Index: /issm/oecreview/Archive/11510-11530/Date.tex =================================================================== --- /issm/oecreview/Archive/11510-11530/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11510-11530/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11510-11530/ISSM-11510-11511.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11510-11511.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11510-11511.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11510) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11511) +@@ -77,7 +77,7 @@ + dnl mex -v gives all the flags for compilation of mex files + dnl if matlab version is 7.10 or more, we must use mexmaci64 (64 bits) + MEXLINK="-O -Wl,-flat_namespace -undefined suppress -arch i386 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" +- MEXLIB=" mexversion.o -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" ++ MEXLIB=" -L$MATLAB_ROOT/bin/maci/ -lmx -lmex -lmat -lstdc++ -largeArrayDims" + if test $MATLAB_MAJOR -ge 7; then + if test $MATLAB_MINOR -ge 10; then + MEXLINK="-O -Wl,-flat_namespace -undefined suppress -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci64/mexFunction.map" Index: /issm/oecreview/Archive/11510-11530/ISSM-11511-11512.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11511-11512.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11511-11512.diff (revision 11991) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11511) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11512) +@@ -150,7 +150,9 @@ + double f,gnorm,cnorm,xdiff; + + TaoGetSolutionStatus(tao, &its, &f, &gnorm, &cnorm, &xdiff, NULL); +- printf("Iteration %3i: Function value: %12.7g, Residual: %g\n",its,f,gnorm); ++ if(its==0)printf("Iter Function Residual\n"); ++ printf("%4i %12.7g %12.7g\n",its,f,gnorm); ++ printf("iter: %i\n",tao->niter); + return 0; + } + Index: /issm/oecreview/Archive/11510-11530/ISSM-11512-11513.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11512-11513.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11512-11513.diff (revision 11991) @@ -0,0 +1,61 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11512) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11513) +@@ -16,8 +16,8 @@ + #include + + /*Local prototype*/ +-int FormFunctionGradient(TaoSolver tao,Vec,double*,Vec,void*); +-int IssmMonitor(TaoSolver,void *); ++int FormFunctionGradient(TaoSolver,Vec,double*,Vec,void*); ++int IssmMonitor(TaoSolver,void*); + typedef struct { + FemModel* femmodel; + } AppCtx; +@@ -59,7 +59,7 @@ + //TaoSetType(tao,"tao_lmvm"); + + /*Prepare all TAO parameters*/ +- TaoSetMonitor(tao,IssmMonitor,NULL,NULL); ++ TaoSetMonitor(tao,IssmMonitor,&user,NULL); + TaoSetMaximumFunctionEvaluations(tao,maxiter); + TaoSetMaximumIterations(tao,nsteps); + TaoSetTolerances(tao,0.,0.,0.,0.,0.); +@@ -145,14 +145,30 @@ + } + int IssmMonitor(TaoSolver tao, void *userCtx){ + +- AppCtx *user = (AppCtx *)userCtx; +- int its; +- double f,gnorm,cnorm,xdiff; ++ int i,its,num_responses; ++ double f,gnorm,cnorm,xdiff; ++ AppCtx *user = (AppCtx *)userCtx; ++ FemModel *femmodel = user->femmodel; ++ Element *element = NULL; ++ int *responses = NULL; + ++ femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); ++ femmodel->parameters->FindParam(&responses,NULL,NULL,StepResponsesEnum); ++ + TaoGetSolutionStatus(tao, &its, &f, &gnorm, &cnorm, &xdiff, NULL); +- if(its==0)printf("Iter Function Residual\n"); +- printf("%4i %12.7g %12.7g\n",its,f,gnorm); +- printf("iter: %i\n",tao->niter); ++ if(its==0) _printf_(true,"Iter Function Residual | List of contributions\n"); ++ if(its==0) _printf_(true,"-----------------------------------+-----------------------\n"); ++ _printf_(true,"%4i %12.7g %12.7g | ",its,f,gnorm); ++ ++ /*Retrieve objective functions independently*/ ++ for(i=0;ielements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,EnumToStringx(responses[i]),false,i); ++ _printf_(true," %12.7g ","",f); ++ } ++ _printf_(true,"\n"); ++ ++ /*Clean-up and return*/ ++ xfree((void**)&responses); + return 0; + } + Index: /issm/oecreview/Archive/11510-11530/ISSM-11516-11517.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11516-11517.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11516-11517.diff (revision 11991) @@ -0,0 +1,226 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.sh (revision 11516) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.sh (revision 11517) +@@ -1,69 +0,0 @@ +-declare -x ALLUSERSPROFILE="C:\\ProgramData" +-declare -x APPDATA="C:\\Users\\larour\\AppData\\Roaming" +-declare -x APPVER="6.1" +-declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319" +-declare -x COMMONPROGRAMFILES="C:\\Program Files (x86)\\Common Files" +-declare -x COMPUTERNAME="WIN-IH1FCG0JVB1" +-declare -x COMSPEC="C:\\Windows\\system32\\cmd.exe" +-declare -x CURRENT_CPU="x64" +-declare -x CommandPromptType="Native" +-declare -x CommonProgramW6432="C:\\Program Files\\Common Files" +-declare -x Configuration="Debug" +-declare -x FP_NO_HOST_CHECK="NO" +-declare -x FrameworkVersion="v4.0.30319" +-declare -x GREP_COLOR="00;38;5;226" +-declare -x GREP_OPTIONS="--binary-file=without-match" +-declare -x HOME="/home/larour" +-declare -x HOMEDRIVE="C:" +-declare -x HOMEPATH="\\Users\\larour" +-declare -x HOSTNAME="WIN-IH1FCG0JVB1" +-declare -x INCLUDE="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;" +-declare -x INFOPATH="/usr/local/info:/usr/share/info:/usr/info:" +-declare -x LANG="C.UTF-8" +-declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib\\X64;" +-declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework64\\v3.5;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;" +-declare -x LOCALAPPDATA="C:\\Users\\larour\\AppData\\Local" +-declare -x LOGONSERVER="\\\\WIN-IH1FCG0JVB1" +-declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" +-declare -x NUMBER_OF_PROCESSORS="1" +-declare -x OLDPWD="/cygdrive/c/issm-uci/trunk-jpl/externalpackages" +-declare -x OS="Windows_NT" +-declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/c/MATLAB/R2011b/bin" +-declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" +-declare -x PRINTER="137.78.140.129#:1" +-declare -x PROCESSOR_ARCHITECTURE="x86" +-declare -x PROCESSOR_ARCHITEW6432="AMD64" +-declare -x PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 42 Stepping 7, GenuineIntel" +-declare -x PROCESSOR_LEVEL="6" +-declare -x PROCESSOR_REVISION="2a07" +-declare -x PROGRAMFILES="C:\\Program Files (x86)" +-declare -x PROMPT="\$P\$G" +-declare -x PS1="\\[\\e]0;\\w\\a\\]\\n\\[\\e[32m\\]\\u@\\h \\[\\e[33m\\]\\w\\[\\e[0m\\]\\n\\\$ " +-declare -x PSModulePath="C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\" +-declare -x PUBLIC="C:\\Users\\Public" +-declare -x PWD="/cygdrive/c/issm-uci/trunk-jpl/externalpackages/win7" +-declare -x PlatformToolset="Windows7.1SDK" +-declare -x ProgramData="C:\\ProgramData" +-declare -x ProgramW6432="C:\\Program Files" +-declare -x REPO="jpl" +-declare -x SESSIONNAME="Console" +-declare -x SHLVL="1" +-declare -x SYSTEMDRIVE="C:" +-declare -x SYSTEMROOT="C:\\Windows" +-declare -x TARGET_CPU="x64" +-declare -x TARGET_PLATFORM="WIN7" +-declare -x TEMP="/tmp" +-declare -x TERM="cygwin" +-declare -x TMP="/tmp" +-declare -x ToolsVersion="4.0" +-declare -x USER="larour" +-declare -x USERDOMAIN="WIN-IH1FCG0JVB1" +-declare -x USERNAME="larour" +-declare -x USERPROFILE="C:\\Users\\larour" +-declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" +-declare -x WINDIR="C:\\Windows" +-declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" +-declare -x WindowsSDKVersionOverride="v7.1" +-declare -x sdkdir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" +-declare -x windows_tracing_flags="3" +-declare -x windows_tracing_logfile="C:\\BVTBin\\Tests\\installpackage\\csilogfile.log" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.32bits.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.32bits.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.32bits.sh (revision 11517) +@@ -0,0 +1,73 @@ ++declare -x ALLUSERSPROFILE="C:\\ProgramData" ++declare -x APPDATA="C:\\Users\\larour\\AppData\\Roaming" ++declare -x APPVER="6.1" ++declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319" ++declare -x COMMONPROGRAMFILES="C:\\Program Files (x86)\\Common Files" ++declare -x COMPUTERNAME="WIN-IH1FCG0JVB1" ++declare -x COMSPEC="C:\\Windows\\system32\\cmd.exe" ++declare -x CURRENT_CPU="x64" ++declare -x CommandPromptType="Cross" ++declare -x CommonProgramW6432="C:\\Program Files\\Common Files" ++declare -x Configuration="Debug" ++declare -x FP_NO_HOST_CHECK="NO" ++declare -x FrameworkVersion="v4.0.30319" ++declare -x GREP_COLOR="00;38;5;226" ++declare -x GREP_OPTIONS="--binary-file=without-match" ++declare -x HOME="/home/larour" ++declare -x HOMEDRIVE="C:" ++declare -x HOMEPATH="\\Users\\larour" ++declare -x HOSTNAME="WIN-IH1FCG0JVB1" ++declare -x INCLUDE="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\INCLUDE;" ++declare -x INFOPATH="/usr/local/info:/usr/share/info:/usr/info:" ++declare -x LANG="en_US.UTF-8" ++declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\ATLMFC\\LIB;" ++declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib;" ++declare -x LOCALAPPDATA="C:\\Users\\larour\\AppData\\Local" ++declare -x LOGONSERVER="\\\\WIN-IH1FCG0JVB1" ++declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" ++declare -x NUMBER_OF_PROCESSORS="8" ++declare -x OS="Windows_NT" ++declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b32/runtime/win32:/cygdrive/c/MATLAB/R2011b32/bin:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/c/MATLAB/R2011b/bin:/cygdrive/c/Program Files (x86)/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/Tools/Binn:/cygdrive/c/Program Files/Microsoft SQL Server/100/DTS/Binn:/cygdrive/c/Program Files/Microsoft Network Monitor 3" ++declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" ++declare -x PRINTER="137.78.140.129#:1" ++declare -x PROCESSOR_ARCHITECTURE="x86" ++declare -x PROCESSOR_ARCHITEW6432="AMD64" ++declare -x PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 42 Stepping 7, GenuineIntel" ++declare -x PROCESSOR_LEVEL="6" ++declare -x PROCESSOR_REVISION="2a07" ++declare -x PROGRAMFILES="C:\\Program Files (x86)" ++declare -x PROMPT="\$P\$G" ++declare -x PS1="\\[\\e]0;\\w\\a\\]\\n\\[\\e[32m\\]\\u@\\h \\[\\e[33m\\]\\w\\[\\e[0m\\]\\n\\\$ " ++declare -x PSModulePath="C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\" ++declare -x PUBLIC="C:\\Users\\Public" ++declare -x PWD="/cygdrive/c/issm-uci/trunk-jpl-32/externalpackages/win7" ++declare -x PlatformToolset="Windows7.1SDK" ++declare -x ProgramData="C:\\ProgramData" ++declare -x ProgramW6432="C:\\Program Files" ++declare -x REPO="jpl" ++declare -x SESSIONNAME="Console" ++declare -x SHELL="/bin/bash" ++declare -x SHLVL="1" ++declare -x SVN_EDITOR="/usr/bin/vim" ++declare -x SYSTEMDRIVE="C:" ++declare -x SYSTEMROOT="C:\\Windows" ++declare -x TARGET_CPU="x86" ++declare -x TARGET_PLATFORM="WIN7" ++declare -x TEMP="/tmp" ++declare -x TERM="cygwin" ++declare -x TMP="/tmp" ++declare -x TZ="America/Los_Angeles" ++declare -x ToolsVersion="4.0" ++declare -x USER="larour" ++declare -x USERDOMAIN="WIN-IH1FCG0JVB1" ++declare -x USERNAME="larour" ++declare -x USERPROFILE="C:\\Users\\larour" ++declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" ++declare -x WINDIR="C:\\Windows" ++declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" ++declare -x WindowsSDKVersionOverride="v7.1" ++declare -x sdkdir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" ++declare -x temp="C:\\Users\\larour\\AppData\\Local\\Temp" ++declare -x tmp="C:\\Users\\larour\\AppData\\Local\\Temp" ++declare -x windows_tracing_flags="3" ++declare -x windows_tracing_logfile="C:\\BVTBin\\Tests\\installpackage\\csilogfile.log" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.64bits.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.64bits.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/win7/sdk7.1.64bits.sh (revision 11517) +@@ -0,0 +1,69 @@ ++declare -x ALLUSERSPROFILE="C:\\ProgramData" ++declare -x APPDATA="C:\\Users\\larour\\AppData\\Roaming" ++declare -x APPVER="6.1" ++declare -x CL="/AI C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319" ++declare -x COMMONPROGRAMFILES="C:\\Program Files (x86)\\Common Files" ++declare -x COMPUTERNAME="WIN-IH1FCG0JVB1" ++declare -x COMSPEC="C:\\Windows\\system32\\cmd.exe" ++declare -x CURRENT_CPU="x64" ++declare -x CommandPromptType="Native" ++declare -x CommonProgramW6432="C:\\Program Files\\Common Files" ++declare -x Configuration="Debug" ++declare -x FP_NO_HOST_CHECK="NO" ++declare -x FrameworkVersion="v4.0.30319" ++declare -x GREP_COLOR="00;38;5;226" ++declare -x GREP_OPTIONS="--binary-file=without-match" ++declare -x HOME="/home/larour" ++declare -x HOMEDRIVE="C:" ++declare -x HOMEPATH="\\Users\\larour" ++declare -x HOSTNAME="WIN-IH1FCG0JVB1" ++declare -x INCLUDE="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\INCLUDE\\gl;" ++declare -x INFOPATH="/usr/local/info:/usr/share/info:/usr/info:" ++declare -x LANG="C.UTF-8" ++declare -x LIB="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\Lib\\X64;" ++declare -x LIBPATH="C:\\Windows\\Microsoft.NET\\Framework64\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework\\v4.0.30319;C:\\Windows\\Microsoft.NET\\Framework64\\v3.5;C:\\Windows\\Microsoft.NET\\Framework\\v3.5;;C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\Lib\\amd64;" ++declare -x LOCALAPPDATA="C:\\Users\\larour\\AppData\\Local" ++declare -x LOGONSERVER="\\\\WIN-IH1FCG0JVB1" ++declare -x MANPATH="/usr/local/man:/usr/share/man:/usr/man:" ++declare -x NUMBER_OF_PROCESSORS="1" ++declare -x OLDPWD="/cygdrive/c/issm-uci/trunk-jpl/externalpackages" ++declare -x OS="Windows_NT" ++declare -x PATH="/usr/local/bin:/usr/bin:/cygdrive/c/Windows/Microsoft.NET/Framework64/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework/v4.0.30319:/cygdrive/c/Windows/Microsoft.NET/Framework64/v3.5:/cygdrive/c/Windows/Microsoft.NET/Framework/v3.5:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/IDE:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/Common7/Tools:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/amd64:/cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/Bin/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/NETFX 4.0 Tools/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin/x64:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v7.1/Bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files/Microsoft Windows Performance Toolkit:/cygdrive/c/MATLAB/R2011b/runtime/win64:/cygdrive/c/MATLAB/R2011b/bin" ++declare -x PATHEXT=".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC" ++declare -x PRINTER="137.78.140.129#:1" ++declare -x PROCESSOR_ARCHITECTURE="x86" ++declare -x PROCESSOR_ARCHITEW6432="AMD64" ++declare -x PROCESSOR_IDENTIFIER="Intel64 Family 6 Model 42 Stepping 7, GenuineIntel" ++declare -x PROCESSOR_LEVEL="6" ++declare -x PROCESSOR_REVISION="2a07" ++declare -x PROGRAMFILES="C:\\Program Files (x86)" ++declare -x PROMPT="\$P\$G" ++declare -x PS1="\\[\\e]0;\\w\\a\\]\\n\\[\\e[32m\\]\\u@\\h \\[\\e[33m\\]\\w\\[\\e[0m\\]\\n\\\$ " ++declare -x PSModulePath="C:\\Windows\\system32\\WindowsPowerShell\\v1.0\\Modules\\" ++declare -x PUBLIC="C:\\Users\\Public" ++declare -x PWD="/cygdrive/c/issm-uci/trunk-jpl/externalpackages/win7" ++declare -x PlatformToolset="Windows7.1SDK" ++declare -x ProgramData="C:\\ProgramData" ++declare -x ProgramW6432="C:\\Program Files" ++declare -x REPO="jpl" ++declare -x SESSIONNAME="Console" ++declare -x SHLVL="1" ++declare -x SYSTEMDRIVE="C:" ++declare -x SYSTEMROOT="C:\\Windows" ++declare -x TARGET_CPU="x64" ++declare -x TARGET_PLATFORM="WIN7" ++declare -x TEMP="/tmp" ++declare -x TERM="cygwin" ++declare -x TMP="/tmp" ++declare -x ToolsVersion="4.0" ++declare -x USER="larour" ++declare -x USERDOMAIN="WIN-IH1FCG0JVB1" ++declare -x USERNAME="larour" ++declare -x USERPROFILE="C:\\Users\\larour" ++declare -x VS100COMNTOOLS="C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\Common7\\Tools\\" ++declare -x WINDIR="C:\\Windows" ++declare -x WindowsSDKDir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" ++declare -x WindowsSDKVersionOverride="v7.1" ++declare -x sdkdir="C:\\Program Files\\Microsoft SDKs\\Windows\\v7.1\\" ++declare -x windows_tracing_flags="3" ++declare -x windows_tracing_logfile="C:\\BVTBin\\Tests\\installpackage\\csilogfile.log" Index: /issm/oecreview/Archive/11510-11530/ISSM-11517-11518.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11517-11518.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11517-11518.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/ISSM.aic +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/ISSM.aic (revision 11517) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/ISSM.aic (revision 11518) +@@ -1,17 +0,0 @@ +-;aic +-SetVersion "1.0" +-SetPackageName "ISSM.msi" +-AddFile APPDIR C:\issm-uci\trunk-jpl\bin\config.h +-AddFile APPDIR C:\issm-uci\trunk-jpl\bin\matlabissm.bat +-AddFile APPDIR C:\issm-uci\trunk-jpl\bin\startup.m +-AddFolder PersonalFolder C:/issm-uci/trunk-jpl\test +-AddFolder APPDIR C:/issm-uci/trunk-jpl\bin +-SetPackageType x64 +-DelEnvironment ISSM_TESTS +-NewEnvironment -name ISSM_TESTS -value [test_Dir] +-DelEnvironment ISSM_TIER +-NewEnvironment -name ISSM_TIER -value [APPDIR] +-DelEnvironment ISSM_TIER_WIN +-NewEnvironment -name ISSM_TIER_WIN -value [APPDIR] +-Save +-Rebuild Index: /issm/oecreview/Archive/11510-11530/ISSM-11518-11519.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11518-11519.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11518-11519.diff (revision 11991) @@ -0,0 +1,28 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11518) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11519) +@@ -12,12 +12,11 @@ + SetPackageName "ISSM.msi" + END + +-ls $ISSM_TIER_WIN/bin/*.bat $ISSM_TIER_WIN/bin/startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic ++ls $ISSM_TIER_WIN/scripts/*.bat $ISSM_TIER_WIN/bin/startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic + + cat << END >> ISSM.aic + AddFolder PersonalFolder $ISSM_TIER_WIN\test + AddFolder APPDIR $ISSM_TIER_WIN\bin +-SetPackageType x64 + DelEnvironment ISSM_TESTS + NewEnvironment -name ISSM_TESTS -value [test_Dir] + DelEnvironment ISSM_TIER +@@ -33,4 +32,4 @@ + + #Get rid of temporary files: + cp ISSM-SetupFiles/ISSM.msi ./ +-rm -rf ISSM.aip ISSM-SetupFiles ++rm -rf ISSM.aip ISSM-SetupFiles ISSM.aic +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/ISSM.initial.aip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/xml Index: /issm/oecreview/Archive/11510-11530/ISSM-11519-11520.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11519-11520.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11519-11520.diff (revision 11991) @@ -0,0 +1,30 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/bin +___________________________________________________________________ +Modified: svn:ignore + - *.mexa64 +*.mexw64 +Makefile +Makefile.in +issm.exe +*.m +*.h +@pairoptions +@modellist +*.bat +*.rtf + + + *.mexa64 +*.mexw64 +*.mexw32 +Makefile +Makefile.in +issm.exe +*.m +*.h +@pairoptions +@modellist +*.bat +*.rtf + + Index: /issm/oecreview/Archive/11510-11530/ISSM-11520-11521.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11520-11521.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11520-11521.diff (revision 11991) @@ -0,0 +1,36 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex +___________________________________________________________________ +Modified: svn:ignore + - Makefile +.ignore.txt +Makefile.in +*.mexa64 +.deps +*.exe +*.exp +*.lib +*.obj +*.mexw64 +*.mexw64.manifest +*.mexw64.map +*.exe.manifest + + + Makefile +.ignore.txt +Makefile.in +*.mexa64 +.deps +*.exe +*.exp +*.lib +*.obj +*.mexw64 +*.mexw64.manifest +*.mexw64.map +*.mexw32 +*.mexw32.manifest +*.mexw32.map +*.exe.manifest + + Index: /issm/oecreview/Archive/11510-11530/ISSM-11521-11522.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11521-11522.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11521-11522.diff (revision 11991) @@ -0,0 +1,460 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/plot +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/display +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/parameterization +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/partition +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/solvers +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Basins +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/ImageProcessing +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Cluster +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Analysis +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Kml +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/BC +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Numerics +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Math +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Geometry +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Mesh +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Ecco3 +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Model +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/LatLong +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Interp +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/consistency +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/qmu +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Miscellaneous +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Meca +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/DataProcessing +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/String +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Array +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Plot +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/kml +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/planet +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/shared +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/@modellist +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/clusters +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/@pairoptions +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solvers +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m +___________________________________________________________________ +Modified: svn:ignore + - Makefile.in + + + Makefile.in +Makefile + + Index: /issm/oecreview/Archive/11510-11530/ISSM-11522-11523.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11522-11523.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11522-11523.diff (revision 11991) @@ -0,0 +1,157 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11522) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11523) +@@ -41,6 +41,50 @@ + dnl }}} + + dnl ISSM's externalpackages ++ dnl vendor{{{1 ++ AC_ARG_WITH([vendor], ++ AS_HELP_STRING([--with-vendor = VENDOR], [vendor name, ex: intel]), [VENDOR=$withval],[VENDOR=""]) ++ AC_MSG_CHECKING(for vendor compilers) ++ if test -n "$VENDOR"; then ++ ++ if test $VENDOR = intel-win32; then ++ export CC=icl ++ export CXX=icl ++ export CFLAGS="-DWIN32 -D_INTEL_WIN_" ++ export CXXFLAGS="-DWIN32 -D_INTEL_WIN_" ++ elif test $VENDOR = intel-win7-32; then ++ export CC=cccl ++ export CXX=cccl ++ export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc" ++ export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc" ++ export AR=lib ++ export RANLIB=true ++ OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib" ++ elif test $VENDOR = intel-win7-64; then ++ export CC=cccl ++ export CXX=cccl ++ export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc" ++ export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc" ++ export AR=lib ++ export RANLIB=true ++ OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib" ++ elif test $VENDOR = intel-linux; then ++ export CC=icc ++ export CXX=icpc ++ export CFLAGS=" -D_INTEL_LINUX_" ++ export CXXFLAGS=" -D_INTEL_LINUX_" ++ elif test $VENDOR = intel-pleiades; then ++ export CC=icc ++ export CXX=icpc ++ export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ " ++ export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " ++ else ++ AC_MSG_ERROR([unknow compiler vendor!]) ++ fi ++ fi ++ AC_SUBST([OSLIBS]) ++ AC_MSG_RESULT(done) ++ dnl }}} + dnl Matlab {{{1 + AC_ARG_WITH([matlab-dir], + AS_HELP_STRING([--with-matlab-dir = DIR], +@@ -91,10 +135,12 @@ + dnl Old MEXLINK + dnl MEXLINK="-Wl,-twolevel_namespace -undefined error -arch i386 -Wl,-syslibroot,/Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -bundle -Wl,-exported_symbols_list,$MATLAB_ROOT/extern/lib/maci/mexFunction.map" + ;; +- *cygwin*) +- MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win64\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" +- +- ++ *cygwin*) ++ if test $VENDOR = intel-win7-32; then ++ MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win32\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" ++ elif test $VENDOR = intel-win7-64; then ++ MEXLIB="-dll -export:mexFunction -LIBPATH:\"$MATLAB_ROOT\extern\lib\win64\microsoft\" libmx.lib libmex.lib libmat.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib -NOLOGO -INCREMENTAL:NO -manifest" ++ fi + MEXEXT=`$MATLAB_ROOT/bin/mexext.bat` + MEXEXT=".$MEXEXT" + ;; +@@ -843,42 +889,6 @@ + fi + AC_MSG_RESULT(done) + dnl }}} +- dnl vendor{{{1 +- AC_ARG_WITH([vendor], +- AS_HELP_STRING([--with-vendor = VENDOR], [vendor name, ex: intel]), [VENDOR=$withval],[VENDOR=""]) +- AC_MSG_CHECKING(for vendor compilers) +- if test -n "$VENDOR"; then +- +- if test $VENDOR = intel-win32; then +- export CC=icl +- export CXX=icl +- export CFLAGS="-DWIN32 -D_INTEL_WIN_" +- export CXXFLAGS="-DWIN32 -D_INTEL_WIN_" +- elif test $VENDOR = intel-win7; then +- export CC=cccl +- export CXX=cccl +- export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc" +- export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc" +- export AR=lib +- export RANLIB=true +- OSLIBS="kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib" +- elif test $VENDOR = intel-linux; then +- export CC=icc +- export CXX=icpc +- export CFLAGS=" -D_INTEL_LINUX_" +- export CXXFLAGS=" -D_INTEL_LINUX_" +- elif test $VENDOR = intel-pleiades; then +- export CC=icc +- export CXX=icpc +- export CXXFLAGS=" -O3 -xS -D_INTEL_LINUX_ " +- export CFLAGS=" -O3 -xS -D_INTEL_LINUX_ " +- else +- AC_MSG_ERROR([unknow compiler vendor!]) +- fi +- fi +- AC_SUBST([OSLIBS]) +- AC_MSG_RESULT(done) +- dnl }}} + dnl with-steadystate{{{1 + AC_ARG_WITH([steadystate],AS_HELP_STRING([--with-steadystate = YES], [compile with steadystate capabilities (default is yes)]),[STEADYSTATE=$withval],[STEADYSTATE=yes]) + AC_MSG_CHECKING(for steadystate capability compilation) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7.sh (revision 11522) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7.sh (revision 11523) +@@ -1,5 +0,0 @@ +-#!/bin/sh +- +- +-#get configure.sh to pick up the win7 Visual Studio compiler +-./configure --prefix=$ISSM_TIER --with-vendor=intel-win7 --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER_WIN/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER_WIN/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER_WIN/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ --with-mpi-lib=$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib --with-mpi-include=$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh (revision 11523) +@@ -0,0 +1,5 @@ ++#!/bin/sh ++ ++ ++#get configure.sh to pick up the win7 Visual Studio compiler ++./configure --prefix=$ISSM_TIER --with-vendor=intel-win7-32 --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER_WIN/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER_WIN/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER_WIN/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ --with-mpi-lib=$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib --with-mpi-include=$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh (revision 11523) +@@ -0,0 +1,5 @@ ++#!/bin/sh ++ ++ ++#get configure.sh to pick up the win7 Visual Studio compiler ++./configure --prefix=$ISSM_TIER --with-vendor=intel-win7-64 --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER_WIN/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER_WIN/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER_WIN/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ --with-mpi-lib=$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib --with-mpi-include=$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11510-11530/ISSM-11524-11525.diff =================================================================== --- /issm/oecreview/Archive/11510-11530/ISSM-11524-11525.diff (revision 11991) +++ /issm/oecreview/Archive/11510-11530/ISSM-11524-11525.diff (revision 11991) @@ -0,0 +1,258 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh (revision 11524) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mpich2/install-1.4-macosx32.sh (revision 11525) +@@ -13,16 +13,16 @@ + + #Configure mpich2 + cd src +-export CFLAGS=" -arch i386" ++export FFLAGS=" -m32" ++export CFLAGS=" -m32" + export CXXFLAGS=" -arch i386" + export CPPFLAGS=" -arch i386" +-export FFLAGS=" -arch i386" + ./configure \ + --prefix="$ISSM_TIER/externalpackages/mpich2/install" \ + --enable-f91=gfortran \ + --enable-sharedlibs=osx-gcc \ + --enable-shared \ +- --enable-fc="/usr/local/bin/gfortran" ++ --enable-fc + + #Compile mpich2 + if [ -z $1 ]; then +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 11524) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 11525) +@@ -179,6 +179,8 @@ + bool results_as_patches; + int numberofvertices,numberofelements; + int numberofresults,vectorsize; ++ int rank; ++ int minrank; + + /*Recover parameters: */ + parameters->FindParam(&io_gather,SettingsIoGatherEnum); +@@ -189,25 +191,31 @@ + if(!results_as_patches){ + /*No patch here, we prepare vectors*/ + ++ /*Get rank of first cpu that has results*/ ++ if(this->Size()) rank=my_rank; ++ else rank=num_procs; ++ MPI_Allreduce (&rank,&minrank,1,MPI_INT,MPI_MIN,MPI_COMM_WORLD); ++ + /*see what the first element of this partition has in stock (this is common to all partitions)*/ +- if(my_rank==0){ +- if(this->Size()==0) _error_("Cannot write results because first partition has no element. Maybe too many cpus were requested"); ++ if(my_rank==minrank){ ++ if(this->Size()==0) _error_("Cannot write results because there is no element??"); + Element* element=(Element*)this->GetObjectByOffset(0); + element->ListResultsInfo(&resultsenums,&resultssizes,&resultstimes,&resultssteps,&numberofresults); + } +- MPI_Bcast(&numberofresults,1,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ MPI_Bcast(&numberofresults,1,MPI_DOUBLE,minrank,MPI_COMM_WORLD); ++ + /*Get out if there is no results. Otherwise broadcast info*/ + if(!numberofresults) return; +- if(my_rank!=0){ ++ if(my_rank!=minrank){ + resultsenums=(int*)xmalloc(numberofresults*sizeof(int)); + resultssizes=(int*)xmalloc(numberofresults*sizeof(int)); + resultstimes=(double*)xmalloc(numberofresults*sizeof(double)); + resultssteps=(int*)xmalloc(numberofresults*sizeof(int)); + } +- MPI_Bcast(resultsenums,numberofresults,MPI_INT,0,MPI_COMM_WORLD); +- MPI_Bcast(resultssizes,numberofresults,MPI_INT,0,MPI_COMM_WORLD); +- MPI_Bcast(resultstimes,numberofresults,MPI_DOUBLE,0,MPI_COMM_WORLD); +- MPI_Bcast(resultssteps,numberofresults,MPI_INT,0,MPI_COMM_WORLD); ++ MPI_Bcast(resultsenums,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); ++ MPI_Bcast(resultssizes,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); ++ MPI_Bcast(resultstimes,numberofresults,MPI_DOUBLE,minrank,MPI_COMM_WORLD); ++ MPI_Bcast(resultssteps,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); + + /*Loop over all results and get nodal vector*/ + for(int i=0;iskip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/u/astrid-r1b/morlighe/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/u/astrid-r1b/morlighe/issm/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=7 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="'benchmark','all'" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win7_larour +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11531-11549/ISSM-11534-11535.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11534-11535.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11534-11535.diff (revision 11991) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmtier.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmtier.m (revision 11534) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Shell/issmtier.m (revision 11535) +@@ -8,7 +8,9 @@ + ISSM_TIER =getenv('ISSM_TIER'); + else + ISSM_TIER =getenv('ISSM_TIER_WIN'); +- ISSM_TIER = ISSM_TIER(1:end-1); %shave off the last '/' ++ if strcmpi(ISSM_TIER(end),'/') | strcmpi(ISSM_TIER(end),'\'), ++ ISSM_TIER = ISSM_TIER(1:end-1); %shave off the last '/' ++ end + end + + if (isempty(ISSM_TIER)), Index: /issm/oecreview/Archive/11531-11549/ISSM-11535-11536.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11535-11536.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11535-11536.diff (revision 11991) @@ -0,0 +1,44 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh (revision 11535) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-32.sh (revision 11536) +@@ -1,5 +1,16 @@ + #!/bin/sh + ++#Dos style path needed for the windows sdk 7.1 cl compiler: ++ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` + + #get configure.sh to pick up the win7 Visual Studio compiler +-./configure --prefix=$ISSM_TIER --with-vendor=intel-win7-32 --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER_WIN/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER_WIN/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER_WIN/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ --with-mpi-lib=$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib --with-mpi-include=$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni ++./configure --prefix=$ISSM_TIER \ ++ --with-vendor=intel-win7-32 \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \ ++ --with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \ ++ --with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ \ ++ --with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ ++ --with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh (revision 11535) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-win7-64.sh (revision 11536) +@@ -1,5 +1,16 @@ + #!/bin/sh + ++#Dos style path needed for the windows sdk 7.1 cl compiler: ++ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` + + #get configure.sh to pick up the win7 Visual Studio compiler +-./configure --prefix=$ISSM_TIER --with-vendor=intel-win7-64 --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_TIER_WIN/externalpackages/triangle/install --with-metis-dir=$ISSM_TIER_WIN/externalpackages/metis/install --with-petsc-dir=$ISSM_TIER_WIN/externalpackages/petsc/install --with-petsc-arch=$ISSM_ARCH --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ --with-mpi-lib=$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib --with-mpi-include=$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni ++./configure --prefix=$ISSM_TIER \ ++ --with-vendor=intel-win7-64 \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir="$ISSM_TIER_WIN/externalpackages/triangle/install" \ ++ --with-metis-dir="$ISSM_TIER_WIN/externalpackages/metis/install" \ ++ --with-petsc-dir="$ISSM_TIER_WIN/externalpackages/petsc/install" \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib/ \ ++ --with-mpi-lib="$ISSM_TIER_WIN/externalpackages/petsc/install/lib/libpetsc.lib" \ ++ --with-mpi-include="$ISSM_TIER_WIN/externalpackages/petsc/install/include/mpiuni" Index: /issm/oecreview/Archive/11531-11549/ISSM-11536-11537.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11536-11537.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11536-11537.diff (revision 11991) @@ -0,0 +1,27 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/issm/cccl +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/issm/cccl (revision 11536) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/cccl/issm/cccl (revision 11537) +@@ -83,7 +83,7 @@ + shift + done + +-echo "$prog $opts" ++#echo "$prog $opts" + exec $prog $opts + exit 0 + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11536) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11537) +@@ -4,6 +4,9 @@ + rm -rf ISSM.aip ISSM-SetupFiles ISSM.msi + cp ISSM.initial.aip ISSM.aip + ++#get windows style path to files ++ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` ++ + #build list of files to put into the installer: + rm -rf ISSM.aic + cat << END > ISSM.aic Index: /issm/oecreview/Archive/11531-11549/ISSM-11537-11538.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11537-11538.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11537-11538.diff (revision 11991) @@ -0,0 +1,62 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m (revision 11537) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m (revision 11538) +@@ -25,35 +25,16 @@ + %the variable ISSM_TIER in this file, in case it is not correctly setup. + + %ISSM path +-addpath(pwd); %add current path first ++addpath([ISSM_TIER '/src/m/utils/']); %loads recursivepath ++addpath([ISSM_TIER '/doc']); ++addpath([ISSM_TIER '/bin']); ++addpath(recursivepath([ISSM_TIER '/src/m'])); ++addpath(recursivepath([ISSM_TIER '/externalpackages/scotch'])); ++addpath(recursivepath([ISSM_TIER '/externalpackages/canos'])); ++addpath(recursivepath([ISSM_TIER '/externalpackages/kml'])); ++addpath(recursivepath([ISSM_TIER '/externalpackages/googleearthtoolbox/'])); ++addpath(recursivepath([ISSM_TIER '/externalpackages/export_fig'])); + +-if exist([ISSM_TIER '/src/m/utils/'],'dir'), +- addpath([ISSM_TIER '/src/m/utils/']); %loads recursivepath +-end +-if exist([ISSM_TIER '/doc'],'dir'), +- addpath([ISSM_TIER '/doc']); +-end +-if exist([ISSM_TIER '/bin'],'dir'), +- addpath([ISSM_TIER '/bin']); +-end +-if exist([ISSM_TIER '/src/m'],'dir'), +- addpath(recursivepath([ISSM_TIER '/src/m'])); +-end +-if exist([ISSM_TIER '/externalpackages/scotch'],'dir'), +- addpath(recursivepath([ISSM_TIER '/externalpackages/scotch'])); +-end +-if exist([ISSM_TIER '/externalpackages/canos'],'dir'), +- addpath(recursivepath([ISSM_TIER '/externalpackages/canos'])); +-end +-if exist([ISSM_TIER '/externalpackages/kml'],'dir'), +- addpath(recursivepath([ISSM_TIER '/externalpackages/kml'])); +-end +-if exist([ISSM_TIER '/externalpackages/googleearthtoolbox/'],'dir'), +- addpath(recursivepath([ISSM_TIER '/externalpackages/googleearthtoolbox/'])); +-end +-if exist([ISSM_TIER '/externalpackages/export_fig'],'dir'), +- addpath(recursivepath([ISSM_TIER '/externalpackages/export_fig'])); +-end + clear ISSM_TIER; + + %Check on any warning messages that might indicate that the paths were not correct. +@@ -85,12 +66,3 @@ + + % no warning if we try to plot while in nojvm (will not be supported in future releases) + warning off MATLAB:HandleGraphics:noJVM +- +-%at the end, get to tests directory if ISSM_TESTS exists: +-if ispc, +- addpath([pwd '\bin']); +- ISSM_TESTS=getenv('ISSM_TESTS'); +- if ~isempty(ISSM_TESTS), +- cd(ISSM_TESTS); +- end +-end Index: /issm/oecreview/Archive/11531-11549/ISSM-11538-11539.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11538-11539.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11538-11539.diff (revision 11991) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 11538) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 11539) +@@ -22,3 +22,7 @@ + else + source $config_dir/intel-winXP.sh + fi ++ ++#finally, out of ISSM_TIER, we need to create an ISSM_TIER_WIN variable for Matlab to pick up on. ++ISSM_TIER_WIN=`cygpath -m $ISSM_TIER` ++ Index: /issm/oecreview/Archive/11531-11549/ISSM-11539-11540.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11539-11540.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11539-11540.diff (revision 11991) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 11539) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/windows_environment.sh (revision 11540) +@@ -25,4 +25,4 @@ + + #finally, out of ISSM_TIER, we need to create an ISSM_TIER_WIN variable for Matlab to pick up on. + ISSM_TIER_WIN=`cygpath -m $ISSM_TIER` +- ++export ISSM_TIER_WIN Index: /issm/oecreview/Archive/11531-11549/ISSM-11540-11541.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11540-11541.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11540-11541.diff (revision 11991) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m (revision 11540) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/startup.m (revision 11541) +@@ -26,7 +26,6 @@ + + %ISSM path + addpath([ISSM_TIER '/src/m/utils/']); %loads recursivepath +-addpath([ISSM_TIER '/doc']); + addpath([ISSM_TIER '/bin']); + addpath(recursivepath([ISSM_TIER '/src/m'])); + addpath(recursivepath([ISSM_TIER '/externalpackages/scotch'])); Index: /issm/oecreview/Archive/11531-11549/ISSM-11541-11542.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11541-11542.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11541-11542.diff (revision 11991) @@ -0,0 +1,26 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun +___________________________________________________________________ +Modified: svn:ignore + - *.tar.gz +*.bin +*.petsc +*.outlog +*.errlog +*.queue + + + *.tar.gz +*.bin +*.petsc +*.outlog +*.errlog +*.queue +*.lock +*settings* +startup.m +*.bat +*.outbin +qmu* +*.bin + + Index: /issm/oecreview/Archive/11531-11549/ISSM-11542-11543.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11542-11543.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11542-11543.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/oshostname.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/oshostname.m (revision 11542) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/oshostname.m (revision 11543) +@@ -6,7 +6,7 @@ + % + + if ispc, +- [status,hostname]=system('hostname');hostname=hostname(1:end-1); ++ [status,hostname]=system('hostname | sed ''s/-//g''');hostname=hostname(1:end-1); + + if status, + error('oshostname error message: could not run hostname command on windows os'); Index: /issm/oecreview/Archive/11531-11549/ISSM-11543-11544.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11543-11544.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11543-11544.diff (revision 11991) @@ -0,0 +1,44 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl +___________________________________________________________________ +Modified: svn:ignore + - autom4te.cache +aclocal.m4 +bin +config.log +config.h +config.h.in +config.status +configure +doxygen +ISSM.paf +ISSM.ppf +ISSM.ppf_cache +libtool +list +Makefile +Makefile.in +stamp-h1 +svn-commit* + + + autom4te.cache +aclocal.m4 +bin +config.log +config.h +config.h.in +config.status +configure +doxygen +ISSM.paf +ISSM.ppf +ISSM.ppf_cache +libtool +list +Makefile +Makefile.in +stamp-h1 +svn-commit* +nightlylog + + Index: /issm/oecreview/Archive/11531-11549/ISSM-11544-11545.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11544-11545.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11544-11545.diff (revision 11991) @@ -0,0 +1,210 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win7_larour +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win7_larour (revision 11544) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win7_larour (revision 11545) +@@ -1,92 +0,0 @@ +-########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ +- +-#-------------------------------# +-# 1: ISSM general configuration # +-#-------------------------------# +- +-#ISSM main directory (full path) +-ISSM_DIR="/u/astrid-r1b/morlighe/issm" +-ISSM_TIER="/u/astrid-r1b/morlighe/issm/trunk-jpl/cron/trunk-jpl" +-#ISSM_TIER="/u/astrid-r1b/morlighe/svn/issm/trunk/cron/issm2.2" +- +-#ISSM Architecture +-ISSM_ARCH="linux-gnu-amd64" +- +-#Machine configuration +-MACHINE="win7" +- +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" +- +-#----------------------# +-# 2: ISSM Installation # +-#----------------------# +- +-#ISSM_INSTALLATION can have 3 values: +-# - "checkout" the existing version of the code will be erased and +-# the latest version will be checked out +-# - "update" the directory won't be erased but ISSM will be updated +-# ->skip to section 3 +-# - "none" leave ISSM as is in its directory +-# ->skip to section 3 +-ISSM_INSTALLATION="checkout" +- +-#SVN repository +-REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +-#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" +- +-#execution path used for parallel runs +-EXECUTION_PATH="/u/astrid-r1b/morlighe/ExecutionNightlyRun" +- +-#-----------------------------------# +-# 3: External packages installation # +-#-----------------------------------# +- +-#ISSM_EXTERNALPACKAGES can have 3 values: +-# - "install" install all external packages listed below +-# - "copy" copy existing directories (EXTERNALPACKAGESDIR) +-# - "none" leave external packages as is +-# ->skip to section 4 +-ISSM_EXTERNALPACKAGES="install" +-EXTERNALPACKAGESDIR="/u/astrid-r1b/morlighe/issm/trunk-jpl/externalpackages" +- +-#List of external pakages to be installed +-EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" +- +-#---------------------# +-# 4: ISSM Compilation # +-#---------------------# +- +-#ISSM_COMPILATION can have 2 values: +-# - "yes" compile ISSM +-# - "no" do not compile ISSM +-ISSM_COMPILATION="yes" +- +-#----------------------# +-# 5: Mail notification # +-#----------------------# +- +-#Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_TIER/cron/mailinglist. +-SKIPMAIL="no" +- +-#Sender email address +-EMAIL_ADRESS="mathieu.morlighem@jpl.nasa.gov" +- +-#------------------------# +-# 6: Nightly run options # +-#------------------------# +- +-#number of cpus used in ISSM installation and compilation (one is usually +-#safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=1 +- +-#number of cpus used in the nightly runs. +-NUMCPUS_RUN=7 +- +-#Nightly run options. The matlab routine nightlyrun.m will be called +-#as follows: nightlyrun($NROPTIONS). The options must be understandable +-#by Matlab and nightlyrun.m +-#ex: "'id',[101 102 103]" +- +-NROPTIONS="'benchmark','all'" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732_larour +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732_larour (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732_larour (revision 11545) +@@ -0,0 +1,102 @@ ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/cygdrive/c/issm-uci" ++ISSM_TIER="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="cygwin-intel" ++ ++#Machine configuration ++MACHINE="win7" ++ ++#MATLAB path ++MATLAB_PATH="C:/MATLAB/R2011b32/" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-win7-32.sh" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="none" ++ ++#SVN repository ++REPOSITORY="http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/cygdrive/c/issm-uci/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="none" ++EXTERNALPACKAGESDIR="/cygdrive/c/issm-uci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES=" autoconf automake petsc metis triangle cccl" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install-3.1-win7.sh install-4.0-win7.sh install-win7.sh install-win7.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="no" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="eric.larour@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=8 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=1 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="'benchmark','all'" ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++MATLABBIN=/cygdrive/c/MATLAB/R2011b32/bin/matlab + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win732_larour +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11531-11549/ISSM-11545-11546.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11545-11546.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11545-11546.diff (revision 11991) @@ -0,0 +1,7 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron +___________________________________________________________________ +Added: svn:ignore + + trunk-jpl + + Index: /issm/oecreview/Archive/11531-11549/ISSM-11546-11547.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11546-11547.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11546-11547.diff (revision 11991) @@ -0,0 +1,70 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11546) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11547) +@@ -15,7 +15,7 @@ + SetPackageName "ISSM.msi" + END + +-ls $ISSM_TIER_WIN/scripts/*.bat $ISSM_TIER_WIN/bin/startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic ++ls $ISSM_TIER_WIN/scripts/*.bat startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic + + cat << END >> ISSM.aic + AddFolder PersonalFolder $ISSM_TIER_WIN\test +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/startup.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/startup.m (revision 11547) +@@ -0,0 +1,46 @@ ++%STARTUP - Matlab startup script ++% ++% startup.m is a script run by matlab at the beginning of a session, just ++% before handing over the prompt to the user. This delivery startup.m script ++% has been customized here for the ISSM code. This startup script should be ++% run by users before trying to use ISSM. The best way to do that is to put ++% the startup file in the location where Matlab starts and established its ++% root directory. ++ ++% clear the last warning to focus on the warnings of the ISSM path ++lastwarn(''); ++ ++%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++ISSM_TIER=getenv('ISSM_TIER_WIN'); ++ ++if (isempty(ISSM_TIER)), ++ error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++end ++ ++%Now add all issm code paths necessary to run issm smoothly. ++%We capture the error output, so that we can warn the user to update ++%the variable ISSM_TIER in this file, in case it is not correctly setup. ++ ++%ISSM path ++addpath(pwd); %add current path first ++addpath([pwd '\bin']); ++ ++%Check on any warning messages that might indicate that the paths were not correct. ++if ~isempty(lastwarn), ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); ++else ++ fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); ++end ++ ++%disable matlab bell! ++beep off; ++ ++% no warning if we try to plot while in nojvm (will not be supported in future releases) ++warning off MATLAB:HandleGraphics:noJVM ++ ++%at the end, get to tests directory if ISSM_TESTS exists: ++ISSM_TESTS=getenv('ISSM_TESTS'); ++if ~isempty(ISSM_TESTS), ++ cd(ISSM_TESTS); ++end + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/startup.m +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11531-11549/ISSM-11547-11548.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11547-11548.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11547-11548.diff (revision 11991) @@ -0,0 +1,356 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new (revision 11548) +@@ -0,0 +1,345 @@ ++#!/bin/bash ++#This bash script calls the nightlyrun.m matlab file to run our nightly test decks. ++#It then processes the results and sends an email to the Ice developpers. ++ ++#some functions ++function timer() #{{{1 ++{ ++ if [[ $# -eq 0 ]]; then ++ echo $(date '+%s') ++ else ++ local stime=$1 ++ etime=$(date '+%s') ++ ++ if [[ -z "$stime" ]]; then stime=$etime; fi ++ ++ dt=$((etime - stime)) ++ ds=$((dt % 60)) ++ dm=$(((dt / 60) % 60)) ++ dh=$((dt / 3600)) ++ printf '%d:%02d:%02d' $dh $dm $ds ++ fi ++} #}}} ++function todaydate() #{{{1 ++{ ++ suffix=`date | awk '{printf("%s-%s-%s %s",$2,$3,$6,$4);}'` ++ echo $suffix; ++} #}}} ++function host_name() #{{{1 ++{ ++ #return host name depending on the OS ++ if [ "$1" = "win7" ] ++ then ++ HOST_NAME=`hostname | sed 's/-//g'`; ++ else ++ HOST_NAME=`hostname -s | sed 's/-//g'`; ++ fi ++ echo $HOST_NAME; ++} #}}} ++function pause() #{{{1 ++{ ++pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'` ++ ++while [ -n "$pid" ] ++do ++ pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'` ++done ++} ++#}}} ++#Get configuration ++#Source config file{{{1 ++if [ $# -ne 1 ]; ++then ++ #no config file specified: exit ++ echo "no config file specified. Exiting..." >&2 # Error message to stderr. ++ exit 1 ++fi ++if [ ! -f "$1" ] ++then ++ echo "File $1 not found!" >&2 # Error message to stderr. ++ exit 1 ++fi ++source $1; ++#}}} ++#Export ISSM_* variables{{{1 ++export ISSM_DIR ++export ISSM_TIER ++export ISSM_ARCH ++#}}} ++#Initialize variables {{{1 ++TODAY=$(todaydate); ++HOST_NAME=$(host_name $MACHINE); ++START_TIME=$(timer); ++ISSM_RELEASE=$(basename $(echo $REPOSITORY)); ++USER=$(whoami); ++INIT_PATH=$(pwd); ++#}}} ++ ++#Lauch installation ++#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{1 ++if [ "$ISSM_INSTALLATION" == "checkout" ] ++then ++ ++ #Erase previous code and Fetch the new one ++ rm -rf $ISSM_RELEASE ++ svn checkout "$REPOSITORY" ++ ++elif [ "$ISSM_INSTALLATION" == "update" ] ++then ++ ++ #only update ISSM ++ cd $ISSM_TIER ++ svn update ++ ++elif [ "$ISSM_INSTALLATION" == "none" ] ++then ++ ++ #do nothing ++ echo "Skipping ISSM installation" ++ ++else ++ ++ #Error message ++ echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr. ++ exit 1 ++ ++fi ++#}}} ++#Create cluster's settings{{{1 ++#create simpler cluster.rc file, with only the cluster we are interested in. ++cd $ISSM_TIER/test/NightlyRun/ ++if [ "$MACHINE" = "win7" ]; then ++cat << END > $HOST_NAME"_settings.m" ++cluster.login='$USER'; ++cluster.codepath='`cygpath -m $ISSM_TIER/bin`'; ++cluster.executionpath='`cygpath -m $EXECUTION_PATH`'; ++END ++else ++cat << END > $HOST_NAME"_settings.m" ++cluster.login='$USER'; ++cluster.codepath='$ISSM_TIER/bin'; ++cluster.executionpath='$EXECUTION_PATH'; ++END ++fi ++#}}} ++#Source environment variables with new matlab path {{{1 ++cd $ISSM_TIER/etc ++source environment.sh MATLAB_DIR=$MATLAB_PATH ++#}}} ++#install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 ++if [ "$ISSM_EXTERNALPACKAGES" == "install" ] ++then ++ ++ cd $ISSM_TIER/externalpackages ++ #number of packages: ++ numpackages=`echo $EXTERNALPACKAGES | wc -w` ++ ++ for (( i=1; i<=$numpackages; i++ )) ++ do ++ package=`echo $EXTERNALPACKAGES | cut -d " " -f $i-$i` ++ package_config=`echo $EXTERNALPACKAGES_CONFIGS | cut -d " " -f $i-$i` ++ package_numcpus=`echo $EXTERNALPACKAGES_NUMCPUS | cut -d " " -f $i-$i` ++ ++ cd $package ++ $package_config $package_numcpus ++ cd .. ++ done ++ ++ ++elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ] ++then ++ ++ #erase externapackages, and link with externalpackages_dir ++ cd $ISSM_TIER ++ rm -rf externalpackages ++ cp -Rf $EXTERNALPACKAGESDIR ./ ++ ++elif [ "$ISSM_EXTERNALPACKAGES" == "none" ] ++then ++ ++ #Do nothing ++ echo "Skipping external packages installation" ++ ++else ++ ++ #Error message ++ echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr. ++ exit 1 ++ ++fi ++#}}} ++#ISSM compilation yes/no (ISSM_COMPILATION) {{{1 ++if [ "$ISSM_COMPILATION" == "yes" ] ++then ++ ++ cd $ISSM_TIER ++ make clean ++ make distclean ++ ./scripts/automakererun.sh ++ source ./configs/$COMPILE_CONFIG_FILE ++ ++ make -j $NUMCPUS_INSTALL ++ make -j $NUMCPUS_INSTALL install ++ ++elif [ "$ISSM_COMPILATION" == "no" ] ++then ++ echo "Skipping ISSM compilation" ++else ++ echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr. ++ exit 1 ++fi ++#}}} ++ ++#Prepare run ++#create softlink to startup {{{1 ++cd $ISSM_TIER/test/NightlyRun/ ++if [ "$MACHINE" = "win7" ]; then ++ cp $ISSM_TIER/startup.m . ++else ++ ln -s $ISSM_TIER/startup.m . ++fi ++#}}} ++#Create nightlylog directory and info.log {{{1 ++#put installation elapsed time in info.log ++INSTALL_TIME=$(timer) ++ELAPSED_INSTALL=$(timer $START_TIME) ++rm -rf $ISSM_TIER/nightlylog ++mkdir $ISSM_TIER/nightlylog ++cat << END > $ISSM_TIER/nightlylog/info.log ++today: $(echo $TODAY) ++user: $(echo $USER) ++host: $(echo $HOST_NAME) ++OS: $(echo $MACHINE) ++release: $(echo $ISSM_RELEASE) ++init_path: $(echo $INIT_PATH) ++elapsed_install: $(echo $ELAPSED_INSTALL) ++END ++#}}} ++#check NUMCPUS_RUN options {{{1 ++if [ "$NUMCPUS_RUN" = "" ] ++then ++ echo "NUMCPUS_RUN option not found, defaulting to NUMCPUS_RUN = 1" ++ NUMCPUS_RUN=1 ++fi ++#}}} ++ ++#Run tests ++#on Matlab and windows machines, we'll need a windows style path: {{{ ++if [ "$MACHINE" = "win7" ]; then ++ MATLAB_TIER=`cygpath -m $ISSM_TIER` ++else ++ MATLAB_TIER=$ISSM_TIER ++fi ++ ++#}}} ++#Launch all tests on different cpus {{{1 ++for (( i=1;i<=$NUMCPUS_RUN;i++ )) ++do ++ #Launch matlab and the nightly run script ++ cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF ++ warning off %necessary to avoid a info.log of several Go for parallel runs ++ try, ++ cd $MATLAB_TIER/test/NightlyRun ++ startup; ++ $(if [ "$NROPTIONS" = "" ] ++ then ++ echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" ++ else ++ #echo "runme('id',[101 102]);" ++ echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" ++ fi ++ ) ++ catch me, ++ %An error occured, get report and exit ++ message=getReport(me) ++ directory=strsplit(pwd,'/'); ++ fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); ++ fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); ++ fprintf(fid,'%s',message); ++ fclose(fid); ++ end ++ disp('MATLABEXITEDCORRECTLY'); ++ exit ++EOF ++ ++ #Start run from nightlylog directory ++ cd $ISSM_TIER/nightlylog/ ++ ++ #Start test ++ $MATLABBIN -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & ++ ++done ++ ++#wait until matlab closes ++if [ "$MACHINE" = "win7" ]; then ++ pause MATLAB ++else ++ wait ++fi ++ ++#}}} ++#concatenate all reports {{{1 ++cd $ISSM_TIER/nightlylog/ ++mv matlab_log1.log matlab_log.log ++for (( i=2;i<=$NUMCPUS_RUN;i++ )) ++do ++ cat matlab_log.log matlab_log$i.log > matlab_log.log.bak ++ mv matlab_log.log.bak matlab_log.log ++done ++#}}} ++#Complete info.log {{{1 ++if [ $(cat matlab_log.log | grep "MATLABEXITEDCORRECTLY" | wc -l) -eq $NUMCPUS_RUN ] ++then ++ MATLABCRASH=0 ++else ++ MATLABCRASH=1 ++fi ++ELAPSED_RUN=$(timer $INSTALL_TIME) ++ELAPSED_TOTAL=$(timer $START_TIME) ++cat << END >> $ISSM_TIER/nightlylog/info.log ++elapsed_run: $(echo $ELAPSED_RUN) ++elapsed_total: $(echo $ELAPSED_TOTAL) ++matlab_crash: $(echo $MATLABCRASH) ++END ++#}}} ++ ++#Send Report ++#Build html report {{{1 ++cd $ISSM_TIER/nightlylog/ ++sh ../scripts/report.sh ++echo "html report located in $ISSM_TIER/nightlylog/report.html" ++#}}} ++#send mail if requested (SKIPMAIL) {{{1 ++if [ "$SKIPMAIL" != "yes" ] ++then ++ echo "sending report..." ++ source $ISSM_TIER/cron/mailinglist ++ for i in `echo $MAILINGLIST`; do ++ ++ if [ "$MACHINE" = "win7" ] ++ then ++ echo $i ++ email -html -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/nightlylog/report.html ++ else ++ if [ "$MACHINE" = "astrid" ] ++ then ++cat - $ISSM_TIER/nightlylog/report.html < ++To: $i ++Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. ++Mime-Version: 1.0 ++Content-Type: text/html ++HERE ++ else ++cat - $ISSM_TIER/nightlylog/report.html < ++To: $i ++Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. ++Mime-Version: 1.0 ++Content-Type: text/html ++HERE ++ fi ++ fi ++ done ++fi ++#}}} + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11531-11549/ISSM-11548-11549.diff =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-11548-11549.diff (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-11548-11549.diff (revision 11991) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/expopen.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/expopen.m (revision 11548) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/expopen.m (revision 11549) +@@ -1,10 +0,0 @@ +-function struct=expopen(newname,oldname) +-%EXPOPEN - read in an exp file, and open all the contours. +-% +-% Usage: +-% expopen(newname,oldname) +-% +- +- +-a=expread(oldname,0); %0 for opening. +-expwrite(a,newname); Index: /issm/oecreview/Archive/11531-11549/ISSM-DocReview-11531-11549.tex =================================================================== --- /issm/oecreview/Archive/11531-11549/ISSM-DocReview-11531-11549.tex (revision 11991) +++ /issm/oecreview/Archive/11531-11549/ISSM-DocReview-11531-11549.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11531-11549/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11531-11549/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11531-11549/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11531-11549 Index: /issm/oecreview/Archive/11531-11549/Makefile =================================================================== --- /issm/oecreview/Archive/11531-11549/Makefile (revision 11991) +++ /issm/oecreview/Archive/11531-11549/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11531-11549 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11531-11549/log.tex =================================================================== --- /issm/oecreview/Archive/11531-11549/log.tex (revision 11991) +++ /issm/oecreview/Archive/11531-11549/log.tex (revision 11991) @@ -0,0 +1,34 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11531-11532.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/win7/README A /issm/trunk-jpl/externalpackages/win7/configs A /issm/trunk-jpl/externalpackages/win7/configs/intel-win7.sh A /issm/trunk-jpl/externalpackages/win7/configs/intel-winXP.sh A /issm/trunk-jpl/externalpackages/win7/configs/sdk7.1.win7-32.sh A /issm/trunk-jpl/externalpackages/win7/configs/sdk7.1.win7-64.sh D /issm/trunk-jpl/externalpackages/win7/notes D /issm/trunk-jpl/externalpackages/win7/sdk7.1.32bits.sh D /issm/trunk-jpl/externalpackages/win7/sdk7.1.64bits.sh D /issm/trunk-jpl/externalpackages/win7/vs10.0.sh A /issm/trunk-jpl/externalpackages/win7/win7.sdk7.1.exe A /issm/trunk-jpl/externalpackages/win7/windows\_environment.sh D /issm/trunk-jpl/externalpackages/win7/winsdk\_web.exe \\ Export determination: 6. \\Rationale: Reorganizing different compiler configurations +M /issm/trunk-jpl/etc/environment.sh D /issm/trunk-jpl/externalpackages/win7 A /issm/trunk-jpl/externalpackages/windows (from /issm/trunk-jpl/externalpackages/win7:11523) A /issm/trunk-jpl/externalpackages/windows/README (from /issm/trunk-jpl/externalpackages/win7/README:11531) A /issm/trunk-jpl/externalpackages/windows/configs (from /issm/trunk-jpl/externalpackages/win7/configs:11531) D /issm/trunk-jpl/externalpackages/windows/notes D /issm/trunk-jpl/externalpackages/windows/sdk7.1.32bits.sh D /issm/trunk-jpl/externalpackages/windows/sdk7.1.64bits.sh D /issm/trunk-jpl/externalpackages/windows/vs10.0.sh A /issm/trunk-jpl/externalpackages/windows/win7.sdk7.1.exe (from /issm/trunk-jpl/externalpackages/win7/win7.sdk7.1.exe:11531) A /issm/trunk-jpl/externalpackages/windows/windows\_environment.sh (from /issm/trunk-jpl/externalpackages/win7/windows\_environment.sh:11531) D /issm/trunk-jpl/externalpackages/windows/winsdk\_web.exe Moved win7 to more general windows configuration files for windows compilers. Introduced setup of windows compilers at the /etc/environment.sh level. \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11532-11533.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh D /issm/trunk-jpl/externalpackages/win7 A /issm/trunk-jpl/externalpackages/windows (from /issm/trunk-jpl/externalpackages/win7:11523) A /issm/trunk-jpl/externalpackages/windows/README (from /issm/trunk-jpl/externalpackages/win7/README:11531) A /issm/trunk-jpl/externalpackages/windows/configs (from /issm/trunk-jpl/externalpackages/win7/configs:11531) D /issm/trunk-jpl/externalpackages/windows/notes D /issm/trunk-jpl/externalpackages/windows/sdk7.1.32bits.sh D /issm/trunk-jpl/externalpackages/windows/sdk7.1.64bits.sh D /issm/trunk-jpl/externalpackages/windows/vs10.0.sh A /issm/trunk-jpl/externalpackages/windows/win7.sdk7.1.exe (from /issm/trunk-jpl/externalpackages/win7/win7.sdk7.1.exe:11531) A /issm/trunk-jpl/externalpackages/windows/windows\_environment.sh (from /issm/trunk-jpl/externalpackages/win7/windows\_environment.sh:11531) D /issm/trunk-jpl/externalpackages/windows/winsdk\_web.exe \\ Export determination: 6. \\Rationale: Moved win7 to more general windows configuration files for windows compilers. Introduced setup of windows compilers at the /etc/environment.sh level. \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11533-11534.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/win7\_larour \\ Export determination: 6. \\Rationale: Nightly runs for windows \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11534-11535.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/win7\_larour \\ Export determination: 6. \\Rationale: Nightly runs for windows +M /issm/trunk-jpl/src/m/utils/Shell/issmtier.m More nuanced way of getting rid of the trailing "" or "/" \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11535-11536.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/Shell/issmtier.m \\ Export determination: 6. \\Rationale: More nuanced way of getting rid of the trailing "" or "/" +M /issm/trunk-jpl/configs/config-win7-32.sh M /issm/trunk-jpl/configs/config-win7-64.sh New configuration files, more flexible \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11536-11537.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-win7-32.sh M /issm/trunk-jpl/configs/config-win7-64.sh \\ Export determination: 6. \\Rationale: New configuration files, more flexible +M /issm/trunk-jpl/externalpackages/cccl/issm/cccl M /issm/trunk-jpl/installers/win7/aic.sh Work without the ISSM\_TIER\_WIN environment variable. Stop cccl to output so much. \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11537-11538.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/cccl/issm/cccl M /issm/trunk-jpl/installers/win7/aic.sh \\ Export determination: 6. \\Rationale: Work without the ISSM\_TIER\_WIN environment variable. Stop cccl to output so much. +M /issm/trunk-jpl/startup.m Back to previous startup, with some windows flavor still \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11538-11539.diff: \\ Function name: \\M /issm/trunk-jpl/startup.m \\ Export determination: 6. \\Rationale: Back to previous startup, with some windows flavor still +M /issm/trunk-jpl/externalpackages/windows/windows\_environment.sh Creation of ISSM\_TIER\_WIN embedded into windows\_environment.sh script \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11539-11540.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/windows/windows\_environment.sh \\ Export determination: 6. \\Rationale: Creation of ISSM\_TIER\_WIN embedded into windows\_environment.sh script +M /issm/trunk-jpl/externalpackages/windows/windows\_environment.sh Forgot export \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11540-11541.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/windows/windows\_environment.sh \\ Export determination: 6. \\Rationale: Forgot export +M /issm/trunk-jpl/startup.m doc now deleted \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11541-11542.diff: \\ Function name: \\M /issm/trunk-jpl/startup.m \\ Export determination: 6. \\Rationale: doc now deleted +M /issm/trunk-jpl/test/NightlyRun Ignoring more files in test directory \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11542-11543.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun \\ Export determination: 6. \\Rationale: Ignoring more files in test directory +M /issm/trunk-jpl/src/m/utils/OS/oshostname.m Get rid of - for windows machines too \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11543-11544.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/OS/oshostname.m \\ Export determination: 6. \\Rationale: Get rid of - for windows machines too +M /issm/trunk-jpl Ignoring some files \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11544-11545.diff: \\ Function name: \\M /issm/trunk-jpl \\ Export determination: 6. \\Rationale: Ignoring some files +A /issm/trunk-jpl/cron/configs/win732\_larour D /issm/trunk-jpl/cron/configs/win7\_larour New configuration file for new nightly run \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11545-11546.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/win732\_larour D /issm/trunk-jpl/cron/configs/win7\_larour \\ Export determination: 6. \\Rationale: New configuration file for new nightly run +M /issm/trunk-jpl/cron Ignoring new files \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11546-11547.diff: \\ Function name: \\M /issm/trunk-jpl/cron \\ Export determination: 6. \\Rationale: Ignoring new files +M /issm/trunk-jpl/installers/win7/aic.sh A /issm/trunk-jpl/installers/win7/startup.m Picking up simple startup file for windows locally. Reverting trunk startup to original startup \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11547-11548.diff: \\ Function name: \\M /issm/trunk-jpl/installers/win7/aic.sh A /issm/trunk-jpl/installers/win7/startup.m \\ Export determination: 6. \\Rationale: Picking up simple startup file for windows locally. Reverting trunk startup to original startup +A /issm/trunk-jpl/cron/nightlyrun.sh.new New nightly run prototype, works with configs/win732\_larour. Please look at it and comment \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-11548-11549.diff: \\ Function name: \\A /issm/trunk-jpl/cron/nightlyrun.sh.new \\ Export determination: 6. \\Rationale: New nightly run prototype, works with configs/win732\_larour. Please look at it and comment +D /issm/trunk-jpl/src/m/utils/Exp/expopen.m useless \\\\ Index: /issm/oecreview/Archive/11531-11549/r1.tex =================================================================== --- /issm/oecreview/Archive/11531-11549/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11531-11549/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11531 Index: /issm/oecreview/Archive/11531-11549/r2.tex =================================================================== --- /issm/oecreview/Archive/11531-11549/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11531-11549/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11549 Index: /issm/oecreview/Archive/11550-11568/Date.tex =================================================================== --- /issm/oecreview/Archive/11550-11568/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11550-11568/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11550-11568/ISSM-11550-11551.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11550-11551.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11550-11551.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 11550) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp (revision 11551) +@@ -144,7 +144,7 @@ + if (!isnan(bamgopts->hmaxVertices[i])){ + Metric M=BTh.vertices[i].m; + EigenMetric Vp(M/coef); +- Vp.Minh(bamgopts->hmaxVertices[i]); ++ Vp.Maxh(bamgopts->hmaxVertices[i]); + BTh.vertices[i].m=Vp; + } + } Index: /issm/oecreview/Archive/11550-11568/ISSM-11551-11552.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11551-11552.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11551-11552.diff (revision 11991) @@ -0,0 +1,547 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new (revision 11551) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh.new (revision 11552) +@@ -1,345 +0,0 @@ +-#!/bin/bash +-#This bash script calls the nightlyrun.m matlab file to run our nightly test decks. +-#It then processes the results and sends an email to the Ice developpers. +- +-#some functions +-function timer() #{{{1 +-{ +- if [[ $# -eq 0 ]]; then +- echo $(date '+%s') +- else +- local stime=$1 +- etime=$(date '+%s') +- +- if [[ -z "$stime" ]]; then stime=$etime; fi +- +- dt=$((etime - stime)) +- ds=$((dt % 60)) +- dm=$(((dt / 60) % 60)) +- dh=$((dt / 3600)) +- printf '%d:%02d:%02d' $dh $dm $ds +- fi +-} #}}} +-function todaydate() #{{{1 +-{ +- suffix=`date | awk '{printf("%s-%s-%s %s",$2,$3,$6,$4);}'` +- echo $suffix; +-} #}}} +-function host_name() #{{{1 +-{ +- #return host name depending on the OS +- if [ "$1" = "win7" ] +- then +- HOST_NAME=`hostname | sed 's/-//g'`; +- else +- HOST_NAME=`hostname -s | sed 's/-//g'`; +- fi +- echo $HOST_NAME; +-} #}}} +-function pause() #{{{1 +-{ +-pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'` +- +-while [ -n "$pid" ] +-do +- pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'` +-done +-} +-#}}} +-#Get configuration +-#Source config file{{{1 +-if [ $# -ne 1 ]; +-then +- #no config file specified: exit +- echo "no config file specified. Exiting..." >&2 # Error message to stderr. +- exit 1 +-fi +-if [ ! -f "$1" ] +-then +- echo "File $1 not found!" >&2 # Error message to stderr. +- exit 1 +-fi +-source $1; +-#}}} +-#Export ISSM_* variables{{{1 +-export ISSM_DIR +-export ISSM_TIER +-export ISSM_ARCH +-#}}} +-#Initialize variables {{{1 +-TODAY=$(todaydate); +-HOST_NAME=$(host_name $MACHINE); +-START_TIME=$(timer); +-ISSM_RELEASE=$(basename $(echo $REPOSITORY)); +-USER=$(whoami); +-INIT_PATH=$(pwd); +-#}}} +- +-#Lauch installation +-#Checkout/update/none ISSM if requested (ISSM_INSTALLATION){{{1 +-if [ "$ISSM_INSTALLATION" == "checkout" ] +-then +- +- #Erase previous code and Fetch the new one +- rm -rf $ISSM_RELEASE +- svn checkout "$REPOSITORY" +- +-elif [ "$ISSM_INSTALLATION" == "update" ] +-then +- +- #only update ISSM +- cd $ISSM_TIER +- svn update +- +-elif [ "$ISSM_INSTALLATION" == "none" ] +-then +- +- #do nothing +- echo "Skipping ISSM installation" +- +-else +- +- #Error message +- echo "ISSM_INSTALLATION supported values are: checkout, update and none. Exiting..." >&2 # Error message to stderr. +- exit 1 +- +-fi +-#}}} +-#Create cluster's settings{{{1 +-#create simpler cluster.rc file, with only the cluster we are interested in. +-cd $ISSM_TIER/test/NightlyRun/ +-if [ "$MACHINE" = "win7" ]; then +-cat << END > $HOST_NAME"_settings.m" +-cluster.login='$USER'; +-cluster.codepath='`cygpath -m $ISSM_TIER/bin`'; +-cluster.executionpath='`cygpath -m $EXECUTION_PATH`'; +-END +-else +-cat << END > $HOST_NAME"_settings.m" +-cluster.login='$USER'; +-cluster.codepath='$ISSM_TIER/bin'; +-cluster.executionpath='$EXECUTION_PATH'; +-END +-fi +-#}}} +-#Source environment variables with new matlab path {{{1 +-cd $ISSM_TIER/etc +-source environment.sh MATLAB_DIR=$MATLAB_PATH +-#}}} +-#install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 +-if [ "$ISSM_EXTERNALPACKAGES" == "install" ] +-then +- +- cd $ISSM_TIER/externalpackages +- #number of packages: +- numpackages=`echo $EXTERNALPACKAGES | wc -w` +- +- for (( i=1; i<=$numpackages; i++ )) +- do +- package=`echo $EXTERNALPACKAGES | cut -d " " -f $i-$i` +- package_config=`echo $EXTERNALPACKAGES_CONFIGS | cut -d " " -f $i-$i` +- package_numcpus=`echo $EXTERNALPACKAGES_NUMCPUS | cut -d " " -f $i-$i` +- +- cd $package +- $package_config $package_numcpus +- cd .. +- done +- +- +-elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ] +-then +- +- #erase externapackages, and link with externalpackages_dir +- cd $ISSM_TIER +- rm -rf externalpackages +- cp -Rf $EXTERNALPACKAGESDIR ./ +- +-elif [ "$ISSM_EXTERNALPACKAGES" == "none" ] +-then +- +- #Do nothing +- echo "Skipping external packages installation" +- +-else +- +- #Error message +- echo "ISSM_EXTERNALPACKAGES supported values are: install, copy and none. Exiting..." >&2 # Error message to stderr. +- exit 1 +- +-fi +-#}}} +-#ISSM compilation yes/no (ISSM_COMPILATION) {{{1 +-if [ "$ISSM_COMPILATION" == "yes" ] +-then +- +- cd $ISSM_TIER +- make clean +- make distclean +- ./scripts/automakererun.sh +- source ./configs/$COMPILE_CONFIG_FILE +- +- make -j $NUMCPUS_INSTALL +- make -j $NUMCPUS_INSTALL install +- +-elif [ "$ISSM_COMPILATION" == "no" ] +-then +- echo "Skipping ISSM compilation" +-else +- echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr. +- exit 1 +-fi +-#}}} +- +-#Prepare run +-#create softlink to startup {{{1 +-cd $ISSM_TIER/test/NightlyRun/ +-if [ "$MACHINE" = "win7" ]; then +- cp $ISSM_TIER/startup.m . +-else +- ln -s $ISSM_TIER/startup.m . +-fi +-#}}} +-#Create nightlylog directory and info.log {{{1 +-#put installation elapsed time in info.log +-INSTALL_TIME=$(timer) +-ELAPSED_INSTALL=$(timer $START_TIME) +-rm -rf $ISSM_TIER/nightlylog +-mkdir $ISSM_TIER/nightlylog +-cat << END > $ISSM_TIER/nightlylog/info.log +-today: $(echo $TODAY) +-user: $(echo $USER) +-host: $(echo $HOST_NAME) +-OS: $(echo $MACHINE) +-release: $(echo $ISSM_RELEASE) +-init_path: $(echo $INIT_PATH) +-elapsed_install: $(echo $ELAPSED_INSTALL) +-END +-#}}} +-#check NUMCPUS_RUN options {{{1 +-if [ "$NUMCPUS_RUN" = "" ] +-then +- echo "NUMCPUS_RUN option not found, defaulting to NUMCPUS_RUN = 1" +- NUMCPUS_RUN=1 +-fi +-#}}} +- +-#Run tests +-#on Matlab and windows machines, we'll need a windows style path: {{{ +-if [ "$MACHINE" = "win7" ]; then +- MATLAB_TIER=`cygpath -m $ISSM_TIER` +-else +- MATLAB_TIER=$ISSM_TIER +-fi +- +-#}}} +-#Launch all tests on different cpus {{{1 +-for (( i=1;i<=$NUMCPUS_RUN;i++ )) +-do +- #Launch matlab and the nightly run script +- cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF +- warning off %necessary to avoid a info.log of several Go for parallel runs +- try, +- cd $MATLAB_TIER/test/NightlyRun +- startup; +- $(if [ "$NROPTIONS" = "" ] +- then +- echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" +- else +- #echo "runme('id',[101 102]);" +- echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" +- fi +- ) +- catch me, +- %An error occured, get report and exit +- message=getReport(me) +- directory=strsplit(pwd,'/'); +- fid=fopen([ISSM_TIER '/nightlylog/matlaberror.log'], 'at'); +- fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end}); +- fprintf(fid,'%s',message); +- fclose(fid); +- end +- disp('MATLABEXITEDCORRECTLY'); +- exit +-EOF +- +- #Start run from nightlylog directory +- cd $ISSM_TIER/nightlylog/ +- +- #Start test +- $MATLABBIN -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & +- +-done +- +-#wait until matlab closes +-if [ "$MACHINE" = "win7" ]; then +- pause MATLAB +-else +- wait +-fi +- +-#}}} +-#concatenate all reports {{{1 +-cd $ISSM_TIER/nightlylog/ +-mv matlab_log1.log matlab_log.log +-for (( i=2;i<=$NUMCPUS_RUN;i++ )) +-do +- cat matlab_log.log matlab_log$i.log > matlab_log.log.bak +- mv matlab_log.log.bak matlab_log.log +-done +-#}}} +-#Complete info.log {{{1 +-if [ $(cat matlab_log.log | grep "MATLABEXITEDCORRECTLY" | wc -l) -eq $NUMCPUS_RUN ] +-then +- MATLABCRASH=0 +-else +- MATLABCRASH=1 +-fi +-ELAPSED_RUN=$(timer $INSTALL_TIME) +-ELAPSED_TOTAL=$(timer $START_TIME) +-cat << END >> $ISSM_TIER/nightlylog/info.log +-elapsed_run: $(echo $ELAPSED_RUN) +-elapsed_total: $(echo $ELAPSED_TOTAL) +-matlab_crash: $(echo $MATLABCRASH) +-END +-#}}} +- +-#Send Report +-#Build html report {{{1 +-cd $ISSM_TIER/nightlylog/ +-sh ../scripts/report.sh +-echo "html report located in $ISSM_TIER/nightlylog/report.html" +-#}}} +-#send mail if requested (SKIPMAIL) {{{1 +-if [ "$SKIPMAIL" != "yes" ] +-then +- echo "sending report..." +- source $ISSM_TIER/cron/mailinglist +- for i in `echo $MAILINGLIST`; do +- +- if [ "$MACHINE" = "win7" ] +- then +- echo $i +- email -html -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/nightlylog/report.html +- else +- if [ "$MACHINE" = "astrid" ] +- then +-cat - $ISSM_TIER/nightlylog/report.html < +-To: $i +-Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. +-Mime-Version: 1.0 +-Content-Type: text/html +-HERE +- else +-cat - $ISSM_TIER/nightlylog/report.html < +-To: $i +-Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. +-Mime-Version: 1.0 +-Content-Type: text/html +-HERE +- fi +- fi +- done +-fi +-#}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11551) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11552) +@@ -28,15 +28,24 @@ + function host_name() #{{{1 + { + #return host name depending on the OS +- if [ "$1" = "wineric" ] ++ if [ "$1" = "win7" ] + then +- HOST_NAME=`hostname`; ++ HOST_NAME=`hostname | sed 's/-//g'`; + else +- HOST_NAME=`hostname -s`; ++ HOST_NAME=`hostname -s | sed 's/-//g'`; + fi + echo $HOST_NAME; + } #}}} ++function pause() #{{{1 ++{ ++pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'` + ++while [ -n "$pid" ] ++do ++ pid=`ps aux -W | grep $1 | awk '{printf("%s\n",$1);}'` ++done ++} ++#}}} + #Get configuration + #Source config file{{{1 + if [ $# -ne 1 ]; +@@ -73,7 +82,7 @@ + + #Erase previous code and Fetch the new one + rm -rf $ISSM_RELEASE +- svn checkout $REPOSITORY ++ svn checkout "$REPOSITORY" + + elif [ "$ISSM_INSTALLATION" == "update" ] + then +@@ -99,11 +108,19 @@ + #Create cluster's settings{{{1 + #create simpler cluster.rc file, with only the cluster we are interested in. + cd $ISSM_TIER/test/NightlyRun/ ++if [ "$MACHINE" = "win7" ]; then + cat << END > $HOST_NAME"_settings.m" + cluster.login='$USER'; ++cluster.codepath='`cygpath -m $ISSM_TIER/bin`'; ++cluster.executionpath='`cygpath -m $EXECUTION_PATH`'; ++END ++else ++cat << END > $HOST_NAME"_settings.m" ++cluster.login='$USER'; + cluster.codepath='$ISSM_TIER/bin'; + cluster.executionpath='$EXECUTION_PATH'; + END ++fi + #}}} + #Source environment variables with new matlab path {{{1 + cd $ISSM_TIER/etc +@@ -112,21 +129,23 @@ + #install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 + if [ "$ISSM_EXTERNALPACKAGES" == "install" ] + then ++ + cd $ISSM_TIER/externalpackages +- for ep in $EXTERNALPACKAGES +- do +- cd $ep +- case $ep in +- "mpich2" ) ./install-1.0.2-linux64.sh ;; +- "petsc" ) ./install-3.2-linux64.sh ;; +- "metis" ) ./install-4.0-linux64.sh ;; +- "triangle" ) ./install-linux64.sh ;; +- "dakota" ) ./install-linux64-astrid.sh ;; +- *) ./install.sh $NUMCPUS_INSTALL +- esac ++ #number of packages: ++ numpackages=`echo $EXTERNALPACKAGES | wc -w` ++ ++ for (( i=1; i<=$numpackages; i++ )) ++ do ++ package=`echo $EXTERNALPACKAGES | cut -d " " -f $i-$i` ++ package_config=`echo $EXTERNALPACKAGES_CONFIGS | cut -d " " -f $i-$i` ++ package_numcpus=`echo $EXTERNALPACKAGES_NUMCPUS | cut -d " " -f $i-$i` ++ ++ cd $package ++ $package_config $package_numcpus + cd .. + done + ++ + elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ] + then + +@@ -157,20 +176,10 @@ + make clean + make distclean + ./scripts/automakererun.sh +- ./configs/config-linux64-astrid.sh ++ source ./configs/$COMPILE_CONFIG_FILE + +- #4: compile and install ISSM +- if [ "$MACHINE" = "wineric" ] +- then +- cd $ISSM_TIER/src/c +- ./intel-compile.sh +- cd $ISSM_TIER/src/mex +- make install +- cd $ISSM_TIER +- else +- make -j $NUMCPUS_INSTALL +- make -j $NUMCPUS_INSTALL install +- fi ++ make -j $NUMCPUS_INSTALL ++ make -j $NUMCPUS_INSTALL install + + elif [ "$ISSM_COMPILATION" == "no" ] + then +@@ -184,7 +193,11 @@ + #Prepare run + #create softlink to startup {{{1 + cd $ISSM_TIER/test/NightlyRun/ +-ln -s $ISSM_TIER/startup.m . ++if [ "$MACHINE" = "win7" ]; then ++ cp $ISSM_TIER/startup.m . ++else ++ ln -s $ISSM_TIER/startup.m . ++fi + #}}} + #Create nightlylog directory and info.log {{{1 + #put installation elapsed time in info.log +@@ -211,6 +224,14 @@ + #}}} + + #Run tests ++#on Matlab and windows machines, we'll need a windows style path: {{{ ++if [ "$MACHINE" = "win7" ]; then ++ MATLAB_TIER=`cygpath -m $ISSM_TIER` ++else ++ MATLAB_TIER=$ISSM_TIER ++fi ++ ++#}}} + #Launch all tests on different cpus {{{1 + for (( i=1;i<=$NUMCPUS_RUN;i++ )) + do +@@ -218,12 +239,13 @@ + cat > $ISSM_TIER/nightlylog/matlab_run$i.m << EOF + warning off %necessary to avoid a info.log of several Go for parallel runs + try, +- cd $ISSM_TIER/test/NightlyRun ++ cd $MATLAB_TIER/test/NightlyRun + startup; + $(if [ "$NROPTIONS" = "" ] + then + echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" + else ++ #echo "runme('id',[101 102]);" + echo "runme($NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);" + fi + ) +@@ -244,12 +266,17 @@ + cd $ISSM_TIER/nightlylog/ + + #Start test +- MATLAB_VERSION="7.6" #7.2,7.4,7.6 and 7.8 +- /usr/local/pkgs/matlab-$MATLAB_VERSION/bin/matlab -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & ++ $MATLABBIN -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & ++ + done + + #wait until matlab closes +-wait ++if [ "$MACHINE" = "win7" ]; then ++ pause MATLAB ++else ++ wait ++fi ++ + #}}} + #concatenate all reports {{{1 + cd $ISSM_TIER/nightlylog/ +@@ -289,9 +316,10 @@ + source $ISSM_TIER/cron/mailinglist + for i in `echo $MAILINGLIST`; do + +- if [ "$MACHINE" = "wineric" ] ++ if [ "$MACHINE" = "win7" ] + then +- email -html -f "ISSM Nightly run $EMAIL_ADRESS" -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/test/Verification/NightlyRun/report.html ++ echo $i ++ email -html -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/nightlylog/report.html + else + if [ "$MACHINE" = "astrid" ] + then Index: /issm/oecreview/Archive/11550-11568/ISSM-11552-11553.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11552-11553.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11552-11553.diff (revision 11991) @@ -0,0 +1,63 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11553) +@@ -0,0 +1,52 @@ ++Installing Matlab: ++ ++-Make sure that when you install Matlab, you choose C:\MATLAB\R2011b as directory ++for the installation. Failing to do so could preclude the sdk compiler from ++finding the Matlab header files. ++ ++-Also pay attention to what version of Matlab you are using, 32 or 64 bits, ++as this will need to be reflected onto the sdk compiler settings. ++ ++Win7: ++-Be sure to use an account name that does not have spaces in it, as this could be an ++issue with Cygwin. ++ ++ ++Cygwin: ++ ++-You will need cygwin installed on your Windows platform to manage the compilation. ++The compilation will still be carried out by the windows sdk compiler, but the ++environment driving the compilation will be the unix-like cygwin. When you download ++cygwin, make sure that you install it in the C:\Cygwin directory. ++ ++-You will find the cygwin setup executable on the www.cygwin.com webpage. Here is a link ++to it: http://cygwin.com/setup.exe. Download this file to C:\cygwin and be sure to reuse ++it when you want to update your current cygwin installation. Do not download setup.exe ++twice! ++ ++- You will need the following packages downloaded to carry out the compilation of ISSM ++ successfully, so be sure to include them in your cygwin install: ++ ++subversion ++autotools ++automake ++vim (or any other editor) ++ ++ ++ ++Compiler: ++ ++you will need the Windows SDK 7.1 compiler, which you can find at the following link ++http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=8279 ++This compiler is compatible with Matlab, as detailed in the following webpage: ++http://www.mathworks.com/support/compilers/R2011b/win64.html#n2 ++ ++ ++Downloading issm: ++ ++Download issm onto the C:\ directory. Do not download it in your Documents or Desktop ++folder. ++ ++In cygwin: ++cd /cygdrive/c/ ++svn co http://issm.ess.uci.edi/svn/issm/issm + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11550-11568/ISSM-11553-11554.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11553-11554.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11553-11554.diff (revision 11991) @@ -0,0 +1,173 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp (revision 11553) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp (revision 11554) +@@ -47,6 +47,7 @@ + KML_Polygon* kpoly =NULL; + KML_LinearRing* kring =NULL; + KML_LineString* kline =NULL; ++ KML_Point* kpoint=NULL; + + FILE* fid=NULL; + +@@ -59,8 +60,11 @@ + + /* read exp file */ + +- if (!DomainOutlineRead(&nprof,&pnvert,&pprofx,&pprofy,&closed,filexp,false)) ++ if (!DomainOutlineRead(&nprof,&pnvert,&pprofx,&pprofy,&closed,filexp,true)) + _error_("Error reading exp file."); ++ _printf_(true,"Exp2Kmlx -- Reading %d exp profiles from file \"%s\".\n",nprof,filexp); ++// for (i=0; incoord =pnvert[i]; +- kring->coords =(double (*)[3]) xmalloc(pnvert[i]*3*sizeof(double)); +- for (j=0; jncoord =pnvert[i]-1; ++ lat=(double *) xmalloc(kring->ncoord*sizeof(double)); ++ lon=(double *) xmalloc(kring->ncoord*sizeof(double)); ++ Xy2llx(lat,lon,pprofx[i],pprofy[i],kring->ncoord,sgn,cm,sp); ++ kring->coords =(double (*)[3]) xmalloc(kring->ncoord*3*sizeof(double)); ++ for (j=0; jncoord; j++) { + kring->coords[j][0]=lon[j]; + kring->coords[j][1]=lat[j]; + kring->coords[j][2]=0.; +@@ -155,19 +158,19 @@ + kring =NULL; + + for (i=1; incoord =pnvert[i]; +- kring->coords =(double (*)[3]) xmalloc(pnvert[i]*3*sizeof(double)); +- for (j=0; jncoord =pnvert[i]-1; ++ lat=(double *) xmalloc(kring->ncoord*sizeof(double)); ++ lon=(double *) xmalloc(kring->ncoord*sizeof(double)); ++ Xy2llx(lat,lon,pprofx[i],pprofy[i],kring->ncoord,sgn,cm,sp); ++ kring->coords =(double (*)[3]) xmalloc(kring->ncoord*3*sizeof(double)); ++ for (j=0; jncoord; j++) { + kring->coords[j][0]=lon[j]; + kring->coords[j][1]=lat[j]; + kring->coords[j][2]=0.; +@@ -191,7 +194,7 @@ + for (i=0; i 1 && pprofx[i][pnvert[i]-1] == pprofx[i][0] && pprofy[i][pnvert[i]-1] == pprofy[i][0]) { + sprintf(kplace->name ,"Polygon %d",i+1); + kplace->visibility=true; + sprintf(kplace->styleurl ,"#BlackLineRandomPoly"); +@@ -199,13 +202,12 @@ + kpoly =new KML_Polygon(); + kring =new KML_LinearRing(); + +- lat=(double *) xmalloc(pnvert[i]*sizeof(double)); +- lon=(double *) xmalloc(pnvert[i]*sizeof(double)); +- Xy2llx(lat,lon,pprofx[i],pprofy[i],pnvert[i],sgn,cm,sp); +- +- kring->ncoord =pnvert[i]; +- kring->coords =(double (*)[3]) xmalloc(pnvert[i]*3*sizeof(double)); +- for (j=0; jncoord =pnvert[i]-1; ++ lat=(double *) xmalloc(kring->ncoord*sizeof(double)); ++ lon=(double *) xmalloc(kring->ncoord*sizeof(double)); ++ Xy2llx(lat,lon,pprofx[i],pprofy[i],kring->ncoord,sgn,cm,sp); ++ kring->coords =(double (*)[3]) xmalloc(kring->ncoord*3*sizeof(double)); ++ for (j=0; jncoord; j++) { + kring->coords[j][0]=lon[j]; + kring->coords[j][1]=lat[j]; + kring->coords[j][2]=0.; +@@ -220,20 +222,19 @@ + kpoly =NULL; + } + +- else { ++ else if (pnvert[i] > 1) { + sprintf(kplace->name ,"LineString %d",i+1); + kplace->visibility=true; + sprintf(kplace->styleurl ,"#RandomLineEmptyPoly"); + + kline =new KML_LineString(); + +- lat=(double *) xmalloc(pnvert[i]*sizeof(double)); +- lon=(double *) xmalloc(pnvert[i]*sizeof(double)); +- Xy2llx(lat,lon,pprofx[i],pprofy[i],pnvert[i],sgn,cm,sp); +- + kline->ncoord =pnvert[i]; +- kline->coords =(double (*)[3]) xmalloc(pnvert[i]*3*sizeof(double)); +- for (j=0; jncoord*sizeof(double)); ++ lon=(double *) xmalloc(kline->ncoord*sizeof(double)); ++ Xy2llx(lat,lon,pprofx[i],pprofy[i],kline->ncoord,sgn,cm,sp); ++ kline->coords =(double (*)[3]) xmalloc(kline->ncoord*3*sizeof(double)); ++ for (j=0; jncoord; j++) { + kline->coords[j][0]=lon[j]; + kline->coords[j][1]=lat[j]; + kline->coords[j][2]=0.; +@@ -245,6 +246,26 @@ + kline =NULL; + } + ++ else if (pnvert[i]) { ++ sprintf(kplace->name ,"Point %d",i+1); ++ kplace->visibility=true; ++ sprintf(kplace->styleurl ,"#RandomLineEmptyPoly"); ++ ++ kpoint=new KML_Point(); ++ ++ lat=(double *) xmalloc(sizeof(double)); ++ lon=(double *) xmalloc(sizeof(double)); ++ Xy2llx(lat,lon,pprofx[i],pprofy[i],1,sgn,cm,sp); ++ kpoint->coords[0]=lon[0]; ++ kpoint->coords[1]=lat[0]; ++ kpoint->coords[2]=0.; ++ xfree((void**)&lon); ++ xfree((void**)&lat); ++ ++ (kplace->geometry )->AddObject((Object*)kpoint); ++ kpoint =NULL; ++ } ++ + (kfold ->feature )->AddObject((Object*)kplace); + kplace=NULL; + } +@@ -259,7 +280,7 @@ + + /* write kml file */ + +- _printf_(true,"Writing kml document to file.\n"); ++ _printf_(true,"Exp2Kmlx -- Writing kml document to file \"%s\".\n",filkml); + fid=fopen(filkml,"w"); + fprintf(fid,"\n"); + kfile->Write(fid,indent); Index: /issm/oecreview/Archive/11550-11568/ISSM-11554-11555.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11554-11555.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11554-11555.diff (revision 11991) @@ -0,0 +1,174 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/Sdk1.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/Sdk1.png +___________________________________________________________________ +Added: svn:executable + + * +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/Sdk2.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/Sdk2.png +___________________________________________________________________ +Added: svn:executable + + * +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11554) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11555) +@@ -1,3 +1,8 @@ ++Win7: ++-Be sure to use an account name that does not have spaces in it, as this could be an ++issue with Cygwin. ++ ++ + Installing Matlab: + + -Make sure that when you install Matlab, you choose C:\MATLAB\R2011b as directory +@@ -7,9 +12,6 @@ + -Also pay attention to what version of Matlab you are using, 32 or 64 bits, + as this will need to be reflected onto the sdk compiler settings. + +-Win7: +--Be sure to use an account name that does not have spaces in it, as this could be an +-issue with Cygwin. + + + Cygwin: +@@ -20,7 +22,7 @@ + cygwin, make sure that you install it in the C:\Cygwin directory. + + -You will find the cygwin setup executable on the www.cygwin.com webpage. Here is a link +-to it: http://cygwin.com/setup.exe. Download this file to C:\cygwin and be sure to reuse ++to it: http://cygwin.com/setup.exe. Download this file to C:\Cygwin and be sure to reuse + it when you want to update your current cygwin installation. Do not download setup.exe + twice! + +@@ -31,17 +33,39 @@ + autotools + automake + vim (or any other editor) ++patchutils ++make: The GNU version of the 'make' utility ++automake 1.11 and automake:Wrapper scripts ++autoconf ++python: Python language interpreter ++unzip + + + + Compiler: + +-you will need the Windows SDK 7.1 compiler, which you can find at the following link ++You need Visual Studio Express 2010 for C++, which you can find here: ++http://www.microsoft.com/visualstudio/en-us/products/2010-editions/visual-cpp-express ++ ++you will also need the Windows SDK 7.1 compiler, which you can find at the following link + http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=8279 + This compiler is compatible with Matlab, as detailed in the following webpage: + http://www.mathworks.com/support/compilers/R2011b/win64.html#n2 + ++Be careful not to download the sdk before Visual Studio Express, as this could lead to ++environment setup issues. + ++ ++Before you do anything related to ISSM! You have to capture the settings of your compiler. ++This is by far the most tricky part. ++ ++Follow Figure 2 for more details. You have to launch sdk 7.1 command prompt, go to the ++cygwin directory and fire up Cygwin by executing Cygwin.bat. Once this is done,dump the ++results of the export command onto a file, called sdk7.1.win7.64.sh ++you will need this file later in the ISSM install. ++ ++ ++ + Downloading issm: + + Download issm onto the C:\ directory. Do not download it in your Documents or Desktop +@@ -50,3 +74,75 @@ + In cygwin: + cd /cygdrive/c/ + svn co http://issm.ess.uci.edi/svn/issm/issm ++ ++Once you download it, in your home directory, edit .bashrc: ++and add the following lines: ++export ISSM_DIR=/cygdrive/c/issm ++export ISSM_TIER=$ISSM_DIR/trunk-jpl ++export ISSM_ARCH=cygwin-intel ++ ++#source ++source $ISSM_TIER/etc/environment.sh ++ ++ ++Getting the cl.exe compiler to work: ++before trying to compile the externalpackages, you need to be sure that your compiler cl.exe ++(the sdk compiler)works. To make sure, create a simple hello world file: ++ ++hello.cpp ++ ++#include ++int main(){ ++printf("%s\n","hello"); ++return 1; ++} ++ ++and try to compile it by doing: ++cl hello.cpp ++ ++If this does not work, do not go any further! The settings of your cl compiler are found ++in externalpackages/windows/configs/ ++if there is a significant different between you sdk7.1.win7.64.sh file (see above section Compiler) ++and the file that is being sourced in the windows/configs directory, place your new file in ++the configs directory. Relaunch bash, and try to run cl hello.cpp again. Beware, you might ++have to erase some lines in your file, as cygwin might not like some of the stuff that your ++Windows platform is trying to define. ++ ++ ++ ++ ++Once the cl.exe compiler works, you can start installing the following packages: ++petsc metis triangle and cccl ++ ++For petsc, use install-3.1-win7.sh ++For metis, use install-4.0-win7.sh ++For cccl, use install-win7.sh ++For triangle, use install-win7.sh ++ ++Once these externlapackages have been compiled, you can compile issm: ++ ++./scripts/autoremakererun.sh ++./configs/config-win7-64.sh ++make install ++ ++This should compile both parallel and serial versions of ISSM. Beware though, the parallel ++version cannot be run on multi-core platforms yet! We are actively working on it. ++ ++ ++ ++ ++ ++One note about 32 vs 64 bit compile: ++depending on your Matlab version, you will need to do a 32 or 64 bit compile. The only ++difference between both compiles is the setup of the cl.exe compiler. For ease of use, ++you will find in externalpackages/windows/windows_environment.sh a switch to go from 32 ++to 64 bit compile. When you type cl.exe \help at the command prompt, cl.exe should report ++what system it is compiling for. ++Beware, switching 32 to 64 or vice-versa implies recompiling everything from scratch. ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file Index: /issm/oecreview/Archive/11550-11568/ISSM-11555-11556.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11555-11556.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11555-11556.diff (revision 11991) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dyson/ldap.pl +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dyson/ldap.pl (revision 11555) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dyson/ldap.pl (revision 11556) +@@ -1,25 +1,25 @@ +-#!/usr/bin/perl +-# +-# LDAP.PL - Acquire JPL LDAP data and pare down to user IDs - 2011-08-01 +-# +-$cat="/bin/cat"; $srt="/bin/sort"; $ldb="/usr/bin/ldapsearch"; # Binary locations (change as needed) +-$lds="ldap.jpl.nasa.gov"; $ou="ou=personnel,dc=dir,dc=jpl,dc=nasa,dc=gov"; # Define LDAP server & organization +-$bn="jplbadgenumber"; $txt="$bn".".txt"; $db="jplusers.db"; # Initialize values +-# +-system(`$ldb -x -h $lds -b $ou uid=* filter $bn > $txt`); # Execute LDAPsearch, write to file +-# +-open(I,"<$txt"); # Open input file handle +- open(O,">badges.tmp"); # Open output file handle +- while () { chomp($_); # Spool through input file +- if ($_=~"^uid=") { # If line begins with UID value, +- $_=~s/uid=//; $_=~s/,(.*)$//; $_=~s/\n//; # strip line of extraneous data +- if (!($_=~/^\d\d\d\d\d\d/)) { print O "$_\n"; } # If UID is non-numeric, print output +- } # Close condition +- } # Close spool +- close(O); # Close output file handle +-close(I); # Close input file handle +-# +-system(`$cat badges.tmp |$srt -u > $db 2>/dev/null`); # Sort output +-unlink("badges.tmp"); unlink("$txt"); # Unlink temp files +-# +-# EOF - 2011-08-01 - Jay Dyson ++#!/usr/bin/perl ++# ++# LDAP.PL - Acquire JPL LDAP data and pare down to user IDs - 2011-08-01 ++# ++$cat="/bin/cat"; $srt="/bin/sort"; $ldb="/usr/bin/ldapsearch"; # Binary locations (change as needed) ++$lds="ldap.jpl.nasa.gov"; $ou="ou=personnel,dc=dir,dc=jpl,dc=nasa,dc=gov"; # Define LDAP server & organization ++$bn="jplbadgenumber"; $txt="$bn".".txt"; $db="jplusers.db"; # Initialize values ++# ++system(`$ldb -x -h $lds -b $ou uid=* uid > $txt`); # Execute LDAPsearch, write to file ++# ++open(I,"<$txt"); # Open input file handle ++ open(O,">badges.tmp"); # Open output file handle ++ while () { chomp($_); # Spool through input file ++ if ($_ =~ "^uid: ") { # If line begins with UID value, ++ $_=~s/uid: //; $_=~s/,(.*)$//; $_=~s/\n//; # strip line of extraneous data ++ if (!($_=~/^\d\d\d\d\d\d/)) { print O "$_\n"; } # If UID is non-numeric, print output ++ } # Close condition ++ } # Close spool ++ close(O); # Close output file handle ++close(I); # Close input file handle ++# ++system(`$cat badges.tmp |$srt -u > $db 2>/dev/null`); # Sort output ++unlink("badges.tmp"); unlink("$txt"); # Unlink temp files ++# ++# EOF - 2011-08-01 - Jay Dyson Index: /issm/oecreview/Archive/11550-11568/ISSM-11556-11557.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11556-11557.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11556-11557.diff (revision 11991) @@ -0,0 +1,204 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.appscript +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.appscript (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.appscript (revision 11557) +@@ -0,0 +1 @@ ++do shell script "open /Library/ISSM/bin/matlabissm" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/issm.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/issm.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist (revision 11557) +@@ -0,0 +1,44 @@ ++ ++ ++ ++ ++ CFBundleAllowMixedLocalizations ++ ++ CFBundleDevelopmentRegion ++ English ++ CFBundleExecutable ++ applet ++ CFBundleIconFile ++ applet ++ CFBundleInfoDictionaryVersion ++ 6.0 ++ CFBundleName ++ ISSM ++ CFBundlePackageType ++ APPL ++ CFBundleSignature ++ aplt ++ LSMinimumSystemVersionByArchitecture ++ ++ x86_64 ++ 10.6 ++ ++ LSRequiresCarbon ++ ++ WindowState ++ ++ dividerCollapsed ++ ++ eventLogLevel ++ -1 ++ name ++ ScriptWindowState ++ positionOfDivider ++ 333 ++ savedFrame ++ 1006 323 602 597 0 0 1680 1028 ++ selectedTabView ++ result ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 11557) +@@ -0,0 +1,4 @@ ++{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf230 ++{\fonttbl} ++{\colortbl;\red255\green255\blue255;} ++} +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo (revision 11557) +@@ -0,0 +1 @@ ++APPLaplt +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pkg +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pkg +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm (revision 11557) +@@ -0,0 +1,2 @@ ++#/bin/bash ++matlab -r "addpath /Library/ISSM/bin/; startup" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m (revision 11557) +@@ -0,0 +1,46 @@ ++%STARTUP - Matlab startup script ++% ++% startup.m is a script run by matlab at the beginning of a session, just ++% before handing over the prompt to the user. This delivery startup.m script ++% has been customized here for the ISSM code. This startup script should be ++% run by users before trying to use ISSM. The best way to do that is to put ++% the startup file in the location where Matlab starts and established its ++% root directory. ++ ++% clear the last warning to focus on the warnings of the ISSM path ++lastwarn(''); ++ ++%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++ISSM_TIER=getenv('ISSM_TIER'); ++ ++if (isempty(ISSM_TIER)), ++ error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++end ++ ++%Now add all issm code paths necessary to run issm smoothly. ++%We capture the error output, so that we can warn the user to update ++%the variable ISSM_TIER in this file, in case it is not correctly setup. ++ ++%ISSM path ++addpath(pwd); %add current path first ++addpath([pwd '\bin']); ++ ++%Check on any warning messages that might indicate that the paths were not correct. ++if ~isempty(lastwarn), ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); ++else ++ fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); ++end ++ ++%disable matlab bell! ++beep off; ++ ++% no warning if we try to plot while in nojvm (will not be supported in future releases) ++warning off MATLAB:HandleGraphics:noJVM ++ ++%at the end, get to tests directory if ISSM_TESTS exists: ++ISSM_TESTS=getenv('ISSM_TESTS'); ++if ~isempty(ISSM_TESTS), ++ cd(ISSM_TESTS); ++end + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11550-11568/ISSM-11557-11558.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11557-11558.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11557-11558.diff (revision 11991) @@ -0,0 +1,23 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11557) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11558) +@@ -523,7 +523,7 @@ + + if(stabilization==2){ + /*Streamline upwinding*/ +- vel=sqrt(pow(vx,2.)+pow(vy,2.)); ++ vel=sqrt(pow(vx,2.)+pow(vy,2.))+1.e-8; + K[0][0]=h/(2*vel)*vx*vx; + K[1][0]=h/(2*vel)*vy*vx; + K[0][1]=h/(2*vel)*vx*vy; +@@ -3666,8 +3666,8 @@ + // vx_input->GetInputValue(&vx,gauss); + // vy_input->GetInputValue(&vy,gauss); + // grade_g[iv]=-2*drag*alpha_complement*((lambda*vx+mu*vy)); +- // VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,INSERT_VALUES); + //} ++ //VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,INSERT_VALUES); + /*End Analytical gradient*/ + + VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); Index: /issm/oecreview/Archive/11550-11568/ISSM-11558-11559.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11558-11559.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11558-11559.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.m (revision 11558) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/prognostic.m (revision 11559) +@@ -49,7 +49,7 @@ + + checkfield(md,'prognostic.spcthickness','forcing',1); + checkfield(md,'prognostic.hydrostatic_adjustment','values',{'Absolute' 'Incremental'}); +- checkfield(md,'prognostic.stabilization','values',[0 1 3]); ++ checkfield(md,'prognostic.stabilization','values',[0 1 2 3]); + checkfield(md,'prognostic.min_thickness','>',0); + + end % }}} +@@ -58,7 +58,7 @@ + fielddisplay(obj,'spcthickness','thickness constraints (NaN means no constraint)'); + fielddisplay(obj,'min_thickness','minimum ice thickness allowed'); + fielddisplay(obj,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' '); +- fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 3->discontinuous Galerkin'); ++ fielddisplay(obj,'stabilization','0->no, 1->artificial_diffusivity, 2->streamline upwinding, 3->discontinuous Galerkin'); + + disp(sprintf('\n %s','Penalty options:')); + fielddisplay(obj,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset'); Index: /issm/oecreview/Archive/11550-11568/ISSM-11559-11560.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11559-11560.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11559-11560.diff (revision 11991) @@ -0,0 +1,28 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/historyISSM.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/historyISSM.m (revision 11559) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/scripts/historyISSM.m (revision 11560) +@@ -1,18 +1,13 @@ + !vim runme.m +-md=runme('id',101); + runme('id',[101]); +-md.numberofelements +-md.numberofnodes ++md.mesh.numberofelements + md=mesh(md,'DomainOutline.exp',5000); +-md=geography(md,'',''); +-md=geography(md,'Iceshelves.exp','Islands.exp'); +-md=setelementstype(md,'macayeal','all'); +-md=setelementstype(md,'pattyn','all','stokes','all'); +-md=solve(md,ThermalSolutionEnum); ++md=setmask(md,'',''); ++md=setflowequation(md,'macayeal','all'); ++md=setflowequation(md,'pattyn','all','stokes','all'); ++md=solve(md,TransientSolutionEnum); + md=solve(md,BalancedthicknessSolutionEnum); + md=solve(md,DiagnosticSolutionEnum); + md=loadresultsfromcluster(md); +-md=tres(md,ThermalSolutionEnum); +-md=tres(md,DiagnosticSolutionEnum); + plotmodel(md,'data',md.results.DiagnosticSolution.Vel) + plotmodel(md,'data',) Index: /issm/oecreview/Archive/11550-11568/ISSM-11560-11561.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11560-11561.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11560-11561.diff (revision 11991) @@ -0,0 +1,118 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11560) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11561) +@@ -15,8 +15,8 @@ + #Machine configuration + MACHINE="astrid" + +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + + #----------------------# + # 2: ISSM Installation # +@@ -53,6 +53,10 @@ + #List of external pakages to be installed + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" + ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ + #---------------------# + # 4: ISSM Compilation # + #---------------------# +@@ -90,3 +94,12 @@ + #ex: "'id',[101 102 103]" + + NROPTIONS="'benchmark','all'" ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily (revision 11560) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily (revision 11561) +@@ -16,8 +16,8 @@ + #Machine configuration + MACHINE="astrid" + +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + + #----------------------# + # 2: ISSM Installation # +@@ -54,6 +54,10 @@ + #List of external pakages to be installed + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_NUMCPUS=" 8 8 8 8 8 8" ++ + #---------------------# + # 4: ISSM Compilation # + #---------------------# +@@ -91,3 +95,12 @@ + #ex: "'id',[101 102 103]" + + NROPTIONS="" ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly (revision 11560) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly (revision 11561) +@@ -16,8 +16,8 @@ + #Machine configuration + MACHINE="astrid" + +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + + #----------------------# + # 2: ISSM Installation # +@@ -54,6 +54,10 @@ + #List of external pakages to be installed + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ + #---------------------# + # 4: ISSM Compilation # + #---------------------# +@@ -91,3 +95,13 @@ + #ex: "'id',[101 102 103]" + + NROPTIONS="" ++ ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" Index: /issm/oecreview/Archive/11550-11568/ISSM-11561-11562.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11561-11562.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11561-11562.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11561) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11562) +@@ -145,4 +145,7 @@ + + + +- +\ No newline at end of file ++How to setup a Cron job? ++downlaod exim and cron from cygwin. run exim-config (don't forget to launch your cygwin terminal as ++Administrator). If asked for a daemon name, type ntsec. Also, if cron complains about sendmail, ++symlink /usr/lib/sendmail and /usr/bin/exim. Index: /issm/oecreview/Archive/11550-11568/ISSM-11562-11563.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11562-11563.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11562-11563.diff (revision 11991) @@ -0,0 +1,31 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11562) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11563) +@@ -3596,6 +3596,7 @@ + int i,ig; + int analysis_type; + int doflist1[NUMVERTICES]; ++ int connectivity[NUMVERTICES]; + double vx,vy,lambda,mu,alpha_complement,Jdet; + double bed,thickness,Neff,drag; + double xyz_list[NUMVERTICES][3]; +@@ -3613,6 +3614,7 @@ + parameters->FindParam(&analysis_type,AnalysisTypeEnum); + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); + GradientIndexing(&doflist1[0],control_index); ++ this->GetConnectivityList(&connectivity[0]); + + /*Build frictoin element, needed later: */ + friction=new Friction("2d",inputs,matpar,analysis_type); +@@ -3665,9 +3667,8 @@ + // adjointy_input->GetInputValue(&mu, gauss); + // vx_input->GetInputValue(&vx,gauss); + // vy_input->GetInputValue(&vy,gauss); +- // grade_g[iv]=-2*drag*alpha_complement*((lambda*vx+mu*vy)); ++ // grade_g[iv] = -2*drag*alpha_complement*(lambda*vx+mu*vy)/((double)connectivity[iv]); + //} +- //VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,INSERT_VALUES); + /*End Analytical gradient*/ + + VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); Index: /issm/oecreview/Archive/11550-11568/ISSM-11563-11564.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11563-11564.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11563-11564.diff (revision 11991) @@ -0,0 +1,92 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11563) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/aic.sh (revision 11564) +@@ -1,38 +0,0 @@ +-#!/bin/bash +- +-#get brand new project: +-rm -rf ISSM.aip ISSM-SetupFiles ISSM.msi +-cp ISSM.initial.aip ISSM.aip +- +-#get windows style path to files +-ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` +- +-#build list of files to put into the installer: +-rm -rf ISSM.aic +-cat << END > ISSM.aic +-;aic +-SetVersion "1.0" +-SetPackageName "ISSM.msi" +-END +- +-ls $ISSM_TIER_WIN/scripts/*.bat startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic +- +-cat << END >> ISSM.aic +-AddFolder PersonalFolder $ISSM_TIER_WIN\test +-AddFolder APPDIR $ISSM_TIER_WIN\bin +-DelEnvironment ISSM_TESTS +-NewEnvironment -name ISSM_TESTS -value [test_Dir] +-DelEnvironment ISSM_TIER +-NewEnvironment -name ISSM_TIER -value [APPDIR] +-DelEnvironment ISSM_TIER_WIN +-NewEnvironment -name ISSM_TIER_WIN -value [APPDIR] +-Save +-Rebuild +-END +- +-#Run installer: +-"C:/Program Files (x86)/Caphyon/Advanced Installer 8.9/bin/x86/AdvancedInstaller.com" /execute ./ISSM.aip ./ISSM.aic +- +-#Get rid of temporary files: +-cp ISSM-SetupFiles/ISSM.msi ./ +-rm -rf ISSM.aip ISSM-SetupFiles ISSM.aic +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/package.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/package.sh (revision 11564) +@@ -0,0 +1,38 @@ ++#!/bin/bash ++ ++#get brand new project: ++rm -rf ISSM.aip ISSM-SetupFiles ISSM.msi ++cp ISSM.initial.aip ISSM.aip ++ ++#get windows style path to files ++ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` ++ ++#build list of files to put into the installer: ++rm -rf ISSM.aic ++cat << END > ISSM.aic ++;aic ++SetVersion "1.0" ++SetPackageName "ISSM.msi" ++END ++ ++ls $ISSM_TIER_WIN/scripts/*.bat startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic ++ ++cat << END >> ISSM.aic ++AddFolder PersonalFolder $ISSM_TIER_WIN\test ++AddFolder APPDIR $ISSM_TIER_WIN\bin ++DelEnvironment ISSM_TESTS ++NewEnvironment -name ISSM_TESTS -value [test_Dir] ++DelEnvironment ISSM_TIER ++NewEnvironment -name ISSM_TIER -value [APPDIR] ++DelEnvironment ISSM_TIER_WIN ++NewEnvironment -name ISSM_TIER_WIN -value [APPDIR] ++Save ++Rebuild ++END ++ ++#Run installer: ++"C:/Program Files (x86)/Caphyon/Advanced Installer 8.9/bin/x86/AdvancedInstaller.com" /execute ./ISSM.aip ./ISSM.aic ++ ++#Get rid of temporary files: ++cp ISSM-SetupFiles/ISSM.msi ./ ++rm -rf ISSM.aip ISSM-SetupFiles ISSM.aic + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/win7/package.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11550-11568/ISSM-11565-11566.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11565-11566.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11565-11566.diff (revision 11991) @@ -0,0 +1,305 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.appscript +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.appscript (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.appscript (revision 11566) +@@ -0,0 +1 @@ ++do shell script "open /Library/ISSM/bin/matlabissm" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/package.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/package.sh (revision 11566) +@@ -0,0 +1,6 @@ ++#/bin/bash ++ ++#Package using the Package Maker from OSX, driven by command line. ++rm -rf ISSM.pkg ++ ++PackageMaker -d ISSM.pmdoc -o ISSM.pkg + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/package.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/issm.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/issm.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist (revision 11566) +@@ -0,0 +1,44 @@ ++ ++ ++ ++ ++ CFBundleAllowMixedLocalizations ++ ++ CFBundleDevelopmentRegion ++ English ++ CFBundleExecutable ++ applet ++ CFBundleIconFile ++ applet ++ CFBundleInfoDictionaryVersion ++ 6.0 ++ CFBundleName ++ ISSM ++ CFBundlePackageType ++ APPL ++ CFBundleSignature ++ aplt ++ LSMinimumSystemVersionByArchitecture ++ ++ x86_64 ++ 10.6 ++ ++ LSRequiresCarbon ++ ++ WindowState ++ ++ dividerCollapsed ++ ++ eventLogLevel ++ -1 ++ name ++ ScriptWindowState ++ positionOfDivider ++ 333 ++ savedFrame ++ 1006 323 602 597 0 0 1680 1028 ++ selectedTabView ++ result ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 11566) +@@ -0,0 +1,4 @@ ++{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf230 ++{\fonttbl} ++{\colortbl;\red255\green255\blue255;} ++} +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo (revision 11566) +@@ -0,0 +1 @@ ++APPLaplt +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pkg +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pkg +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 11566) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup.xml (revision 11566) +@@ -0,0 +1 @@ ++ISSM.startup.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/startup.m/Library/ISSM/bin/installTo.pathrelocatableparentinstallToidentifier03startup-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11566) +@@ -0,0 +1 @@ ++groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 11566) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/index.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/index.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/index.xml (revision 11566) +@@ -0,0 +1 @@ ++ISSM/Users/larour/issm-uci/trunk-jpl/installers/macosx/ISSM.pkghttp://issm.jpl.nasa.govIce Sheet System Model01issm.xml02matlabissm.xml03startup.xml04bin.xmlproperties.titleproperties.userDomaindescriptionproperties.anywhereDomain +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 11566) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm.xml (revision 11566) +@@ -0,0 +1 @@ ++ISSM.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/ISSM.app/ApplicationsrequireAuthorizationidentifierinstallTorelocatableincludeRootparent01issm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin.xml (revision 11566) +@@ -0,0 +1 @@ ++issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/bin/Library/ISSM/bininstallTo.pathparentinstallToidentifier04bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 11566) +@@ -0,0 +1 @@ ++ISSM.matlabissm.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/matlabissm/Library/ISSM/bin/installTo.isRelativeTypeinstallTorelocatableinstallTo.isAbsoluteTypeidentifierparentinstallTo.path02matlabissm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm (revision 11566) +@@ -0,0 +1,2 @@ ++#/bin/bash ++matlab -r "addpath /Library/ISSM/bin/; startup" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/matlabissm +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/README (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/README (revision 11566) +@@ -0,0 +1,16 @@ ++Files needsed to package ISSM into a MacOSX delivery: ++ ++ISSM.appscript : applescript file used by Script Editor to build ISSM.app. Just edit using applescript, and save ++as application. ++ ++ISSM.app: result of above. ++ ++ISSM.pmdoc: Package Maker project, which outputs ISSM.pkg ++ ++ISSM.pkg: result of above. ++ ++Package Maker can be command line driven, using the pmdoc project directly. This is what package.sh does. ++ ++issm.icns: icon file for ISSM install. ++matlabissm: used by the Package Maker to launch matlab with ISSM path sourced. ++startup.m: needed to be sourced by Matlab to point towards mac executables. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m (revision 11566) +@@ -0,0 +1,46 @@ ++%STARTUP - Matlab startup script ++% ++% startup.m is a script run by matlab at the beginning of a session, just ++% before handing over the prompt to the user. This delivery startup.m script ++% has been customized here for the ISSM code. This startup script should be ++% run by users before trying to use ISSM. The best way to do that is to put ++% the startup file in the location where Matlab starts and established its ++% root directory. ++ ++% clear the last warning to focus on the warnings of the ISSM path ++lastwarn(''); ++ ++%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++ISSM_TIER=getenv('ISSM_TIER'); ++ ++if (isempty(ISSM_TIER)), ++ error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++end ++ ++%Now add all issm code paths necessary to run issm smoothly. ++%We capture the error output, so that we can warn the user to update ++%the variable ISSM_TIER in this file, in case it is not correctly setup. ++ ++%ISSM path ++addpath(pwd); %add current path first ++addpath([pwd '\bin']); ++ ++%Check on any warning messages that might indicate that the paths were not correct. ++if ~isempty(lastwarn), ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); ++else ++ fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); ++end ++ ++%disable matlab bell! ++beep off; ++ ++% no warning if we try to plot while in nojvm (will not be supported in future releases) ++warning off MATLAB:HandleGraphics:noJVM ++ ++%at the end, get to tests directory if ISSM_TESTS exists: ++ISSM_TESTS=getenv('ISSM_TESTS'); ++if ~isempty(ISSM_TESTS), ++ cd(ISSM_TESTS); ++end + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/installers/macosx/startup.m +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11550-11568/ISSM-11566-11567.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11566-11567.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11566-11567.diff (revision 11991) @@ -0,0 +1,435 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/package.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/package.sh (revision 11567) +@@ -0,0 +1,38 @@ ++#!/bin/bash ++ ++#get brand new project: ++rm -rf ISSM.aip ISSM-SetupFiles ISSM.msi ++cp ISSM.initial.aip ISSM.aip ++ ++#get windows style path to files ++ISSM_TIER_WIN=`cygpath -m "$ISSM_TIER"` ++ ++#build list of files to put into the installer: ++rm -rf ISSM.aic ++cat << END > ISSM.aic ++;aic ++SetVersion "1.0" ++SetPackageName "ISSM.msi" ++END ++ ++ls $ISSM_TIER_WIN/scripts/*.bat startup.m $ISSM_TIER_WIN/bin/*.h | awk '{printf("AddFile APPDIR %s\n",$1);}' | sed 's/\//\\/g' >> ISSM.aic ++ ++cat << END >> ISSM.aic ++AddFolder PersonalFolder $ISSM_TIER_WIN\test ++AddFolder APPDIR $ISSM_TIER_WIN\bin ++DelEnvironment ISSM_TESTS ++NewEnvironment -name ISSM_TESTS -value [test_Dir] ++DelEnvironment ISSM_TIER ++NewEnvironment -name ISSM_TIER -value [APPDIR] ++DelEnvironment ISSM_TIER_WIN ++NewEnvironment -name ISSM_TIER_WIN -value [APPDIR] ++Save ++Rebuild ++END ++ ++#Run installer: ++"C:/Program Files (x86)/Caphyon/Advanced Installer 8.9/bin/x86/AdvancedInstaller.com" /execute ./ISSM.aip ./ISSM.aic ++ ++#Get rid of temporary files: ++cp ISSM-SetupFiles/ISSM.msi ./ ++rm -rf ISSM.aip ISSM-SetupFiles ISSM.aic + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/package.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/ISSMlogo.ico +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = image/x-icon + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/ISSMlogo.ico +___________________________________________________________________ +Added: svn:mime-type + + image/x-icon +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/ISSM.initial.aip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/xml + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/ISSM.initial.aip +___________________________________________________________________ +Added: svn:mime-type + + application/xml +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/startup.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/startup.m (revision 11567) +@@ -0,0 +1,46 @@ ++%STARTUP - Matlab startup script ++% ++% startup.m is a script run by matlab at the beginning of a session, just ++% before handing over the prompt to the user. This delivery startup.m script ++% has been customized here for the ISSM code. This startup script should be ++% run by users before trying to use ISSM. The best way to do that is to put ++% the startup file in the location where Matlab starts and established its ++% root directory. ++ ++% clear the last warning to focus on the warnings of the ISSM path ++lastwarn(''); ++ ++%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++ISSM_TIER=getenv('ISSM_TIER_WIN'); ++ ++if (isempty(ISSM_TIER)), ++ error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++end ++ ++%Now add all issm code paths necessary to run issm smoothly. ++%We capture the error output, so that we can warn the user to update ++%the variable ISSM_TIER in this file, in case it is not correctly setup. ++ ++%ISSM path ++addpath(pwd); %add current path first ++addpath([pwd '\bin']); ++ ++%Check on any warning messages that might indicate that the paths were not correct. ++if ~isempty(lastwarn), ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); ++else ++ fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); ++end ++ ++%disable matlab bell! ++beep off; ++ ++% no warning if we try to plot while in nojvm (will not be supported in future releases) ++warning off MATLAB:HandleGraphics:noJVM ++ ++%at the end, get to tests directory if ISSM_TESTS exists: ++ISSM_TESTS=getenv('ISSM_TESTS'); ++if ~isempty(ISSM_TESTS), ++ cd(ISSM_TESTS); ++end + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/win7/startup.m +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.appscript +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.appscript (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.appscript (revision 11567) +@@ -0,0 +1 @@ ++do shell script "open /Library/ISSM/bin/matlabissm" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11567) +@@ -0,0 +1,6 @@ ++#/bin/bash ++ ++#Package using the Package Maker from OSX, driven by command line. ++rm -rf ISSM.pkg ++ ++PackageMaker -d ISSM.pmdoc -o ISSM.pkg + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/issm.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/issm.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS/applet +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS/applet +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist (revision 11567) +@@ -0,0 +1,44 @@ ++ ++ ++ ++ ++ CFBundleAllowMixedLocalizations ++ ++ CFBundleDevelopmentRegion ++ English ++ CFBundleExecutable ++ applet ++ CFBundleIconFile ++ applet ++ CFBundleInfoDictionaryVersion ++ 6.0 ++ CFBundleName ++ ISSM ++ CFBundlePackageType ++ APPL ++ CFBundleSignature ++ aplt ++ LSMinimumSystemVersionByArchitecture ++ ++ x86_64 ++ 10.6 ++ ++ LSRequiresCarbon ++ ++ WindowState ++ ++ dividerCollapsed ++ ++ eventLogLevel ++ -1 ++ name ++ ScriptWindowState ++ positionOfDivider ++ 333 ++ savedFrame ++ 1006 323 602 597 0 0 1680 1028 ++ selectedTabView ++ result ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 11567) +@@ -0,0 +1,4 @@ ++{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf230 ++{\fonttbl} ++{\colortbl;\red255\green255\blue255;} ++} +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.rsrc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.rsrc +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo (revision 11567) +@@ -0,0 +1 @@ ++APPLaplt +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pkg +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pkg +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 11567) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml (revision 11567) +@@ -0,0 +1 @@ ++ISSM.startup.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/startup.m/Library/ISSM/bin/installTo.pathrelocatableparentinstallToidentifier03startup-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11567) +@@ -0,0 +1 @@ ++groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 11567) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml (revision 11567) +@@ -0,0 +1 @@ ++ISSM/Users/larour/issm-uci/trunk-jpl/installers/macosx/ISSM.pkghttp://issm.jpl.nasa.govIce Sheet System Model01issm.xml02matlabissm.xml03startup.xml04bin.xmlproperties.titleproperties.userDomaindescriptionproperties.anywhereDomain +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 11567) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml (revision 11567) +@@ -0,0 +1 @@ ++ISSM.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/ISSM.app/ApplicationsrequireAuthorizationidentifierinstallTorelocatableincludeRootparent01issm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml (revision 11567) +@@ -0,0 +1 @@ ++issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/bin/Library/ISSM/bininstallTo.pathparentinstallToidentifier04bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 11567) +@@ -0,0 +1 @@ ++ISSM.matlabissm.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/matlabissm/Library/ISSM/bin/installTo.isRelativeTypeinstallTorelocatableinstallTo.isAbsoluteTypeidentifierparentinstallTo.path02matlabissm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11567) +@@ -0,0 +1,2 @@ ++#/bin/bash ++matlab -r "addpath /Library/ISSM/bin/; startup" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/README (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/README (revision 11567) +@@ -0,0 +1,16 @@ ++Files needsed to package ISSM into a MacOSX delivery: ++ ++ISSM.appscript : applescript file used by Script Editor to build ISSM.app. Just edit using applescript, and save ++as application. ++ ++ISSM.app: result of above. ++ ++ISSM.pmdoc: Package Maker project, which outputs ISSM.pkg ++ ++ISSM.pkg: result of above. ++ ++Package Maker can be command line driven, using the pmdoc project directly. This is what package.sh does. ++ ++issm.icns: icon file for ISSM install. ++matlabissm: used by the Package Maker to launch matlab with ISSM path sourced. ++startup.m: needed to be sourced by Matlab to point towards mac executables. +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m (revision 11567) +@@ -0,0 +1,46 @@ ++%STARTUP - Matlab startup script ++% ++% startup.m is a script run by matlab at the beginning of a session, just ++% before handing over the prompt to the user. This delivery startup.m script ++% has been customized here for the ISSM code. This startup script should be ++% run by users before trying to use ISSM. The best way to do that is to put ++% the startup file in the location where Matlab starts and established its ++% root directory. ++ ++% clear the last warning to focus on the warnings of the ISSM path ++lastwarn(''); ++ ++%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++ISSM_TIER=getenv('ISSM_TIER'); ++ ++if (isempty(ISSM_TIER)), ++ error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++end ++ ++%Now add all issm code paths necessary to run issm smoothly. ++%We capture the error output, so that we can warn the user to update ++%the variable ISSM_TIER in this file, in case it is not correctly setup. ++ ++%ISSM path ++addpath(pwd); %add current path first ++addpath([pwd '\bin']); ++ ++%Check on any warning messages that might indicate that the paths were not correct. ++if ~isempty(lastwarn), ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); ++else ++ fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); ++end ++ ++%disable matlab bell! ++beep off; ++ ++% no warning if we try to plot while in nojvm (will not be supported in future releases) ++warning off MATLAB:HandleGraphics:noJVM ++ ++%at the end, get to tests directory if ISSM_TESTS exists: ++ISSM_TESTS=getenv('ISSM_TESTS'); ++if ~isempty(ISSM_TESTS), ++ cd(ISSM_TESTS); ++end + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11550-11568/ISSM-11567-11568.diff =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-11567-11568.diff (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-11567-11568.diff (revision 11991) @@ -0,0 +1,107 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh (revision 11568) +@@ -0,0 +1,96 @@ ++#!/bin/bash ++ ++#Get number of cpus ++NUMCPUS=$1; ++ ++#Some cleanup ++rm -rf Dakota ++rm -rf src ++rm -rf install ++mkdir src install ++ ++#Untar ++tar -zxvf Dakota_4_3.src.tar.gz ++ ++#Move Dakota to src directory ++mv Dakota/* src ++rm -rf Dakota ++ ++#Apply patches ++patch src/src/ParallelLibrary.C ./ParallelLibrary.C.patch ++patch src/src/ParallelLibrary.H ./ParallelLibrary.H.patch ++patch src/src/NIDRProblemDescDB.C ./NIDRProblemDescDB.C.patch ++patch src/src/NonDSampling.C ./NonDSampling.C.patch ++patch src/src/NonDLocalReliability.C ./NonDLocalReliability.C.patch ++patch src/src/NonDUnilevelRBDO.C ./NonDUnilevelRBDO.C.patch # source not even used? ++#patch -R src/packages/Pecos/src/LHSDriver.cpp ./LHSDriver.cpp.patch ++ ++#Configure dakota ++cd src ++./configure \ ++ --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --without-graphics \ ++ --with-pic \ ++ --disable-mpi \ ++ --with-blas=/usr/lib64/libblas.so.3.1.1 \ ++ --with-lapack=/usr/lib64/liblapack.so.3.1.1 ++cd .. ++ ++#Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages ++#do not register -fPIC in Dakota, which is a problem. Edit the faulty Makefiles and add the -fPIC ++#flag to the compilation. ++cat ./src/methods/NCSUOpt/Makefile | sed 's/FFLAGS = -g -O2/FFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/NCSUOpt/Makefile ++ ++cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/pebbl/src/Makefile ++ ++cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-nappspack/Makefile ++ ++cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-cddlib/Makefile ++ ++cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-shared/Makefile ++ ++cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-shared/Makefile ++ ++cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-conveyor/Makefile ++ ++cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/methods/hopspack/src-appspack/Makefile ++ ++cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/colin/src/Makefile ++ ++cat ./src/methods/acro/packages/coliny/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/coliny/src/Makefile ++ ++cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CFLAGS = -O2/CFLAGS = -O2 -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/tpl/3po/Makefile ++ ++cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp ++mv temp ./src/methods/acro/packages/tpl/3po/Makefile ++ ++cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++mv temp ./src/packages/ampl/Makefile ++ ++#Compile and install dakota ++cd src ++if [ -z $NUMCPUS ]; ++then ++ make ++ make install ++else ++ make -j $NUMCPUS ++ make -j $NUMCPUS install ++fi ++cd .. ++ ++#Weird behaviour of Dakota: libamplsolver.a and amplsolver.a are not the same thing! ++cd install/lib ++mv libamplsolver.a libamplsolver.a.bak ++ln -s ../../src/packages/ampl/amplsolver.a ./libamplsolver.a + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11550-11568/ISSM-DocReview-11550-11568.tex =================================================================== --- /issm/oecreview/Archive/11550-11568/ISSM-DocReview-11550-11568.tex (revision 11991) +++ /issm/oecreview/Archive/11550-11568/ISSM-DocReview-11550-11568.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11550-11568/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11550-11568/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11550-11568/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11550-11568 Index: /issm/oecreview/Archive/11550-11568/Makefile =================================================================== --- /issm/oecreview/Archive/11550-11568/Makefile (revision 11991) +++ /issm/oecreview/Archive/11550-11568/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11550-11568 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11550-11568/log.tex =================================================================== --- /issm/oecreview/Archive/11550-11568/log.tex (revision 11991) +++ /issm/oecreview/Archive/11550-11568/log.tex (revision 11991) @@ -0,0 +1,36 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11550-11551.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun/test1104.m M /issm/trunk-jpl/test/NightlyRun/test1105.m M /issm/trunk-jpl/test/NightlyRun/test1109.m M /issm/trunk-jpl/test/NightlyRun/test1110.m \\ Export determination: 6. \\Rationale: update ISMIP tolerances +M /issm/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp Fixed hmaxVertices option \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11551-11552.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Bamgx/Bamgx.cpp \\ Export determination: 6. \\Rationale: Fixed hmaxVertices option +M /issm/trunk-jpl/cron/nightlyrun.sh D /issm/trunk-jpl/cron/nightlyrun.sh.new New nightly run script compatible with Windows \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11552-11553.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh D /issm/trunk-jpl/cron/nightlyrun.sh.new \\ Export determination: 6. \\Rationale: New nightly run script compatible with Windows +A /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt Windows install instructions \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11553-11554.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt \\ Export determination: 6. \\Rationale: Windows install instructions +M /issm/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp Exp2Kml: Added capability to output kml points. Also removed dependence in Exp2Kmlx on whole parameter and closed flag from DomainOutlineRead. \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11554-11555.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Exp2Kmlx/Exp2Kmlx.cpp \\ Export determination: 6. \\Rationale: Exp2Kml: Added capability to output kml points. Also removed dependence in Exp2Kmlx on whole parameter and closed flag from DomainOutlineRead. +M /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt A /issm/trunk-jpl/externalpackages/windows/Sdk1.png A /issm/trunk-jpl/externalpackages/windows/Sdk2.png Instructions for Windows install \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11555-11556.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt A /issm/trunk-jpl/externalpackages/windows/Sdk1.png A /issm/trunk-jpl/externalpackages/windows/Sdk2.png \\ Export determination: 6. \\Rationale: Instructions for Windows install +M /issm/trunk-jpl/externalpackages/dyson/ldap.pl New script \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11556-11557.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/dyson/ldap.pl \\ Export determination: 6. \\Rationale: New script +A /issm/trunk-jpl/installers/macosx/ISSM.app A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf A /issm/trunk-jpl/installers/macosx/ISSM.appscript A /issm/trunk-jpl/installers/macosx/ISSM.pkg A /issm/trunk-jpl/installers/macosx/issm.icns A /issm/trunk-jpl/installers/macosx/matlabissm A /issm/trunk-jpl/installers/macosx/startup.m All that is needed for a package to be made under MacOSX \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11557-11558.diff: \\ Function name: \\A /issm/trunk-jpl/installers/macosx/ISSM.app A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf A /issm/trunk-jpl/installers/macosx/ISSM.appscript A /issm/trunk-jpl/installers/macosx/ISSM.pkg A /issm/trunk-jpl/installers/macosx/issm.icns A /issm/trunk-jpl/installers/macosx/matlabissm A /issm/trunk-jpl/installers/macosx/startup.m \\ Export determination: 6. \\Rationale: All that is needed for a package to be made under MacOSX +M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp Fixed streamline upwinding in case vel=0 \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11558-11559.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp \\ Export determination: 6. \\Rationale: Fixed streamline upwinding in case vel=0 +M /issm/trunk-jpl/src/m/classes/prognostic.m Allowing streamline upwinding stabilization \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11559-11560.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/prognostic.m \\ Export determination: 6. \\Rationale: Allowing streamline upwinding stabilization +M /issm/trunk-jpl/scripts/historyISSM.m updated history \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11560-11561.diff: \\ Function name: \\M /issm/trunk-jpl/scripts/historyISSM.m \\ Export determination: 6. \\Rationale: updated history +M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_daily M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_nightly M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation New config files that match new cron sh \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11561-11562.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_daily M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_nightly M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation \\ Export determination: 6. \\Rationale: New config files that match new cron sh +M /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt Added cron and exim instructions \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11562-11563.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt \\ Export determination: 6. \\Rationale: Added cron and exim instructions +M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp Fixing analtical gradient \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11563-11564.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp \\ Export determination: 6. \\Rationale: Fixing analtical gradient +D /issm/trunk-jpl/installers/win7/aic.sh A /issm/trunk-jpl/installers/win7/package.sh Moving to better name. \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11564-11565.diff: \\ Function name: \\D /issm/trunk-jpl/installers/win7/aic.sh A /issm/trunk-jpl/installers/win7/package.sh \\ Export determination: 6. \\Rationale: Moving to better name. +D /issm/trunk-jpl/installers/macosx fixing problem with svn server \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11565-11566.diff: \\ Function name: \\D /issm/trunk-jpl/installers/macosx \\ Export determination: 6. \\Rationale: fixing problem with svn server +A /issm/trunk-jpl/installers/macosx A /issm/trunk-jpl/installers/macosx/ISSM.app A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf A /issm/trunk-jpl/installers/macosx/ISSM.appscript A /issm/trunk-jpl/installers/macosx/ISSM.pkg A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/index.xml A /issm/trunk-jpl/installers/macosx/README A /issm/trunk-jpl/installers/macosx/issm.icns A /issm/trunk-jpl/installers/macosx/matlabissm A /issm/trunk-jpl/installers/macosx/package.sh A /issm/trunk-jpl/installers/macosx/startup.m Command line driven package maker for macosx \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11566-11567.diff: \\ Function name: \\A /issm/trunk-jpl/installers/macosx A /issm/trunk-jpl/installers/macosx/ISSM.app A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Info.plist A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/MacOS/applet A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/PkgInfo A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.icns A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/applet.rsrc A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd A /issm/trunk-jpl/installers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf A /issm/trunk-jpl/installers/macosx/ISSM.appscript A /issm/trunk-jpl/installers/macosx/ISSM.pkg A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/01issm.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/02matlabissm.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/03startup.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin-contents.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/04bin.xml A /issm/trunk-jpl/installers/macosx/ISSM.pmdoc/index.xml A /issm/trunk-jpl/installers/macosx/README A /issm/trunk-jpl/installers/macosx/issm.icns A /issm/trunk-jpl/installers/macosx/matlabissm A /issm/trunk-jpl/installers/macosx/package.sh A /issm/trunk-jpl/installers/macosx/startup.m \\ Export determination: 6. \\Rationale: Command line driven package maker for macosx +D /issm/trunk-jpl/installers A /issm/trunk-jpl/packagers (from /issm/trunk-jpl/installers:11498) A /issm/trunk-jpl/packagers/macosx (from /issm/trunk-jpl/installers/macosx:11566) R /issm/trunk-jpl/packagers/win7 (from /issm/trunk-jpl/installers/win7:11563) D /issm/trunk-jpl/packagers/win7/aic.sh A /issm/trunk-jpl/packagers/win7/package.sh (from /issm/trunk-jpl/installers/win7/package.sh:11564) Better name \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-11567-11568.diff: \\ Function name: \\D /issm/trunk-jpl/installers A /issm/trunk-jpl/packagers (from /issm/trunk-jpl/installers:11498) A /issm/trunk-jpl/packagers/macosx (from /issm/trunk-jpl/installers/macosx:11566) R /issm/trunk-jpl/packagers/win7 (from /issm/trunk-jpl/installers/win7:11563) D /issm/trunk-jpl/packagers/win7/aic.sh A /issm/trunk-jpl/packagers/win7/package.sh (from /issm/trunk-jpl/installers/win7/package.sh:11564) \\ Export determination: 6. \\Rationale: Better name +A /issm/trunk-jpl/externalpackages/dakota/install-linux64-murdo.sh Installation file for Dakota on murdo \\\\ Index: /issm/oecreview/Archive/11550-11568/r1.tex =================================================================== --- /issm/oecreview/Archive/11550-11568/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11550-11568/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11550 Index: /issm/oecreview/Archive/11550-11568/r2.tex =================================================================== --- /issm/oecreview/Archive/11550-11568/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11550-11568/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11568 Index: /issm/oecreview/Archive/11569-11580/Date.tex =================================================================== --- /issm/oecreview/Archive/11569-11580/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11569-11580/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11569-11580/ISSM-11569-11570.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11569-11570.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11569-11570.diff (revision 11991) @@ -0,0 +1,110 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour (revision 11569) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour (revision 11570) +@@ -1,22 +1,24 @@ + # +-########### Configuration file for Eric Larour's nightly run on Mac ############ ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ + + #-------------------------------# + # 1: ISSM general configuration # + #-------------------------------# + +-#ISSM main directory (full pathto ISSM trunk) +-ISSM_DIR="/Users/larour/issm/trunk" ++#ISSM main directory (full path) ++ISSM_DIR="/Users/larour/issm-uci" ++ISSM_TIER="/Users/larour/issm-uci/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="macosx-gnu" + +-#Operating System +-OS="macosx64" ++#Machine configuration ++MACHINE="macosx-gil" + +-#MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2008a/" ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-macosx64-mathieu.sh" + ++ + #----------------------# + # 2: ISSM Installation # + #----------------------# +@@ -28,14 +30,13 @@ + # ->skip to section 3 + # - "none" leave ISSM as is in its directory + # ->skip to section 3 +-ISSM_INSTALLATION="update" ++ISSM_INSTALLATION="checkout" + + #SVN repository + REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +-#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" + + #execution path used for parallel runs +-EXECUTION_PATH="" ++EXECUTION_PATH="/Users/larour/ExecutionNightlyRun" + + #-----------------------------------# + # 3: External packages installation # +@@ -46,12 +47,16 @@ + # - "copy" copy existing directories (EXTERNALPACKAGESDIR) + # - "none" leave external packages as is + # ->skip to section 4 +-ISSM_EXTERNALPACKAGES="copy" +-EXTERNALPACKAGESDIR="" ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" + + #List of external pakages to be installed +-EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle" ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ + #---------------------# + # 4: ISSM Compilation # + #---------------------# +@@ -66,11 +71,11 @@ + #----------------------# + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be +-#sent to the adresses present in $ISSM_DIR/cron/mailinglist. ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. + SKIPMAIL="no" + + #Sender email address +-EMAIL_ADRESS="eric.larour@jpl.nasa.gov" ++EMAIL_ADRESS="schlegel@jpl.nasa.gov" + + #------------------------# + # 6: Nightly run options # +@@ -81,7 +86,7 @@ + NUMCPUS_INSTALL=1 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=1 ++NUMCPUS_RUN=7 + + #Nightly run options. The matlab routine nightlyrun.m will be called + #as follows: nightlyrun($NROPTIONS). The options must be understandable +@@ -89,3 +94,13 @@ + #ex: "'id',[101 102 103]" + + NROPTIONS="" ++ ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" Index: /issm/oecreview/Archive/11569-11580/ISSM-11570-11571.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11570-11571.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11570-11571.diff (revision 11991) @@ -0,0 +1,113 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764_larour +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764_larour (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764_larour (revision 11571) +@@ -0,0 +1,102 @@ ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/cygdrive/c/issm-uci" ++ISSM_TIER="/cygdrive/c/issm-uci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="cygwin-intel" ++ ++#Machine configuration ++MACHINE="win7" ++ ++#MATLAB path ++MATLAB_PATH="C:/MATLAB/R2011b/" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-win7-64.sh" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="none" ++ ++#SVN repository ++REPOSITORY="http://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/cygdrive/c/issm-uci/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="none" ++EXTERNALPACKAGESDIR="/cygdrive/c/issm-uci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES=" autoconf automake petsc metis triangle cccl" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install-3.1-win7.sh install-4.0-win7.sh install-win7.sh install-win7.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="no" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="eric.larour@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=8 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=1 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="" ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++MATLABBIN=/cygdrive/c/MATLAB/R2011b32/bin/matlab + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/win764_larour +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11569-11580/ISSM-11571-11572.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11571-11572.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11571-11572.diff (revision 11991) @@ -0,0 +1,87 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11571) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11572) +@@ -46,6 +46,7 @@ + done + } + #}}} ++ + #Get configuration + #Source config file{{{1 + if [ $# -ne 1 ]; +@@ -109,13 +110,13 @@ + #create simpler cluster.rc file, with only the cluster we are interested in. + cd $ISSM_TIER/test/NightlyRun/ + if [ "$MACHINE" = "win7" ]; then +-cat << END > $HOST_NAME"_settings.m" ++ cat << END > $HOST_NAME"_settings.m" + cluster.login='$USER'; + cluster.codepath='`cygpath -m $ISSM_TIER/bin`'; + cluster.executionpath='`cygpath -m $EXECUTION_PATH`'; + END + else +-cat << END > $HOST_NAME"_settings.m" ++ cat << END > $HOST_NAME"_settings.m" + cluster.login='$USER'; + cluster.codepath='$ISSM_TIER/bin'; + cluster.executionpath='$EXECUTION_PATH'; +@@ -138,14 +139,12 @@ + do + package=`echo $EXTERNALPACKAGES | cut -d " " -f $i-$i` + package_config=`echo $EXTERNALPACKAGES_CONFIGS | cut -d " " -f $i-$i` +- package_numcpus=`echo $EXTERNALPACKAGES_NUMCPUS | cut -d " " -f $i-$i` + + cd $package +- $package_config $package_numcpus ++ $package_config + cd .. + done + +- + elif [ "$ISSM_EXTERNALPACKAGES" == "copy" ] + then + +@@ -177,10 +176,8 @@ + make distclean + ./scripts/automakererun.sh + source ./configs/$COMPILE_CONFIG_FILE ++ make install + +- make -j $NUMCPUS_INSTALL +- make -j $NUMCPUS_INSTALL install +- + elif [ "$ISSM_COMPILATION" == "no" ] + then + echo "Skipping ISSM compilation" +@@ -193,11 +190,8 @@ + #Prepare run + #create softlink to startup {{{1 + cd $ISSM_TIER/test/NightlyRun/ +-if [ "$MACHINE" = "win7" ]; then +- cp $ISSM_TIER/startup.m . +-else +- ln -s $ISSM_TIER/startup.m . +-fi ++rm startup.m #in case it alreade exists ++cp $ISSM_TIER/startup.m . + #}}} + #Create nightlylog directory and info.log {{{1 + #put installation elapsed time in info.log +@@ -230,7 +224,6 @@ + else + MATLAB_TIER=$ISSM_TIER + fi +- + #}}} + #Launch all tests on different cpus {{{1 + for (( i=1;i<=$NUMCPUS_RUN;i++ )) +@@ -280,7 +273,7 @@ + #}}} + #concatenate all reports {{{1 + cd $ISSM_TIER/nightlylog/ +-mv matlab_log1.log matlab_log.log ++cp matlab_log1.log matlab_log.log + for (( i=2;i<=$NUMCPUS_RUN;i++ )) + do + cat matlab_log.log matlab_log$i.log > matlab_log.log.bak Index: /issm/oecreview/Archive/11569-11580/ISSM-11572-11573.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11572-11573.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11572-11573.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m (revision 11572) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m (revision 11573) +@@ -214,6 +214,8 @@ + md.mask.elementonwater=project3d(md,'vector',md.mask.elementonwater,'type','element'); + md.mask.vertexonwater=project3d(md,'vector',md.mask.vertexonwater,'type','node'); + if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end; ++if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end; ++if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end; + if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end + + %Put lithostatic pressure if there is an existing pressure Index: /issm/oecreview/Archive/11569-11580/ISSM-11573-11574.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11573-11574.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11573-11574.diff (revision 11991) @@ -0,0 +1,4 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pkg +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/11569-11580/ISSM-11574-11575.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11574-11575.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11574-11575.diff (revision 11991) @@ -0,0 +1,96 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/package.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/package.sh (revision 11575) +@@ -0,0 +1,15 @@ ++#/bin/bash ++ ++#Just tar gz the bin/ directory and test/ directory and put a startup.m file. ++ ++rm -rf ISSM ISSM-Ubuntu32.tar.gz ++ ++mkdir ISSM ++cd ISSM ++ln -s $ISSM_TIER/bin ./bin ++ln -s $ISSM_TIER/test ./test ++cp ../startup.m ./ ++cp ../README.m ./ ++cd .. ++tar zcvfh ISSM-Ubuntu32.tar.gz --exclude='.svn' ./ISSM ++rm -rf ISSM + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/package.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/README (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/README (revision 11575) +@@ -0,0 +1,14 @@ ++To install ISSM, untar ISSM-Ubuntu32.tar.gz ++You will get an ISSM directory. ++ ++You then need to setup the following environment variable in your ++.bashrc or .cshrc: ++ ++in your .bashrc: ++export ISSM_TIER='path_to_untarred_ISSM/bin' ++ ++or in your .cshrc: ++setenv ISSM_TIER 'path_to_untarred_ISSM' ++ ++Once this is done, fireup matlab from inside the ISSM directory: ++matlab -nojvm -r "startup;" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/startup.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/startup.m (revision 11575) +@@ -0,0 +1,40 @@ ++%STARTUP - Matlab startup script ++% ++% startup.m is a script run by matlab at the beginning of a session, just ++% before handing over the prompt to the user. This delivery startup.m script ++% has been customized here for the ISSM code. This startup script should be ++% run by users before trying to use ISSM. The best way to do that is to put ++% the startup file in the location where Matlab starts and established its ++% root directory. ++ ++% clear the last warning to focus on the warnings of the ISSM path ++lastwarn(''); ++ ++%Recover ISSM_TIER , or if on a Windows machine, ISSM_TIER_WIN ++ISSM_TIER=getenv('ISSM_TIER'); ++ ++if (isempty(ISSM_TIER)), ++ error('issmdir error message: ''ISSM_TIER'' environment variable is empty! You should define ISSM_TIER in your .cshrc or .bashrc!'); ++end ++ ++%Now add all issm code paths necessary to run issm smoothly. ++%We capture the error output, so that we can warn the user to update ++%the variable ISSM_TIER in this file, in case it is not correctly setup. ++ ++%ISSM path ++addpath(ISSM_TIER); ++addpath([ISSM_TIER '/bin']); ++ ++%Check on any warning messages that might indicate that the paths were not correct. ++if ~isempty(lastwarn), ++ fprintf('\n Error trying to setup ''ISSM'' code paths. Try and update the ISSM_TIER variable in your .cshrc or .bashrc!\n'); ++ fprintf(' ''ISSM'' will not work at all until this is resolved\n\n'); ++else ++ fprintf('\n To get started with ISSM, type issmdoc at the command prompt.\n\n'); ++end ++ ++%disable matlab bell! ++beep off; ++ ++% no warning if we try to plot while in nojvm (will not be supported in future releases) ++warning off MATLAB:HandleGraphics:noJVM + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/ubuntu/startup.m +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11569-11580/ISSM-11575-11576.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11575-11576.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11575-11576.diff (revision 11991) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.m (revision 11575) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/mesh.m (revision 11576) +@@ -98,6 +98,7 @@ + else + checkfield(md,'mesh.average_vertex_connectivity','>=',24,'message','''mesh.average_vertex_connectivity'' should be at least 24 in 3d'); + end ++ checkfield(md,'mesh.elementconnectivity','size',[md.mesh.numberofelements 3],'NaN',1); + + %Solution specific checks + switch(solution), Index: /issm/oecreview/Archive/11569-11580/ISSM-11577-11578.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11577-11578.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11577-11578.diff (revision 11991) @@ -0,0 +1,32 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/manipulation/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/manipulation/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/manipulation/Makefile.am (revision 11578) +@@ -0,0 +1 @@ ++bin_SCRIPTS=*.m +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/readwrite/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/readwrite/Makefile.am (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/readwrite/Makefile.am (revision 11578) +@@ -0,0 +1 @@ ++bin_SCRIPTS=*.m +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/Makefile.am (revision 11577) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/Makefile.am (revision 11578) +@@ -1 +1,2 @@ ++SUBDIRS = manipulation readwrite + bin_SCRIPTS=*.m +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 11577) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 11578) +@@ -49,6 +49,8 @@ + src/m/utils/DataProcessing/Makefile + src/m/utils/Ecco3/Makefile + src/m/utils/Exp/Makefile ++ src/m/utils/Exp/manipulation/Makefile ++ src/m/utils/Exp/readwrite/Makefile + src/m/utils/Geometry/Makefile + src/m/utils/ImageProcessing/Makefile + src/m/utils/Interp/Makefile Index: /issm/oecreview/Archive/11569-11580/ISSM-11579-11580.diff =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-11579-11580.diff (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-11579-11580.diff (revision 11991) @@ -0,0 +1,4 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/issm.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/11569-11580/ISSM-DocReview-11569-11580.tex =================================================================== --- /issm/oecreview/Archive/11569-11580/ISSM-DocReview-11569-11580.tex (revision 11991) +++ /issm/oecreview/Archive/11569-11580/ISSM-DocReview-11569-11580.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11569-11580/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11569-11580/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11569-11580/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11569-11580 Index: /issm/oecreview/Archive/11569-11580/Makefile =================================================================== --- /issm/oecreview/Archive/11569-11580/Makefile (revision 11991) +++ /issm/oecreview/Archive/11569-11580/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11569-11580 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11569-11580/log.tex =================================================================== --- /issm/oecreview/Archive/11569-11580/log.tex (revision 11991) +++ /issm/oecreview/Archive/11569-11580/log.tex (revision 11991) @@ -0,0 +1,18 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11569-11570.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-linux64-murdo.sh \\ Export determination: 6. \\Rationale: New configuration for murdo +M /issm/trunk-jpl/cron/configs/macosx64\_larour Some settings for macosx64 nightly runs. \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11570-11571.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_larour \\ Export determination: 6. \\Rationale: Some settings for macosx64 nightly runs. +A /issm/trunk-jpl/cron/configs/win764\_larour Reduced set of benchmarks on win7 \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11571-11572.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/win764\_larour \\ Export determination: 6. \\Rationale: Reduced set of benchmarks on win7 +M /issm/trunk-jpl/cron/nightlyrun.sh minor changes \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11572-11573.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: minor changes +M /issm/trunk-jpl/src/m/model/extrude.m Forgot to extrude 2 fields \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11573-11574.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/extrude.m \\ Export determination: 6. \\Rationale: Forgot to extrude 2 fields +D /issm/trunk-jpl/packagers/macosx/ISSM.pkg Not needed, generated dynamically \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11574-11575.diff: \\ Function name: \\D /issm/trunk-jpl/packagers/macosx/ISSM.pkg \\ Export determination: 6. \\Rationale: Not needed, generated dynamically +A /issm/trunk-jpl/packagers/ubuntu A /issm/trunk-jpl/packagers/ubuntu/README A /issm/trunk-jpl/packagers/ubuntu/package.sh A /issm/trunk-jpl/packagers/ubuntu/startup.m Packagere for ubuntu 32 \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11575-11576.diff: \\ Function name: \\A /issm/trunk-jpl/packagers/ubuntu A /issm/trunk-jpl/packagers/ubuntu/README A /issm/trunk-jpl/packagers/ubuntu/package.sh A /issm/trunk-jpl/packagers/ubuntu/startup.m \\ Export determination: 6. \\Rationale: Packagere for ubuntu 32 +M /issm/trunk-jpl/src/m/classes/mesh.m Added check on elementconnectivity to avoid crash \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11576-11577.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/mesh.m \\ Export determination: 6. \\Rationale: Added check on elementconnectivity to avoid crash \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11577-11578.diff: \\ Function name: \\M /issm/trunk-jpl/configure.ac M /issm/trunk-jpl/src/m/utils/Exp/Makefile.am A /issm/trunk-jpl/src/m/utils/Exp/manipulation/Makefile.am A /issm/trunk-jpl/src/m/utils/Exp/readwrite/Makefile.am \\ Export determination: 6. \\Rationale: Forgot to add readwrite and manipulation files for .m file installation. \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11578-11579.diff: \\ Function name: \\M /issm/trunk-jpl/configure.ac M /issm/trunk-jpl/src/m/utils/Exp/Makefile.am A /issm/trunk-jpl/src/m/utils/Exp/manipulation/Makefile.am A /issm/trunk-jpl/src/m/utils/Exp/readwrite/Makefile.am \\ Export determination: 6. \\Rationale: Forgot to add readwrite and manipulation files for .m file installation. \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11579-11580.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/issm.icns \\ Export determination: 6. \\Rationale: Fixed ISSM icon \\\\ Index: /issm/oecreview/Archive/11569-11580/r1.tex =================================================================== --- /issm/oecreview/Archive/11569-11580/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11569-11580/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11569 Index: /issm/oecreview/Archive/11569-11580/r2.tex =================================================================== --- /issm/oecreview/Archive/11569-11580/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11569-11580/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11580 Index: /issm/oecreview/Archive/11581-11588/Date.tex =================================================================== --- /issm/oecreview/Archive/11581-11588/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11581-11588/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11581-11588/ISSM-11582-11583.diff =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-11582-11583.diff (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-11582-11583.diff (revision 11991) @@ -0,0 +1,116 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11583) +@@ -1,6 +1,6 @@ + #/bin/bash + + #Package using the Package Maker from OSX, driven by command line. +-rm -rf ISSM.pkg ++rm -rf ISSM-MacOSX.pkg + +-PackageMaker -d ISSM.pmdoc -o ISSM.pkg ++PackageMaker -d ISSM.pmdoc -o ISSM-MacOSX.pkg +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 11583) +@@ -1 +1 @@ +- +\ No newline at end of file ++groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml (revision 11583) +@@ -0,0 +1 @@ ++issm.test.pkg1.0/Users/larour/issm-uci/trunk-jpl/test/Library/ISSM/testinstallTo.pathparentinstallToidentifier05test-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml (revision 11583) +@@ -1 +1 @@ +-ISSM.startup.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/startup.m/Library/ISSM/bin/installTo.pathrelocatableparentinstallToidentifier03startup-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file ++ISSM.startup.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/startup.m/Library/ISSM/bin/installTo.pathinstallToinstallFrom.pathidentifierrelocatableparent03startup-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11583) +@@ -1 +1 @@ +-groupowner +\ No newline at end of file ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 11583) +@@ -1 +1 @@ +- +\ No newline at end of file ++groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml (revision 11583) +@@ -1 +1 @@ +-ISSM/Users/larour/issm-uci/trunk-jpl/installers/macosx/ISSM.pkghttp://issm.jpl.nasa.govIce Sheet System Model01issm.xml02matlabissm.xml03startup.xml04bin.xmlproperties.titleproperties.userDomaindescriptionproperties.anywhereDomain +\ No newline at end of file ++ISSM/Users/larour/issm-uci/trunk-jpl/packagers/macosx/ISSM.pkghttp://issm.jpl.nasa.govIce Sheet System Model01issm.xml02matlabissm.xml03startup.xml04bin.xml05test.xmlproperties.titleproperties.userDomaindescriptionproperties.anywhereDomain +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 11583) +@@ -1 +1 @@ +- +\ No newline at end of file ++groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml (revision 11583) +@@ -1 +1 @@ +-ISSM.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/ISSM.app/ApplicationsrequireAuthorizationidentifierinstallTorelocatableincludeRootparent01issm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file ++ISSM.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/ISSM.app/ApplicationsinstallTorelocatableinstallFrom.pathidentifierparentincludeRootrequireAuthorization01issm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml (revision 11583) +@@ -1 +1 @@ +-issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/bin/Library/ISSM/bininstallTo.pathparentinstallToidentifier04bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file ++issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/bin/Library/ISSM/bininstallTo.pathparentinstallToidentifier04bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 11583) +@@ -1 +1 @@ +-ISSM.matlabissm.pkg1.0/Users/larour/issm-uci/trunk-jpl/installers/macosx/matlabissm/Library/ISSM/bin/installTo.isRelativeTypeinstallTorelocatableinstallTo.isAbsoluteTypeidentifierparentinstallTo.path02matlabissm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file ++ISSM.matlabissm.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/matlabissm/Library/ISSM/bin/installTo.isRelativeTypeinstallTorelocatableinstallTo.isAbsoluteTypeinstallFrom.pathidentifierparentinstallTo.path02matlabissm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml (revision 11583) +@@ -0,0 +1 @@ ++groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11582) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11583) +@@ -1,2 +1,2 @@ + #/bin/bash +-matlab -r "addpath /Library/ISSM/bin/; startup" ++matlab -r "addpath /Library/ISSM/bin/; startup; cd /Library/ISSM/test;" Index: /issm/oecreview/Archive/11581-11588/ISSM-11583-11584.diff =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-11583-11584.diff (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-11583-11584.diff (revision 11991) @@ -0,0 +1,104 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Triangle.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Triangle.cpp (revision 11583) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Triangle.cpp (revision 11584) +@@ -50,6 +50,57 @@ + AdjacentTriangle Triangle::Adj(int i) const { + return AdjacentTriangle(adj[i],AdjEdgeIndex[i]&3); + };/*}}}*/ ++ /*FUNCTION Triangle::Anisotropy{{{1*/ ++ double Triangle::Anisotropy() const{ ++ ++ double lmin,lmax; ++ ++ /*Get three vertices A,B and C*/ ++ R2 A=*this->vertices[0]; ++ R2 B=*this->vertices[1]; ++ R2 C=*this->vertices[2]; ++ ++ /*Compute edges*/ ++ R2 e1=B-A; ++ R2 e2=C-A; ++ R2 e3=B-C; ++ ++ /*Compute edge length*/ ++ double l1=Norme2(e1); ++ double l2=Norme2(e2); ++ double l3=Norme2(e3); ++ ++ lmin=l1; ++ lmin=min(lmin,l2); ++ lmin=min(lmin,l3); ++ lmax=l1; ++ lmax=max(lmax,l2); ++ lmax=max(lmax,l3); ++ ++ return lmax/lmin; ++ };/*}}}*/ ++ /*FUNCTION Triangle::Length{{{1*/ ++ double Triangle::Length() const{ ++ ++ double l; ++ ++ /*Get three vertices A,B and C*/ ++ R2 A=*this->vertices[0]; ++ R2 B=*this->vertices[1]; ++ R2 C=*this->vertices[2]; ++ ++ /*Compute edges*/ ++ R2 e1=B-A; ++ R2 e2=C-A; ++ R2 e3=B-C; ++ ++ /*Compute edge length*/ ++ l=Norme2(e1); ++ l=max(l,Norme2(e2)); ++ l=max(l,Norme2(e3)); ++ ++ return l; ++ };/*}}}*/ + /*FUNCTION Triangle::Echo {{{1*/ + void Triangle::Echo(void){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Triangle.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Triangle.h (revision 11583) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Triangle.h (revision 11584) +@@ -40,6 +40,8 @@ + + //Methods + void Echo(); ++ double Anisotropy() const; ++ double Length() const; + int swap(short a1,int=0); + long Optim(short a,int =0); + int Locked(int a)const; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.cpp (revision 11583) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Bamg/Mesh.cpp (revision 11584) +@@ -1027,17 +1027,19 @@ + for (i=0;i0 && !(t.Hidden(0)||t.Hidden(1) || t.Hidden(2) )){ +- index[num*3+0]=GetId(t[0])+1; //back to M indexing +- index[num*3+1]=GetId(t[1])+1; //back to M indexing +- index[num*3+2]=GetId(t[2])+1; //back to M indexing +- num=num+1; ++ if(t.Anisotropy()<2 & t.Length()<1.e+5){ ++ index[num*3+0]=GetId(t[0])+1; //back to M indexing ++ index[num*3+1]=GetId(t[1])+1; //back to M indexing ++ index[num*3+2]=GetId(t[2])+1; //back to M indexing ++ num=num+1; ++ } + } + } + } + + /*Assign output pointers*/ + *pindex=index; +- *pnels=k; ++ *pnels=num; + } + /*}}}1*/ + Index: /issm/oecreview/Archive/11581-11588/ISSM-11584-11585.diff =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-11584-11585.diff (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-11584-11585.diff (revision 11991) @@ -0,0 +1,162 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test460.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test460.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test460.m (revision 11585) +@@ -0,0 +1,20 @@ ++md=triangle(model,'../Exp/Square.exp',180000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,3,1); ++md=setflowequation(md,'stokes','all'); ++md.diagnostic.isnewton=1; ++md.diagnostic.restol=0.0001; ++md.cluster=generic('name',oshostname(),'np',3); ++md=solve(md,DiagnosticSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure'}; ++field_tolerances={1e-07,1e-07,1e-06,1e-07,1e-07}; ++field_values={... ++ (md.results.DiagnosticSolution.Vx),... ++ (md.results.DiagnosticSolution.Vy),... ++ (md.results.DiagnosticSolution.Vz),... ++ (md.results.DiagnosticSolution.Vel),... ++ (md.results.DiagnosticSolution.Pressure),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test455.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test455.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test455.m (revision 11585) +@@ -0,0 +1,18 @@ ++md=triangle(model,'../Exp/Square.exp',150000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=setflowequation(md,'macayeal','all'); ++md.diagnostic.isnewton=1; ++md.diagnostic.restol=0.0001; ++md.cluster=none; ++md=solve(md,DiagnosticSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vel','Pressure'}; ++field_tolerances={1e-13,1e-13,1e-13,1e-13}; ++field_values={... ++ (md.results.DiagnosticSolution.Vx),... ++ (md.results.DiagnosticSolution.Vy),... ++ (md.results.DiagnosticSolution.Vel),... ++ (md.results.DiagnosticSolution.Pressure),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test456.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test456.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test456.m (revision 11585) +@@ -0,0 +1,18 @@ ++md=triangle(model,'../Exp/Square.exp',150000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=setflowequation(md,'macayeal','all'); ++md.diagnostic.isnewton=1; ++md.diagnostic.restol=0.0001; ++md.cluster=generic('name',oshostname(),'np',3); ++md=solve(md,DiagnosticSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vel','Pressure'}; ++field_tolerances={1e-13,1e-13,1e-13,1e-13}; ++field_values={... ++ (md.results.DiagnosticSolution.Vx),... ++ (md.results.DiagnosticSolution.Vy),... ++ (md.results.DiagnosticSolution.Vel),... ++ (md.results.DiagnosticSolution.Pressure),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test457.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test457.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test457.m (revision 11585) +@@ -0,0 +1,20 @@ ++md=triangle(model,'../Exp/Square.exp',180000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,5,1); ++md=setflowequation(md,'pattyn','all'); ++md.diagnostic.isnewton=1; ++md.diagnostic.restol=0.0001; ++md.cluster=none; ++md=solve(md,DiagnosticSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure'}; ++field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; ++field_values={... ++ (md.results.DiagnosticSolution.Vx),... ++ (md.results.DiagnosticSolution.Vy),... ++ (md.results.DiagnosticSolution.Vz),... ++ (md.results.DiagnosticSolution.Vel),... ++ (md.results.DiagnosticSolution.Pressure),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/IdToName.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/IdToName.m (revision 11584) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/IdToName.m (revision 11585) +@@ -223,6 +223,12 @@ + case 452, name='SquareSheetShelfGroundingLine3dAgressiceParallel'; + case 453, name='SquareSheetShelfGroundingLine3dSoftSerial'; + case 454, name='SquareSheetShelfGroundingLine3dSoftParallel'; ++ case 455, name='SquareSheetShelfDiagM2dNewtonSerial'; ++ case 456, name='SquareSheetShelfDiagM2dNewtonParallel'; ++ case 457, name='SquareSheetShelfDiagP3dNewtonSerial'; ++ case 458, name='SquareSheetShelfDiagP3dNewtonParallel'; ++ case 459, name='SquareSheetShelfDiagS3dNewtonSerial'; ++ case 460, name='SquareSheetShelfDiagS3dNewtonParallel'; + case 501, name='PigDiagM2dSerial'; + case 502, name='PigDiagM2dParallel'; + case 503, name='PigDiagP3dSerial'; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test458.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test458.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test458.m (revision 11585) +@@ -0,0 +1,20 @@ ++md=triangle(model,'../Exp/Square.exp',180000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,5,1); ++md=setflowequation(md,'pattyn','all'); ++md.diagnostic.isnewton=1; ++md.diagnostic.restol=0.0001; ++md.cluster=generic('name',oshostname(),'np',3); ++md=solve(md,DiagnosticSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure'}; ++field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-09}; ++field_values={... ++ (md.results.DiagnosticSolution.Vx),... ++ (md.results.DiagnosticSolution.Vy),... ++ (md.results.DiagnosticSolution.Vz),... ++ (md.results.DiagnosticSolution.Vel),... ++ (md.results.DiagnosticSolution.Pressure),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test459.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test459.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test459.m (revision 11585) +@@ -0,0 +1,19 @@ ++md=triangle(model,'../Exp/Square.exp',180000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,3,1); ++md=setflowequation(md,'stokes','all'); ++md.diagnostic.isnewton=1; ++md.diagnostic.restol=0.0001; ++md=solve(md,DiagnosticSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure'}; ++field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_values={... ++ (md.results.DiagnosticSolution.Vx),... ++ (md.results.DiagnosticSolution.Vy),... ++ (md.results.DiagnosticSolution.Vz),... ++ (md.results.DiagnosticSolution.Vel),... ++ (md.results.DiagnosticSolution.Pressure),... ++ }; Index: /issm/oecreview/Archive/11581-11588/ISSM-11585-11586.diff =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-11585-11586.diff (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-11585-11586.diff (revision 11991) @@ -0,0 +1,60 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive457.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive457.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive458.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive458.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive455.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive455.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive459.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive459.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive460.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive460.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive456.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive456.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + Index: /issm/oecreview/Archive/11581-11588/ISSM-11586-11587.diff =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-11586-11587.diff (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-11586-11587.diff (revision 11991) @@ -0,0 +1,190 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.appscript +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.appscript (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.appscript (revision 11587) +@@ -1 +1 @@ +-do shell script "open /Library/ISSM/bin/matlabissm" ++do shell script "open ~/ISSM/bin/matlabissm" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package_incomplete.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package_incomplete.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package_incomplete.sh (revision 11587) +@@ -0,0 +1,16 @@ ++#/bin/bash ++ ++#Package using the Package Maker from OSX, driven by command line. ++sudo sh -c "rm -rf ISSM-MacOSX.pkg bin test" ++ ++#We need to copy all the relevant files and set the permissions, as PackageMaker ++#is not good at that. ++cp -Rf $ISSM_TIER/bin ./ ++cp -Rf $ISSM_TIER/test ./ ++cp matlabissm startup.m ./bin ++ ++#Now change group and ownership: ++sudo sh -c "chown -R root ./bin && chgrp -R admin ./bin" ++sudo sh -c "chown -R root ./test && chgrp -R admin ./test" ++ ++#Run PackageMaker now, using the ISSM.pmdoc project + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package_incomplete.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11587) +@@ -1,6 +1,19 @@ + #/bin/bash + + #Package using the Package Maker from OSX, driven by command line. +-rm -rf ISSM-MacOSX.pkg ++sudo sh -c "rm -rf ISSM-MacOSX.pkg bin test" + ++#We need to copy all the relevant files and set the permissions, as PackageMaker ++#is not good at that. ++cp -Rf $ISSM_TIER/bin ./ ++cp -Rf $ISSM_TIER/test ./ ++cp matlabissm startup.m ./bin ++ ++#Now change group and ownership: ++sudo sh -c "chown -R root ./bin && chgrp -R admin ./bin" ++sudo sh -c "chown -R root ./test && chgrp -R admin ./test" ++ + PackageMaker -d ISSM.pmdoc -o ISSM-MacOSX.pkg ++ ++#cleanup ++sudo sh -c "rm -rf ./bin && rm -rf ./test" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml (revision 11587) +@@ -1 +0,0 @@ +-groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml (revision 11587) +@@ -1 +0,0 @@ +-issm.test.pkg1.0/Users/larour/issm-uci/trunk-jpl/test/Library/ISSM/testinstallTo.pathparentinstallToidentifier05test-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml (revision 11587) +@@ -1 +0,0 @@ +-ISSM.startup.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/startup.m/Library/ISSM/bin/installTo.pathinstallToinstallFrom.pathidentifierrelocatableparent03startup-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml (revision 11587) +@@ -1 +0,0 @@ +-groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml (revision 11587) +@@ -1 +0,0 @@ +-groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml (revision 11587) +@@ -1 +0,0 @@ +-issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/bin/Library/ISSM/bininstallTo.pathparentinstallToidentifier04bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml (revision 11587) +@@ -1 +0,0 @@ +-ISSM.matlabissm.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/matlabissm/Library/ISSM/bin/installTo.isRelativeTypeinstallTorelocatableinstallTo.isAbsoluteTypeinstallFrom.pathidentifierparentinstallTo.path02matlabissm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml (revision 11587) +@@ -1 +0,0 @@ +-groupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test.xml (revision 11587) +@@ -0,0 +1 @@ ++issm.test.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/test/ISSM/testinstallTorelocatableinstallFrom.pathscripts.postinstall.pathidentifierparentincludeRootinstallTo.path03test-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml (revision 11587) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11587) +@@ -1 +1 @@ +- +\ No newline at end of file ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml (revision 11587) +@@ -1 +1 @@ +-ISSM/Users/larour/issm-uci/trunk-jpl/packagers/macosx/ISSM.pkghttp://issm.jpl.nasa.govIce Sheet System Model01issm.xml02matlabissm.xml03startup.xml04bin.xml05test.xmlproperties.titleproperties.userDomaindescriptionproperties.anywhereDomain +\ No newline at end of file ++ISSM/Users/larour/issm-uci/trunk-jpl/packagers/macosx/ISSM.pkghttp://issm.jpl.nasa.govIce Sheet System Model01issm.xml02bin.xml03test.xmlproperties.titleproperties.userDomaindescriptionproperties.anywhereDomain +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml (revision 11587) +@@ -0,0 +1 @@ ++issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/bin/ISSM/bininstallTo.pathincludeRootinstallFrom.pathidentifierinstallToparent02bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml (revision 11587) +@@ -1 +1 @@ +-ISSM.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/ISSM.app/ApplicationsinstallTorelocatableinstallFrom.pathidentifierparentincludeRootrequireAuthorization01issm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file ++ISSM.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/ISSM.app/ISSM/installTorelocatableinstallFrom.pathidentifierparentincludeRootrequireAuthorizationinstallTo.path01issm-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml (revision 11587) +@@ -0,0 +1 @@ ++ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11587) +@@ -1,2 +1,2 @@ + #/bin/bash +-matlab -r "addpath /Library/ISSM/bin/; startup; cd /Library/ISSM/test;" ++matlab -r "name=getenv('USER'); issm=['/Users/' name '/ISSM']; cd(issm); cd bin; startup; cd ../;" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m (revision 11586) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/startup.m (revision 11587) +@@ -23,7 +23,6 @@ + + %ISSM path + addpath(pwd); %add current path first +-addpath([pwd '\bin']); + + %Check on any warning messages that might indicate that the paths were not correct. + if ~isempty(lastwarn), Index: /issm/oecreview/Archive/11581-11588/ISSM-11587-11588.diff =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-11587-11588.diff (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-11587-11588.diff (revision 11991) @@ -0,0 +1,108 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS/applet +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS/applet +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist (revision 11588) +@@ -0,0 +1,44 @@ ++ ++ ++ ++ ++ CFBundleAllowMixedLocalizations ++ ++ CFBundleDevelopmentRegion ++ English ++ CFBundleExecutable ++ applet ++ CFBundleIconFile ++ applet ++ CFBundleInfoDictionaryVersion ++ 6.0 ++ CFBundleName ++ ISSM ++ CFBundlePackageType ++ APPL ++ CFBundleSignature ++ aplt ++ LSMinimumSystemVersionByArchitecture ++ ++ x86_64 ++ 10.6 ++ ++ LSRequiresCarbon ++ ++ WindowState ++ ++ dividerCollapsed ++ ++ eventLogLevel ++ -1 ++ name ++ ScriptWindowState ++ positionOfDivider ++ 333 ++ savedFrame ++ 3 428 602 597 0 0 1680 1028 ++ selectedTabView ++ result ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.icns +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.icns +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf (revision 11588) +@@ -0,0 +1,4 @@ ++{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf230 ++{\fonttbl} ++{\colortbl;\red255\green255\blue255;} ++} +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.rsrc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.rsrc +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo (revision 11588) +@@ -0,0 +1 @@ ++APPLaplt +\ No newline at end of file Index: /issm/oecreview/Archive/11581-11588/ISSM-DocReview-11581-11588.tex =================================================================== --- /issm/oecreview/Archive/11581-11588/ISSM-DocReview-11581-11588.tex (revision 11991) +++ /issm/oecreview/Archive/11581-11588/ISSM-DocReview-11581-11588.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11581-11588/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11581-11588/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11581-11588/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11581-11588 Index: /issm/oecreview/Archive/11581-11588/Makefile =================================================================== --- /issm/oecreview/Archive/11581-11588/Makefile (revision 11991) +++ /issm/oecreview/Archive/11581-11588/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11581-11588 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11581-11588/log.tex =================================================================== --- /issm/oecreview/Archive/11581-11588/log.tex (revision 11991) +++ /issm/oecreview/Archive/11581-11588/log.tex (revision 11991) @@ -0,0 +1,12 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11581-11582.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/win7/ISSMlogo.ico \\ Export determination: 6. \\Rationale: Added transparent bg \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11582-11583.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml M /issm/trunk-jpl/packagers/macosx/matlabissm M /issm/trunk-jpl/packagers/macosx/package.sh \\ Export determination: 6. \\Rationale: Some mods on the packager for macosx \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11583-11584.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml M /issm/trunk-jpl/packagers/macosx/matlabissm M /issm/trunk-jpl/packagers/macosx/package.sh \\ Export determination: 6. \\Rationale: Some mods on the packager for macosx +M /issm/trunk-jpl/src/c/objects/Bamg/Mesh.cpp M /issm/trunk-jpl/src/c/objects/Bamg/Triangle.cpp M /issm/trunk-jpl/src/c/objects/Bamg/Triangle.h added functions to remove triangles in a triangulation if the triangles are weird \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11584-11585.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Bamg/Mesh.cpp M /issm/trunk-jpl/src/c/objects/Bamg/Triangle.cpp M /issm/trunk-jpl/src/c/objects/Bamg/Triangle.h \\ Export determination: 6. \\Rationale: added functions to remove triangles in a triangulation if the triangles are weird +M /issm/trunk-jpl/test/NightlyRun/IdToName.m A /issm/trunk-jpl/test/NightlyRun/test455.m A /issm/trunk-jpl/test/NightlyRun/test456.m A /issm/trunk-jpl/test/NightlyRun/test457.m A /issm/trunk-jpl/test/NightlyRun/test458.m A /issm/trunk-jpl/test/NightlyRun/test459.m A /issm/trunk-jpl/test/NightlyRun/test460.m added nightly runs for newton iterations \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11585-11586.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun/IdToName.m A /issm/trunk-jpl/test/NightlyRun/test455.m A /issm/trunk-jpl/test/NightlyRun/test456.m A /issm/trunk-jpl/test/NightlyRun/test457.m A /issm/trunk-jpl/test/NightlyRun/test458.m A /issm/trunk-jpl/test/NightlyRun/test459.m A /issm/trunk-jpl/test/NightlyRun/test460.m \\ Export determination: 6. \\Rationale: added nightly runs for newton iterations +A /issm/trunk-jpl/test/Archives/Archive455.mat A /issm/trunk-jpl/test/Archives/Archive456.mat A /issm/trunk-jpl/test/Archives/Archive457.mat A /issm/trunk-jpl/test/Archives/Archive458.mat A /issm/trunk-jpl/test/Archives/Archive459.mat A /issm/trunk-jpl/test/Archives/Archive460.mat added archives for newton nightly runs \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11586-11587.diff: \\ Function name: \\A /issm/trunk-jpl/test/Archives/Archive455.mat A /issm/trunk-jpl/test/Archives/Archive456.mat A /issm/trunk-jpl/test/Archives/Archive457.mat A /issm/trunk-jpl/test/Archives/Archive458.mat A /issm/trunk-jpl/test/Archives/Archive459.mat A /issm/trunk-jpl/test/Archives/Archive460.mat \\ Export determination: 6. \\Rationale: added archives for newton nightly runs +D /issm/trunk-jpl/packagers/macosx/ISSM.app M /issm/trunk-jpl/packagers/macosx/ISSM.appscript M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml M /issm/trunk-jpl/packagers/macosx/matlabissm M /issm/trunk-jpl/packagers/macosx/package.sh A /issm/trunk-jpl/packagers/macosx/package\_incomplete.sh M /issm/trunk-jpl/packagers/macosx/startup.m Better packager, dumping into the user home directory \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11587-11588.diff: \\ Function name: \\D /issm/trunk-jpl/packagers/macosx/ISSM.app M /issm/trunk-jpl/packagers/macosx/ISSM.appscript M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02matlabissm.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03startup.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml A /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/04bin.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test-contents.xml D /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/05test.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/index.xml M /issm/trunk-jpl/packagers/macosx/matlabissm M /issm/trunk-jpl/packagers/macosx/package.sh A /issm/trunk-jpl/packagers/macosx/package\_incomplete.sh M /issm/trunk-jpl/packagers/macosx/startup.m \\ Export determination: 6. \\Rationale: Better packager, dumping into the user home directory +A /issm/trunk-jpl/packagers/macosx/ISSM.app A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS/applet A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.icns A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.rsrc A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf Different app to launch from home directory \\\\ Index: /issm/oecreview/Archive/11581-11588/r1.tex =================================================================== --- /issm/oecreview/Archive/11581-11588/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11581-11588/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11581 Index: /issm/oecreview/Archive/11581-11588/r2.tex =================================================================== --- /issm/oecreview/Archive/11581-11588/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11581-11588/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11588 Index: /issm/oecreview/Archive/11588-11600/Date.tex =================================================================== --- /issm/oecreview/Archive/11588-11600/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11588-11600/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11588-11600/ISSM-11588-11589.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11588-11589.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11588-11589.diff (revision 11991) @@ -0,0 +1,9 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11588) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11589) +@@ -1,2 +1,4 @@ + #/bin/bash ++user_home=`echo ~`; ++export ISSM_TIER="$user_home/ISSM" + matlab -r "name=getenv('USER'); issm=['/Users/' name '/ISSM']; cd(issm); cd bin; startup; cd ../;" Index: /issm/oecreview/Archive/11588-11600/ISSM-11589-11590.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11589-11590.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11589-11590.diff (revision 11991) @@ -0,0 +1,105 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/steadystate_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/steadystate_core.cpp (revision 11589) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/steadystate_core.cpp (revision 11590) +@@ -24,10 +24,10 @@ + int step; + + /*parameters: */ +- int dim; +- int solution_type; +- int maxiter; +- bool control_analysis; ++ bool control_analysis,isenthalpy; ++ int dim; ++ int solution_type; ++ int maxiter; + int numoutputs = 0; + int *requested_outputs = NULL; + +@@ -37,6 +37,7 @@ + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); + femmodel->parameters->FindParam(&maxiter,SteadystateMaxiterEnum); + femmodel->parameters->FindParam(&numoutputs,SteadystateNumRequestedOutputsEnum); ++ femmodel->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); + if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,SteadystateRequestedOutputsEnum); + + /*intialize counters: */ +@@ -46,7 +47,12 @@ + + _printf_(VerboseSolution(),"%s%i\n"," computing temperature and velocity for step: ",step); + #ifdef _HAVE_THERMAL_ +- thermal_core(femmodel); ++ if(isenthalpy==0){ ++ thermal_core(femmodel); ++ } ++ else{ ++ enthalpy_core(femmodel); ++ } + #else + _error_("ISSM was not compiled with thermal capabilities. Exiting"); + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/AnalysisConfiguration.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/AnalysisConfiguration.cpp (revision 11589) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/AnalysisConfiguration.cpp (revision 11590) +@@ -37,15 +37,16 @@ + break; + + case SteadystateSolutionEnum: +- numanalyses=7; ++ numanalyses=8; + analyses=(int*)xmalloc(numanalyses*sizeof(int)); + analyses[0]=DiagnosticHorizAnalysisEnum; + analyses[1]=DiagnosticVertAnalysisEnum; + analyses[2]=DiagnosticHutterAnalysisEnum; + analyses[3]=SurfaceSlopeAnalysisEnum; + analyses[4]=BedSlopeAnalysisEnum; +- analyses[5]=ThermalAnalysisEnum; +- analyses[6]=MeltingAnalysisEnum; ++ analyses[5]=EnthalpyAnalysisEnum; ++ analyses[6]=ThermalAnalysisEnum; ++ analyses[7]=MeltingAnalysisEnum; + break; + + case ThermalSolutionEnum: +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m (revision 11589) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m (revision 11590) +@@ -9,6 +9,7 @@ + dim=femmodel.parameters.MeshDimension; + control_analysis=femmodel.parameters.InversionIscontrol; + solution_type=femmodel.parameters.SolutionType; ++ isenthalpy=femmodel.parameters.ThermalIsenthalpy; + + %Initialize counter + step=1; +@@ -16,7 +17,11 @@ + while true, + + issmprintf(VerboseSolution,'\n%s%i\n',' computing velocities and temperatures for step: ',step); +- femmodel=thermal_core(femmodel); ++ if (isenthalpy==0), ++ femmodel=thermal_core(femmodel); ++ else ++ femmodel=enthalpy_core(femmodel); ++ end + + issmprintf(VerboseSolution,'\n%s',[' computing new velocity']); + femmodel=diagnostic_core(femmodel); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/AnalysisConfiguration.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/AnalysisConfiguration.m (revision 11589) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/AnalysisConfiguration.m (revision 11590) +@@ -13,8 +13,8 @@ + analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum]; + + case SteadystateSolutionEnum, +- numanalyses=7; +- analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum]; ++ numanalyses=8; ++ analyses=[DiagnosticHorizAnalysisEnum;DiagnosticVertAnalysisEnum;DiagnosticHutterAnalysisEnum;SurfaceSlopeAnalysisEnum;BedSlopeAnalysisEnum;EnthalpyAnalysisEnum;ThermalAnalysisEnum;MeltingAnalysisEnum]; + + case ThermalSolutionEnum, + numanalyses=2; Index: /issm/oecreview/Archive/11588-11600/ISSM-11590-11591.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11590-11591.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11590-11591.diff (revision 11991) @@ -0,0 +1,169 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m (revision 11591) +@@ -0,0 +1,24 @@ ++md=triangle(model,'../Exp/Square.exp',150000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,3,2); ++md=setflowequation(md,'macayeal','all'); ++md.cluster=none; ++md.timestepping.time_step=0; ++md.thermal.isenthalpy=1; ++md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); ++md=solve(md,SteadystateSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; ++field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 ++}; ++field_values={... ++ (md.results.SteadystateSolution.Vx),... ++ (md.results.SteadystateSolution.Vy),... ++ (md.results.SteadystateSolution.Vz),... ++ (md.results.SteadystateSolution.Vel),... ++ (md.results.SteadystateSolution.Pressure),... ++ (md.results.SteadystateSolution.Temperature),... ++ (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test462.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test462.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test462.m (revision 11591) +@@ -0,0 +1,23 @@ ++md=triangle(model,'../Exp/Square.exp',150000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,3,2); ++md=setflowequation(md,'macayeal','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++md.timestepping.time_step=0; ++md.thermal.isenthalpy=1; ++md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); ++md=solve(md,SteadystateSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; ++field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-06}; ++field_values={... ++ (md.results.SteadystateSolution.Vx),... ++ (md.results.SteadystateSolution.Vy),... ++ (md.results.SteadystateSolution.Vz),... ++ (md.results.SteadystateSolution.Vel),... ++ (md.results.SteadystateSolution.Pressure),... ++ (md.results.SteadystateSolution.Temperature),... ++ (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 11591) +@@ -0,0 +1,23 @@ ++md=triangle(model,'../Exp/Square.exp',150000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,3,2); ++md=setflowequation(md,'pattyn','all'); ++md.cluster=none; ++md.timestepping.time_step=0; ++md.thermal.isenthalpy=1; ++md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); ++md=solve(md,SteadystateSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; ++field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; ++field_values={... ++ (md.results.SteadystateSolution.Vx),... ++ (md.results.SteadystateSolution.Vy),... ++ (md.results.SteadystateSolution.Vz),... ++ (md.results.SteadystateSolution.Vel),... ++ (md.results.SteadystateSolution.Pressure),... ++ (md.results.SteadystateSolution.Temperature),... ++ (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m (revision 11591) +@@ -0,0 +1,24 @@ ++md=triangle(model,'../Exp/Square.exp',150000); ++md=setmask(md,'../Exp/SquareShelf.exp',''); ++md=parameterize(md,'../Par/SquareSheetShelf.par'); ++md=extrude(md,3,2); ++md=setflowequation(md,'pattyn','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++md.timestepping.time_step=0; ++md.thermal.isenthalpy=1; ++md.initialization.waterfraction=zeros(md.mesh.numberofvertices,1); ++md=solve(md,SteadystateSolutionEnum); ++ ++%Fields and tolerances to track changes ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; ++field_tolerances={1e-09,1e-09,1e-08,1e-09,1e-09,1e-08,1e-05 ++}; ++field_values={... ++ (md.results.SteadystateSolution.Vx),... ++ (md.results.SteadystateSolution.Vy),... ++ (md.results.SteadystateSolution.Vz),... ++ (md.results.SteadystateSolution.Vel),... ++ (md.results.SteadystateSolution.Pressure),... ++ (md.results.SteadystateSolution.Temperature),... ++ (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/IdToName.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/IdToName.m (revision 11590) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/IdToName.m (revision 11591) +@@ -229,6 +229,10 @@ + case 458, name='SquareSheetShelfDiagP3dNewtonParallel'; + case 459, name='SquareSheetShelfDiagS3dNewtonSerial'; + case 460, name='SquareSheetShelfDiagS3dNewtonParallel'; ++ case 461, name='SquareSheetShelfSteaEnthalpyM3dSerial'; ++ case 462, name='SquareSheetShelfSteaEnthalpyM3dParallel'; ++ case 463, name='SquareSheetShelfSteaEnthalpyP3dSerial'; ++ case 464, name='SquareSheetShelfSteaEnthalpyP3dParallel'; + case 501, name='PigDiagM2dSerial'; + case 502, name='PigDiagM2dParallel'; + case 503, name='PigDiagP3dSerial'; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive462.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive462.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive463.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive463.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive464.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive464.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive461.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive461.mat +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + Index: /issm/oecreview/Archive/11588-11600/ISSM-11591-11592.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11591-11592.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11591-11592.diff (revision 11991) @@ -0,0 +1,40 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11591) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/package.sh (revision 11592) +@@ -1,19 +1,25 @@ + #/bin/bash + + #Package using the Package Maker from OSX, driven by command line. ++echo "Cleanup first" + sudo sh -c "rm -rf ISSM-MacOSX.pkg bin test" + + #We need to copy all the relevant files and set the permissions, as PackageMaker + #is not good at that. ++echo "Copy bin" + cp -Rf $ISSM_TIER/bin ./ ++echo "Copy test" + cp -Rf $ISSM_TIER/test ./ + cp matlabissm startup.m ./bin + + #Now change group and ownership: ++echo "Change group and ownership" + sudo sh -c "chown -R root ./bin && chgrp -R admin ./bin" + sudo sh -c "chown -R root ./test && chgrp -R admin ./test" + ++echo "Launch packagemaker" + PackageMaker -d ISSM.pmdoc -o ISSM-MacOSX.pkg + + #cleanup ++echo "Final cleanup" + sudo sh -c "rm -rf ./bin && rm -rf ./test" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11591) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11592) +@@ -1,4 +1,4 @@ + #/bin/bash + user_home=`echo ~`; +-export ISSM_TIER="$user_home/ISSM" ++export ISSM_TIER="$user_home/ISSM/bin" + matlab -r "name=getenv('USER'); issm=['/Users/' name '/ISSM']; cd(issm); cd bin; startup; cd ../;" Index: /issm/oecreview/Archive/11588-11600/ISSM-11592-11593.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11592-11593.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11592-11593.diff (revision 11991) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/runme.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/runme.m (revision 11592) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/runme.m (revision 11593) +@@ -179,6 +179,7 @@ + fclose(fid); + disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname)); + else ++ disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,fieldname)); + rethrow(me2); + end + end +@@ -203,6 +204,7 @@ + fclose(fid); + disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A')); + else ++ disp(sprintf(['FAILURE difference: N/A test id: %i test name: %s field: %s'],id,id_string,'N/A')); + rethrow(me); + end + end Index: /issm/oecreview/Archive/11588-11600/ISSM-11593-11594.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11593-11594.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11593-11594.diff (revision 11991) @@ -0,0 +1,117 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11594) +@@ -0,0 +1,106 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/Users/larour/issm-uci" ++ISSM_TIER="/Users/larour/issm-uci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="macosx-gnu" ++ ++#Machine configuration ++MACHINE="macosx-gil" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-macosx64-imac.sh" ++ ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/Users/larour/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="schlegel@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=7 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="" ++ ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11588-11600/ISSM-11594-11595.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11594-11595.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11594-11595.diff (revision 11991) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11594) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/matlabissm (revision 11595) +@@ -1,4 +1,4 @@ + #/bin/bash + user_home=`echo ~`; +-export ISSM_TIER="$user_home/ISSM/bin" ++export ISSM_TIER="$user_home/ISSM" + matlab -r "name=getenv('USER'); issm=['/Users/' name '/ISSM']; cd(issm); cd bin; startup; cd ../;" Index: /issm/oecreview/Archive/11588-11600/ISSM-11595-11596.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11595-11596.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11595-11596.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ismumps.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ismumps.m (revision 11595) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ismumps.m (revision 11596) +@@ -5,7 +5,7 @@ + % flag=ismumps(); + + +-configfile=[issmtier() '/config.h']; ++configfile=[issmtier() '/bin/config.h']; %should find it in the install target + if ~exist(configfile,'file'), + error(['File ' configfile ' not found. ISSM has not been configured yet!']); + end Index: /issm/oecreview/Archive/11588-11600/ISSM-11596-11597.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11596-11597.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11596-11597.diff (revision 11991) @@ -0,0 +1,39 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh (revision 11597) +@@ -0,0 +1,28 @@ ++#!/bin/sh ++ ++#petsc 3.2 ++#mpich 1.4 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-numthreads=8 + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11588-11600/ISSM-11597-11598.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11597-11598.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11597-11598.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11597) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11598) +@@ -249,7 +249,7 @@ + dnl defaults + HAVE_DAKOTA=yes + DAKOTAINCL=-I$DAKOTA_ROOT/include +- DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" ++ DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver -L/usr/lib -lblas -llapack" + dnl DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lgslcblas -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src]) + AC_SUBST([DAKOTAINCL]) Index: /issm/oecreview/Archive/11588-11600/ISSM-11598-11599.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11598-11599.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11598-11599.diff (revision 11991) @@ -0,0 +1,57 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh (revision 11598) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh (revision 11599) +@@ -27,11 +27,13 @@ + + #Configure dakota + cd src +-./configure \ +- --prefix="$ISSM_TIER/externalpackages/dakota/install" \ +- --without-graphics \ +- --with-pic \ +- --disable-mpi ++./configure \ ++ --prefix="$ISSM_TIER/externalpackages/dakota/install" \ ++ --without-graphics \ ++ --with-pic \ ++ --disable-mpi \ ++ --with-blas=/usr/lib/libblas.dylib \ ++ --with-lapack=/usr/lib/liblapack.dylib + cd .. + + #Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages +@@ -43,7 +45,7 @@ + cat ./src/methods/acro/packages/pebbl/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp + mv temp ./src/methods/acro/packages/pebbl/src/Makefile + +-cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++cat ./src/methods/hopspack/src-nappspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp + mv temp ./src/methods/hopspack/src-nappspack/Makefile + + cat ./src/methods/hopspack/src-cddlib/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp +@@ -52,13 +54,13 @@ + cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp + mv temp ./src/methods/hopspack/src-shared/Makefile + +-cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++cat ./src/methods/hopspack/src-shared/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp + mv temp ./src/methods/hopspack/src-shared/Makefile + + cat ./src/methods/hopspack/src-conveyor/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp + mv temp ./src/methods/hopspack/src-conveyor/Makefile + +-cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp ++cat ./src/methods/hopspack/src-appspack/Makefile | sed 's/CXXFLAGS = -g -O2/CXXFLAGS = -g -O2 -fPIC/g' > temp + mv temp ./src/methods/hopspack/src-appspack/Makefile + + cat ./src/methods/acro/packages/colin/src/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CXXFLAGS = -O2 -fpermissive -fPIC/g' > temp +@@ -73,7 +75,7 @@ + cat ./src/methods/acro/packages/tpl/3po/Makefile | sed 's/CXXFLAGS = -O2 -fpermissive/CFLAGS = -O2 -fpermissive -fPIC/g' > temp + mv temp ./src/methods/acro/packages/tpl/3po/Makefile + +-cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2/CFLAGS = -g -O2 -fPIC/g' > temp ++cat ./src/packages/ampl/Makefile | sed 's/CFLAGS = -g -O2 -D_NONSTD_SOURCE/CFLAGS = -g -O2 -fPIC/g' > temp + mv temp ./src/packages/ampl/Makefile + + #Compile and install dakota Index: /issm/oecreview/Archive/11588-11600/ISSM-11599-11600.diff =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-11599-11600.diff (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-11599-11600.diff (revision 11991) @@ -0,0 +1,23 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11599) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11600) +@@ -249,7 +249,17 @@ + dnl defaults + HAVE_DAKOTA=yes + DAKOTAINCL=-I$DAKOTA_ROOT/include +- DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver -L/usr/lib -lblas -llapack" ++ case "${host_os}" in ++ *cygwin*) ++ DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" ++ ;; ++ *linux*) ++ DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" ++ ;; ++ *darwin*) ++ DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver -L/usr/lib -lblas -llapack" ++ ;; ++ esac + dnl DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lgslcblas -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src]) + AC_SUBST([DAKOTAINCL]) Index: /issm/oecreview/Archive/11588-11600/ISSM-DocReview-11588-11600.tex =================================================================== --- /issm/oecreview/Archive/11588-11600/ISSM-DocReview-11588-11600.tex (revision 11991) +++ /issm/oecreview/Archive/11588-11600/ISSM-DocReview-11588-11600.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11588-11600/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11588-11600/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11588-11600/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11588-11600 Index: /issm/oecreview/Archive/11588-11600/Makefile =================================================================== --- /issm/oecreview/Archive/11588-11600/Makefile (revision 11991) +++ /issm/oecreview/Archive/11588-11600/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11588-11600 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11588-11600/log.tex =================================================================== --- /issm/oecreview/Archive/11588-11600/log.tex (revision 11991) +++ /issm/oecreview/Archive/11588-11600/log.tex (revision 11991) @@ -0,0 +1,24 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11588-11589.diff: \\ Function name: \\A /issm/trunk-jpl/packagers/macosx/ISSM.app A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Info.plist A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/MacOS/applet A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/PkgInfo A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/Scripts/main.scpt A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.icns A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/applet.rsrc A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd A /issm/trunk-jpl/packagers/macosx/ISSM.app/Contents/Resources/description.rtfd/TXT.rtf \\ Export determination: 6. \\Rationale: Different app to launch from home directory +M /issm/trunk-jpl/packagers/macosx/matlabissm Adding export of ISSM\_TIER \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11589-11590.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/matlabissm \\ Export determination: 6. \\Rationale: Adding export of ISSM\_TIER +M /issm/trunk-jpl/src/c/solutions/AnalysisConfiguration.cpp M /issm/trunk-jpl/src/c/solutions/steadystate\_core.cpp M /issm/trunk-jpl/src/m/solutions/AnalysisConfiguration.m M /issm/trunk-jpl/src/m/solutions/steadystate\_core.m added possibility of using enthalpy in steady state solution \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11590-11591.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/solutions/AnalysisConfiguration.cpp M /issm/trunk-jpl/src/c/solutions/steadystate\_core.cpp M /issm/trunk-jpl/src/m/solutions/AnalysisConfiguration.m M /issm/trunk-jpl/src/m/solutions/steadystate\_core.m \\ Export determination: 6. \\Rationale: added possibility of using enthalpy in steady state solution +A /issm/trunk-jpl/test/Archives/Archive461.mat A /issm/trunk-jpl/test/Archives/Archive462.mat A /issm/trunk-jpl/test/Archives/Archive463.mat A /issm/trunk-jpl/test/Archives/Archive464.mat M /issm/trunk-jpl/test/NightlyRun/IdToName.m A /issm/trunk-jpl/test/NightlyRun/test461.m A /issm/trunk-jpl/test/NightlyRun/test462.m A /issm/trunk-jpl/test/NightlyRun/test463.m A /issm/trunk-jpl/test/NightlyRun/test464.m added nightly runs for steady-state with enthalpy \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11591-11592.diff: \\ Function name: \\A /issm/trunk-jpl/test/Archives/Archive461.mat A /issm/trunk-jpl/test/Archives/Archive462.mat A /issm/trunk-jpl/test/Archives/Archive463.mat A /issm/trunk-jpl/test/Archives/Archive464.mat M /issm/trunk-jpl/test/NightlyRun/IdToName.m A /issm/trunk-jpl/test/NightlyRun/test461.m A /issm/trunk-jpl/test/NightlyRun/test462.m A /issm/trunk-jpl/test/NightlyRun/test463.m A /issm/trunk-jpl/test/NightlyRun/test464.m \\ Export determination: 6. \\Rationale: added nightly runs for steady-state with enthalpy +M /issm/trunk-jpl/packagers/macosx/matlabissm M /issm/trunk-jpl/packagers/macosx/package.sh Wrong determination for ISSM\_TIER \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11592-11593.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/matlabissm M /issm/trunk-jpl/packagers/macosx/package.sh \\ Export determination: 6. \\Rationale: Wrong determination for ISSM\_TIER +M /issm/trunk-jpl/test/NightlyRun/runme.m add failure messages \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11593-11594.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun/runme.m \\ Export determination: 6. \\Rationale: add failure messages +A /issm/trunk-jpl/cron/configs/macosx64\_schlegel use new config file \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11594-11595.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: use new config file +M /issm/trunk-jpl/packagers/macosx/matlabissm Reverting on this \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11595-11596.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/matlabissm \\ Export determination: 6. \\Rationale: Reverting on this +M /issm/trunk-jpl/src/m/utils/OS/ismumps.m This may break some nightlys, legitimate \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11596-11597.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/OS/ismumps.m \\ Export determination: 6. \\Rationale: This may break some nightlys, legitimate +A /issm/trunk-jpl/configs/config-macosx64-imac.sh new config for our desktop imacs \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11597-11598.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-macosx64-imac.sh \\ Export determination: 6. \\Rationale: new config for our desktop imacs +M /issm/trunk-jpl/m4/issm\_options.m4 add option for imac dakota compile \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11598-11599.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: add option for imac dakota compile +M /issm/trunk-jpl/externalpackages/dakota/install-macosx64.sh dakota compiles on mac with new settings \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11599-11600.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/dakota/install-macosx64.sh \\ Export determination: 6. \\Rationale: dakota compiles on mac with new settings +M /issm/trunk-jpl/m4/issm\_options.m4 Change in DakotaLib only for macs \\\\ Index: /issm/oecreview/Archive/11588-11600/r1.tex =================================================================== --- /issm/oecreview/Archive/11588-11600/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11588-11600/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11588 Index: /issm/oecreview/Archive/11588-11600/r2.tex =================================================================== --- /issm/oecreview/Archive/11588-11600/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11588-11600/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11600 Index: /issm/oecreview/Archive/11600-11617/Date.tex =================================================================== --- /issm/oecreview/Archive/11600-11617/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11600-11617/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11600-11617/ISSM-11600-11601.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11600-11601.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11600-11601.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11600) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11601) +@@ -16,7 +16,7 @@ + MACHINE="macosx-gil" + + #COMPILATION CONFIGURATION FILE +-COMPILE_CONFIG_FILE="config-macosx64-imac.sh" ++COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" + + + #----------------------# Index: /issm/oecreview/Archive/11600-11617/ISSM-11601-11602.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11601-11602.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11601-11602.diff (revision 11991) @@ -0,0 +1,72 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh (revision 11601) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-imac.sh (revision 11602) +@@ -1,28 +0,0 @@ +-#!/bin/sh +- +-#petsc 3.2 +-#mpich 1.4 +- +-./configure \ +- --prefix=$ISSM_TIER \ +- --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ +- --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ +- --with-petsc-arch=$ISSM_ARCH \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ +- --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ +- --with-math-lib="/usr/lib/libm.dylib" \ +- --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +- --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ +- --with-numthreads=8 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh (revision 11602) +@@ -0,0 +1,28 @@ ++#!/bin/sh ++ ++#petsc 3.2 ++#mpich 1.4 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-numthreads=8 + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-nicole.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11600-11617/ISSM-11602-11603.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11602-11603.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11602-11603.diff (revision 11991) @@ -0,0 +1,47 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/steadystate_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/steadystate_core.cpp (revision 11602) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/steadystate_core.cpp (revision 11603) +@@ -88,7 +88,9 @@ + InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,VelEnum); + InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,PressureEnum); + InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,TemperatureEnum); +- InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,BasalforcingsMeltingRateEnum); ++ if(isenthalpy) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,WaterfractionEnum); ++ if(isenthalpy) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,EnthalpyEnum); ++ if(!isenthalpy) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,BasalforcingsMeltingRateEnum); + RequestedOutputsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,requested_outputs,numoutputs); + } + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 11602) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 11603) +@@ -63,6 +63,9 @@ + if(solution_type==TransientSolutionEnum && analysis_type==DiagnosticHorizAnalysisEnum && isdiagnostic==false) continue; + if(solution_type==TransientSolutionEnum && analysis_type==DiagnosticVertAnalysisEnum && isdiagnostic==false) continue; + if(solution_type==TransientSolutionEnum && analysis_type==DiagnosticHutterAnalysisEnum && isdiagnostic==false) continue; ++ if(solution_type==SteadystateSolutionEnum && analysis_type==ThermalAnalysisEnum && isenthalpy==true) continue; ++ if(solution_type==SteadystateSolutionEnum && analysis_type==MeltingAnalysisEnum && isenthalpy==true) continue; ++ if(solution_type==SteadystateSolutionEnum && analysis_type==EnthalpyAnalysisEnum && isenthalpy==false) continue; + + _printf_(VerboseMProcessor()," creating datasets for analysis %s\n",EnumToStringx(analysis_type)); + CreateDataSets(&elements,&nodes,&vertices,&materials,&constraints,&loads,¶meters,iomodel,solution_type,analysis_type,nummodels,i); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m (revision 11602) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m (revision 11603) +@@ -50,7 +50,11 @@ + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,VelEnum); + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,PressureEnum); + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,TemperatureEnum); +- femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,BasalforcingsMeltingRateEnum); +- end ++ if (isenthalpy), ++ femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,WaterfractionEnum); ++ femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,EnthalpyEnum); ++ else ++ femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,WaterfractionEnum); ++ end + + end %end of function Index: /issm/oecreview/Archive/11600-11617/ISSM-11603-11604.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11603-11604.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11603-11604.diff (revision 11991) @@ -0,0 +1,110 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m (revision 11603) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test461.m (revision 11604) +@@ -10,9 +10,8 @@ + md=solve(md,SteadystateSolutionEnum); + + %Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13 +-}; ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; ++field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... +@@ -20,5 +19,6 @@ + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ (md.results.SteadystateSolution.Waterfraction),... ++ (md.results.SteadystateSolution.Enthalpy),... + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test462.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test462.m (revision 11603) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test462.m (revision 11604) +@@ -10,8 +10,8 @@ + md=solve(md,SteadystateSolutionEnum); + + %Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-06}; ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; ++field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... +@@ -19,5 +19,6 @@ + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ (md.results.SteadystateSolution.Waterfraction),... ++ (md.results.SteadystateSolution.Enthalpy),... + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 11603) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 11604) +@@ -10,8 +10,8 @@ + md=solve(md,SteadystateSolutionEnum); + + %Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06}; ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; ++field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... +@@ -19,5 +19,6 @@ + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ (md.results.SteadystateSolution.Waterfraction),... ++ (md.results.SteadystateSolution.Enthalpy),... + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m (revision 11603) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m (revision 11604) +@@ -10,9 +10,8 @@ + md=solve(md,SteadystateSolutionEnum); + + %Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-09,1e-09,1e-08,1e-09,1e-09,1e-08,1e-05 +-}; ++field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; ++field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... +@@ -20,5 +19,6 @@ + (md.results.SteadystateSolution.Vel),... + (md.results.SteadystateSolution.Pressure),... + (md.results.SteadystateSolution.Temperature),... +- (md.results.SteadystateSolution.BasalforcingsMeltingRate),... ++ (md.results.SteadystateSolution.Waterfraction),... ++ (md.results.SteadystateSolution.Enthalpy),... + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive462.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive463.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive464.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/Archives/Archive461.mat +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/11600-11617/ISSM-11604-11605.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11604-11605.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11604-11605.diff (revision 11991) @@ -0,0 +1,42 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11604) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11605) +@@ -6,8 +6,8 @@ + #-------------------------------# + + #ISSM main directory (full path) +-ISSM_DIR="/Users/larour/issm-uci" +-ISSM_TIER="/Users/larour/issm-uci/trunk-jpl/cron/trunk-jpl" ++ISSM_DIR="/Users/schlegel/issmuci" ++ISSM_TIER="/Users/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" + + #ISSM Architecture + ISSM_ARCH="macosx-gnu" +@@ -36,7 +36,7 @@ + REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" + + #execution path used for parallel runs +-EXECUTION_PATH="/Users/larour/ExecutionNightlyRun" ++EXECUTION_PATH="/Users/schlegel/ExecutionNightlyRun" + + #-----------------------------------# + # 3: External packages installation # +@@ -48,7 +48,7 @@ + # - "none" leave external packages as is + # ->skip to section 4 + ISSM_EXTERNALPACKAGES="install" +-EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" ++EXTERNALPACKAGESDIR="/Users/schlegel/issmuci/trunk-jpl/externalpackages" + + #List of external pakages to be installed + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" +@@ -93,7 +93,7 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="" ++NROPTIONS="'exclude',[137 527]" + + + #------------------------# Index: /issm/oecreview/Archive/11600-11617/ISSM-11605-11606.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11605-11606.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11605-11606.diff (revision 11991) @@ -0,0 +1,8 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco_njs_notes.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco_njs_notes.txt (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco_njs_notes.txt (revision 11606) +@@ -0,0 +1,3 @@ ++chaco build must be able to see malloc.h ++sudo ln -s /usr/include/malloc/malloc.h /usr/include/malloc.h ++or else make sure you include the malloc directory in path Index: /issm/oecreview/Archive/11600-11617/ISSM-11606-11607.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11606-11607.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11606-11607.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m (revision 11606) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/solutions/steadystate_core.m (revision 11607) +@@ -51,10 +51,10 @@ + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,PressureEnum); + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,TemperatureEnum); + if (isenthalpy), ++ femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,EnthalpyEnum); + femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,WaterfractionEnum); +- femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,EnthalpyEnum); + else +- femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,WaterfractionEnum); ++ femmodel.elements=InputToResult(femmodel.elements,femmodel.nodes,femmodel.vertices,femmodel.loads,femmodel.materials,femmodel.parameters,BasalforcingsMeltingRateEnum); + end + + end %end of function Index: /issm/oecreview/Archive/11600-11617/ISSM-11607-11608.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11607-11608.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11607-11608.diff (revision 11991) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/collapse.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/collapse.m (revision 11607) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/collapse.m (revision 11608) +@@ -91,6 +91,7 @@ + md.geometry.thickness=project2d(md,md.geometry.thickness,1); + md.geometry.bed=project2d(md,md.geometry.bed,1); + md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); ++md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); + md.mask.elementonfloatingice=project2d(md,md.mask.elementonfloatingice,1); + md.mask.vertexonfloatingice=project2d(md,md.mask.vertexonfloatingice,1); + md.mask.elementongroundedice=project2d(md,md.mask.elementongroundedice,1); +@@ -109,6 +110,8 @@ + %Keep a trace of lower and upper nodes + md.mesh.lowervertex=NaN; + md.mesh.uppervertex=NaN; ++md.mesh.lowerelements=NaN; ++md.mesh.upperelements=NaN; + + %Remove old mesh + md.mesh.x2d=NaN; Index: /issm/oecreview/Archive/11600-11617/ISSM-11608-11609.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11608-11609.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11608-11609.diff (revision 11991) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 11608) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test463.m (revision 11609) +@@ -11,7 +11,7 @@ + + %Fields and tolerances to track changes + field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +-field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; ++field_tolerances={1e-09,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m (revision 11608) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/test/NightlyRun/test464.m (revision 11609) +@@ -11,7 +11,7 @@ + + %Fields and tolerances to track changes + field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','Water fraction','Enthalpy'}; +-field_tolerances={1e-10,1e-10,1e-09,1e-10,1e-13,1e-10,1e-10,1e-10}; ++field_tolerances={1e-09,1e-09,1e-09,1e-09,1e-13,1e-10,1e-10,1e-10}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... Index: /issm/oecreview/Archive/11600-11617/ISSM-11609-11610.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11609-11610.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11609-11610.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11609) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11610) +@@ -121,6 +121,12 @@ + cluster.codepath='$ISSM_TIER/bin'; + cluster.executionpath='$EXECUTION_PATH'; + END ++ cat << END > $ISSM_TIER/externalpackages/matlab/install.sh ++#!/bin/bash ++rm -rf install ++ln -s $MATLAB_PATH install ++END ++ + fi + #}}} + #Source environment variables with new matlab path {{{1 Index: /issm/oecreview/Archive/11600-11617/ISSM-11610-11611.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11610-11611.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11610-11611.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11610) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11611) +@@ -101,6 +101,6 @@ + #------------------------# + + #MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++MATLAB_PATH="/Applications/MATLAB_R2011b.app/" + +-MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" ++MATLABBIN="/Applications/MATLAB_R2011b.app/bin/matlab" Index: /issm/oecreview/Archive/11600-11617/ISSM-11611-11612.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11611-11612.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11611-11612.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11611) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11612) +@@ -2,7 +2,7 @@ + SHELL=/bin/bash + + #mail output to Helene +-MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov ++MAILTO=schlegel@jpl.nasa.gov + + #cronjob: issm 9:00pm +-50 9 * * * cd /Users/seroussi/Desktop/backup/svn/issm/trunk/cron/ && ./nightlyrun.sh configs/macosx32_seroussi ++02 12 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/oecreview/Archive/11600-11617/ISSM-11612-11613.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11612-11613.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11612-11613.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11612) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11613) +@@ -2,7 +2,7 @@ + SHELL=/bin/bash + + #mail output to Helene +-MAILTO=schlegel@jpl.nasa.gov ++MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov + + #cronjob: issm 9:00pm +-02 12 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel ++00 18 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/oecreview/Archive/11600-11617/ISSM-11613-11614.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11613-11614.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11613-11614.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11613) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11614) +@@ -54,7 +54,7 @@ + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + + #Corresponding list of installation files to use +-EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" + EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" + + #---------------------# +@@ -86,7 +86,7 @@ + NUMCPUS_INSTALL=1 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=7 ++NUMCPUS_RUN=4 + + #Nightly run options. The matlab routine nightlyrun.m will be called + #as follows: nightlyrun($NROPTIONS). The options must be understandable Index: /issm/oecreview/Archive/11600-11617/ISSM-11615-11616.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11615-11616.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11615-11616.diff (revision 11991) @@ -0,0 +1,16 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11615) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11616) +@@ -1,8 +1,9 @@ + #use /bin/bash to run commands, overriding the default set by cron + SHELL=/bin/bash ++PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/bin + + #mail output to Helene +-MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov ++MAILTO=schlegel@jpl.nasa.gov + + #cronjob: issm 9:00pm +-00 18 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel ++30 15 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/oecreview/Archive/11600-11617/ISSM-11616-11617.diff =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-11616-11617.diff (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-11616-11617.diff (revision 11991) @@ -0,0 +1,16 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11616) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11617) +@@ -2,8 +2,8 @@ + SHELL=/bin/bash + PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/bin + +-#mail output to Helene +-MAILTO=schlegel@jpl.nasa.gov ++#mail output to issm ++MAILTO=MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov + + #cronjob: issm 9:00pm +-30 15 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel ++00 21 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/oecreview/Archive/11600-11617/ISSM-DocReview-11600-11617.tex =================================================================== --- /issm/oecreview/Archive/11600-11617/ISSM-DocReview-11600-11617.tex (revision 11991) +++ /issm/oecreview/Archive/11600-11617/ISSM-DocReview-11600-11617.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11600-11617/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11600-11617/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11600-11617/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11600-11617 Index: /issm/oecreview/Archive/11600-11617/Makefile =================================================================== --- /issm/oecreview/Archive/11600-11617/Makefile (revision 11991) +++ /issm/oecreview/Archive/11600-11617/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11600-11617 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11600-11617/log.tex =================================================================== --- /issm/oecreview/Archive/11600-11617/log.tex (revision 11991) +++ /issm/oecreview/Archive/11600-11617/log.tex (revision 11991) @@ -0,0 +1,32 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11600-11601.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: Change in DakotaLib only for macs +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel change name of config file \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11601-11602.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: change name of config file +D /issm/trunk-jpl/configs/config-macosx64-imac.sh A /issm/trunk-jpl/configs/config-macosx64-nicole.sh (from /issm/trunk-jpl/configs/config-macosx64-imac.sh:11597) change config name \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11602-11603.diff: \\ Function name: \\D /issm/trunk-jpl/configs/config-macosx64-imac.sh A /issm/trunk-jpl/configs/config-macosx64-nicole.sh (from /issm/trunk-jpl/configs/config-macosx64-imac.sh:11597) \\ Export determination: 6. \\Rationale: change config name +M /issm/trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp M /issm/trunk-jpl/src/c/solutions/steadystate\_core.cpp M /issm/trunk-jpl/src/m/solutions/steadystate\_core.m fixed problem caused by steady state enthalpy \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11603-11604.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp M /issm/trunk-jpl/src/c/solutions/steadystate\_core.cpp M /issm/trunk-jpl/src/m/solutions/steadystate\_core.m \\ Export determination: 6. \\Rationale: fixed problem caused by steady state enthalpy +M /issm/trunk-jpl/test/Archives/Archive461.mat M /issm/trunk-jpl/test/Archives/Archive462.mat M /issm/trunk-jpl/test/Archives/Archive463.mat M /issm/trunk-jpl/test/Archives/Archive464.mat M /issm/trunk-jpl/test/NightlyRun/test461.m M /issm/trunk-jpl/test/NightlyRun/test462.m M /issm/trunk-jpl/test/NightlyRun/test463.m M /issm/trunk-jpl/test/NightlyRun/test464.m updated archives enthalpy (mission enthalpy and waterfraction vectors in solution) \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11604-11605.diff: \\ Function name: \\M /issm/trunk-jpl/test/Archives/Archive461.mat M /issm/trunk-jpl/test/Archives/Archive462.mat M /issm/trunk-jpl/test/Archives/Archive463.mat M /issm/trunk-jpl/test/Archives/Archive464.mat M /issm/trunk-jpl/test/NightlyRun/test461.m M /issm/trunk-jpl/test/NightlyRun/test462.m M /issm/trunk-jpl/test/NightlyRun/test463.m M /issm/trunk-jpl/test/NightlyRun/test464.m \\ Export determination: 6. \\Rationale: updated archives enthalpy (mission enthalpy and waterfraction vectors in solution) +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel new config file for macs \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11605-11606.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: new config file for macs +A /issm/trunk-jpl/externalpackages/chaco/chaco\_njs\_notes.txt note to add link for malloc on macs \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11606-11607.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/chaco/chaco\_njs\_notes.txt \\ Export determination: 6. \\Rationale: note to add link for malloc on macs +M /issm/trunk-jpl/src/m/solutions/steadystate\_core.m minor, confused BasalforcingsMeltingRateEnum and WaterfractionEnum \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11607-11608.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/solutions/steadystate\_core.m \\ Export determination: 6. \\Rationale: minor, confused BasalforcingsMeltingRateEnum and WaterfractionEnum +M /issm/trunk-jpl/src/m/model/collapse.m Added collapse of some fields \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11608-11609.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/collapse.m \\ Export determination: 6. \\Rationale: Added collapse of some fields +M /issm/trunk-jpl/test/NightlyRun/test463.m M /issm/trunk-jpl/test/NightlyRun/test464.m tolerances new tests \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11609-11610.diff: \\ Function name: \\M /issm/trunk-jpl/test/NightlyRun/test463.m M /issm/trunk-jpl/test/NightlyRun/test464.m \\ Export determination: 6. \\Rationale: tolerances new tests +M /issm/trunk-jpl/cron/nightlyrun.sh update install.sh script in matlab directory \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11610-11611.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: update install.sh script in matlab directory +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel fix matlab path \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11611-11612.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: fix matlab path +M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile correct install files \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11612-11613.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: correct install files +M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile add all names for e-mail \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11613-11614.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: add all names for e-mail +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel all install files called \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11614-11615.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: all install files called \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11615-11616.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: add path \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11616-11617.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: add path +M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile add emails \\\\ Index: /issm/oecreview/Archive/11600-11617/r1.tex =================================================================== --- /issm/oecreview/Archive/11600-11617/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11600-11617/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11600 Index: /issm/oecreview/Archive/11600-11617/r2.tex =================================================================== --- /issm/oecreview/Archive/11600-11617/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11600-11617/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11617 Index: /issm/oecreview/Archive/11618-11630/Date.tex =================================================================== --- /issm/oecreview/Archive/11618-11630/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11618-11630/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11618-11630/ISSM-11619-11620.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11619-11620.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11619-11620.diff (revision 11991) @@ -0,0 +1,54 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11619) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11620) +@@ -18,6 +18,8 @@ + #COMPILATION CONFIGURATION FILE + COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" + ++#MATLAB path ++MATLAB_PATH="/Applications/MATLAB_R2011b.app/" + + #----------------------# + # 2: ISSM Installation # +@@ -51,11 +53,10 @@ + EXTERNALPACKAGESDIR="/Users/schlegel/issmuci/trunk-jpl/externalpackages" + + #List of external pakages to be installed +-EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle" + + #Corresponding list of installation files to use +-EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" +-EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh" + + #---------------------# + # 4: ISSM Compilation # +@@ -81,10 +82,6 @@ + # 6: Nightly run options # + #------------------------# + +-#number of cpus used in ISSM installation and compilation (one is usually +-#safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=1 +- + #number of cpus used in the nightly runs. + NUMCPUS_RUN=4 + +@@ -93,14 +90,5 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'exclude',[137 527]" ++NROPTIONS="'exclude',[137 235:236 267:268 423:428 434:435 439:440 527]" + +- +-#------------------------# +-# 7: Matlab# +-#------------------------# +- +-#MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2011b.app/" +- +-MATLABBIN="/Applications/MATLAB_R2011b.app/bin/matlab" Index: /issm/oecreview/Archive/11618-11630/ISSM-11620-11621.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11620-11621.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11620-11621.diff (revision 11991) @@ -0,0 +1,136 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11620) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11621) +@@ -18,6 +18,9 @@ + #COMPILATION CONFIGURATION FILE + COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ + #----------------------# + # 2: ISSM Installation # + #----------------------# +@@ -55,7 +58,6 @@ + + #Corresponding list of installation files to use + EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" +-EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" + + #---------------------# + # 4: ISSM Compilation # +@@ -81,10 +83,6 @@ + # 6: Nightly run options # + #------------------------# + +-#number of cpus used in ISSM installation and compilation (one is usually +-#safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=1 +- + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + +@@ -95,11 +93,3 @@ + + NROPTIONS="'benchmark','all'" + +-#------------------------# +-# 7: Matlab# +-#------------------------# +- +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" +- +-MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily (revision 11620) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily (revision 11621) +@@ -19,6 +19,9 @@ + #COMPILATION CONFIGURATION FILE + COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ + #----------------------# + # 2: ISSM Installation # + #----------------------# +@@ -56,7 +59,6 @@ + + #Corresponding list of installation files to use + EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" +-EXTERNALPACKAGES_NUMCPUS=" 8 8 8 8 8 8" + + #---------------------# + # 4: ISSM Compilation # +@@ -82,10 +84,6 @@ + # 6: Nightly run options # + #------------------------# + +-#number of cpus used in ISSM installation and compilation (one is usually +-#safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=8 +- + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + +@@ -96,11 +94,3 @@ + + NROPTIONS="" + +-#------------------------# +-# 7: Matlab# +-#------------------------# +- +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" +- +-MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly (revision 11620) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly (revision 11621) +@@ -19,6 +19,9 @@ + #COMPILATION CONFIGURATION FILE + COMPILE_CONFIG_FILE="config-linux64-astrid.sh" + ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ + #----------------------# + # 2: ISSM Installation # + #----------------------# +@@ -56,7 +59,6 @@ + + #Corresponding list of installation files to use + EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" +-EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" + + #---------------------# + # 4: ISSM Compilation # +@@ -82,10 +84,6 @@ + # 6: Nightly run options # + #------------------------# + +-#number of cpus used in ISSM installation and compilation (one is usually +-#safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=1 +- + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + +@@ -96,12 +94,3 @@ + + NROPTIONS="" + +- +-#------------------------# +-# 7: Matlab# +-#------------------------# +- +-#MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" +- +-MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" Index: /issm/oecreview/Archive/11618-11630/ISSM-11621-11622.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11621-11622.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11621-11622.diff (revision 11991) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11621) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11622) +@@ -131,7 +131,7 @@ + #}}} + #Source environment variables with new matlab path {{{1 + cd $ISSM_TIER/etc +-source environment.sh MATLAB_DIR=$MATLAB_PATH ++source environment.sh + #}}} + #install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 + if [ "$ISSM_EXTERNALPACKAGES" == "install" ] +@@ -264,6 +264,7 @@ + #Start run from nightlylog directory + cd $ISSM_TIER/nightlylog/ + ++ MATLABBIN=$MATLAB_PATH/bin/matlab + #Start test + $MATLABBIN -nojvm -nosplash -r matlab_run$i -logfile matlab_log$i.log & + Index: /issm/oecreview/Archive/11618-11630/ISSM-11622-11623.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11622-11623.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11622-11623.diff (revision 11991) @@ -0,0 +1,48 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11622) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11623) +@@ -57,7 +57,7 @@ + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" + + #Corresponding list of installation files to use +-EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh install.sh" + + #---------------------# + # 4: ISSM Compilation # +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_ucitrunk +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_ucitrunk (revision 11622) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_ucitrunk (revision 11623) +@@ -16,6 +16,9 @@ + #Machine configuration + MACHINE="astrid" + ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" ++ + #MATLAB path + MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" + +@@ -54,6 +57,9 @@ + #List of external pakages to be installed + EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++ + #---------------------# + # 4: ISSM Compilation # + #---------------------# +@@ -78,10 +84,6 @@ + # 6: Nightly run options # + #------------------------# + +-#number of cpus used in ISSM installation and compilation (one is usually +-#safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=1 +- + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + Index: /issm/oecreview/Archive/11618-11630/ISSM-11623-11624.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11623-11624.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11623-11624.diff (revision 11991) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11623) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11624) +@@ -6,4 +6,4 @@ + MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov + + #cronjob: issm 9:00pm +-00 21 * * * cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel ++30 10 * * 1 cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/oecreview/Archive/11618-11630/ISSM-11624-11625.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11624-11625.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11624-11625.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11624) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11625) +@@ -257,7 +257,7 @@ + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + ;; + *darwin*) +- DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver -L/usr/lib -lblas -llapack" ++ DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver " + ;; + esac + dnl DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lgslcblas -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" Index: /issm/oecreview/Archive/11618-11630/ISSM-11625-11626.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11625-11626.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11625-11626.diff (revision 11991) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh (revision 11625) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/install-macosx64.sh (revision 11626) +@@ -32,8 +32,8 @@ + --without-graphics \ + --with-pic \ + --disable-mpi \ +- --with-blas=/usr/lib/libblas.dylib \ +- --with-lapack=/usr/lib/liblapack.dylib ++ --with-blas="-L$ISSM_TIER/externalpackages/petsc/install/lib -lfblas " \ ++ --with-lapack="-L$ISSM_TIER/externalpackages/petsc/install/lib -lflapack -lPLAPACK " + cd .. + + #Before compiling, if running on 64 bits, we need to active fPIC compilation. Some packages Index: /issm/oecreview/Archive/11618-11630/ISSM-11626-11627.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11626-11627.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11626-11627.diff (revision 11991) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/linux_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/linux_cronfile (revision 11626) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/linux_cronfile (revision 11627) +@@ -7,7 +7,7 @@ + #cronjob + 00 09 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily + 30 12 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily +-00 15 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily ++50 15 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily + 00 18 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily + 00 23 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_nightly + 00 20 * * 6 cd /u/astrid-r1b/schlegel/ExecutionNightlyRun && rm -r test* +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11626) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11627) +@@ -131,7 +131,7 @@ + #}}} + #Source environment variables with new matlab path {{{1 + cd $ISSM_TIER/etc +-source environment.sh ++source environment.sh MATLAB_DIR=$MATLAB_PATH + #}}} + #install/copy/none external packages (ISSM_EXTERNALPACKAGES){{{1 + if [ "$ISSM_EXTERNALPACKAGES" == "install" ] Index: /issm/oecreview/Archive/11618-11630/ISSM-11627-11628.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11627-11628.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11627-11628.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/linux_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/linux_cronfile (revision 11627) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/linux_cronfile (revision 11628) +@@ -7,7 +7,7 @@ + #cronjob + 00 09 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily + 30 12 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily +-50 15 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily ++00 15 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily + 00 18 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_daily + 00 23 * * 1-5 cd /u/astrid-r1b/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/linux64_schlegel_nightly + 00 20 * * 6 cd /u/astrid-r1b/schlegel/ExecutionNightlyRun && rm -r test* Index: /issm/oecreview/Archive/11618-11630/ISSM-11628-11629.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11628-11629.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11628-11629.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/SectionValues.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/SectionValues.m (revision 11628) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/SectionValues.m (revision 11629) +@@ -81,7 +81,8 @@ + if (md.mesh.dimension==2) + + %Interpolation of data on specified points +- data_interp=InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,data,X,Y); ++ data_interp=InterpFromMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,data,X,Y); ++ %data_interp=InterpFromMeshToMesh2d(md.mesh.elements,md.mesh.x,md.mesh.y,data,X,Y); + %data_interp=griddata(md.mesh.x,md.mesh.y,data,X,Y); + + %Compute index Index: /issm/oecreview/Archive/11618-11630/ISSM-11629-11630.diff =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-11629-11630.diff (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-11629-11630.diff (revision 11991) @@ -0,0 +1,19 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_write.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_write.m (revision 11629) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_write.m (revision 11630) +@@ -62,12 +62,12 @@ + if ~exist('filei' ,'var') || isempty(filei) + filei=input('Dakota input file to write? ','s'); + end +-[pathstr,name,ext,versn] = fileparts(filei); ++[pathstr,name,ext] = fileparts(filei); + if isempty(ext) + % fileparts only considers '.in' to be the extension, not '.qmu.in' + ext='.qmu.in'; + end +-filei2=fullfile(pathstr,[name ext versn]); ++filei2=fullfile(pathstr,[name ext]); + + display(sprintf('Opening Dakota input file ''%s''.',filei2)); + fidi=fopen(sprintf('%s',filei2),'w'); Index: /issm/oecreview/Archive/11618-11630/ISSM-DocReview-11618-11630.tex =================================================================== --- /issm/oecreview/Archive/11618-11630/ISSM-DocReview-11618-11630.tex (revision 11991) +++ /issm/oecreview/Archive/11618-11630/ISSM-DocReview-11618-11630.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11618-11630/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11618-11630/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11618-11630/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11618-11630 Index: /issm/oecreview/Archive/11618-11630/Makefile =================================================================== --- /issm/oecreview/Archive/11618-11630/Makefile (revision 11991) +++ /issm/oecreview/Archive/11618-11630/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11618-11630 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11618-11630/log.tex =================================================================== --- /issm/oecreview/Archive/11618-11630/log.tex (revision 11991) +++ /issm/oecreview/Archive/11618-11630/log.tex (revision 11991) @@ -0,0 +1,22 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11618-11619.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: try again \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11619-11620.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: remove dakota runs \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11620-11621.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: remove dakota runs +M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_daily M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_nightly M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation move MATLABBIN to nightlyrun.sh \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11621-11622.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_daily M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_nightly M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation \\ Export determination: 6. \\Rationale: move MATLABBIN to nightlyrun.sh +M /issm/trunk-jpl/cron/nightlyrun.sh move MATLAB bin from cron file \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11622-11623.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: move MATLAB bin from cron file +M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_ucitrunk M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation update config files, trunk \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11623-11624.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_ucitrunk M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation \\ Export determination: 6. \\Rationale: update config files, trunk +M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile run monday morning \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11624-11625.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: run monday morning +M /issm/trunk-jpl/m4/issm\_options.m4 remove local library links \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11625-11626.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: remove local library links +M /issm/trunk-jpl/externalpackages/dakota/install-macosx64.sh link with petsc libraries \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11626-11627.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/dakota/install-macosx64.sh \\ Export determination: 6. \\Rationale: link with petsc libraries +M /issm/trunk-jpl/cron/cronfiles/linux\_cronfile M /issm/trunk-jpl/cron/nightlyrun.sh add setting matlab dir back into script \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11627-11628.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/linux\_cronfile M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: add setting matlab dir back into script +M /issm/trunk-jpl/cron/cronfiles/linux\_cronfile run at 3pm \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11628-11629.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/linux\_cronfile \\ Export determination: 6. \\Rationale: run at 3pm +M /issm/trunk-jpl/src/m/model/SectionValues.m Section values blows up on singular meshes, taking a more robust interpolator \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11629-11630.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/SectionValues.m \\ Export determination: 6. \\Rationale: Section values blows up on singular meshes, taking a more robust interpolator +M /issm/trunk-jpl/src/m/qmu/dakota\_in\_write.m matlab no longer allows fullfile version argument \\\\ Index: /issm/oecreview/Archive/11618-11630/r1.tex =================================================================== --- /issm/oecreview/Archive/11618-11630/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11618-11630/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11618 Index: /issm/oecreview/Archive/11618-11630/r2.tex =================================================================== --- /issm/oecreview/Archive/11618-11630/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11618-11630/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11630 Index: /issm/oecreview/Archive/11630-11648/Date.tex =================================================================== --- /issm/oecreview/Archive/11630-11648/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11630-11648/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11630-11648/ISSM-11630-11631.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11630-11631.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11630-11631.diff (revision 11991) @@ -0,0 +1,24 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11630) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11631) +@@ -53,10 +53,10 @@ + EXTERNALPACKAGESDIR="/Users/schlegel/issmuci/trunk-jpl/externalpackages" + + #List of external pakages to be installed +-EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle" ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" + + #Corresponding list of installation files to use +-EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh" ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" + + #---------------------# + # 4: ISSM Compilation # +@@ -90,5 +90,5 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'exclude',[137 235:236 267:268 423:428 434:435 439:440 527]" ++NROPTIONS="'exclude',[137 527]" + Index: /issm/oecreview/Archive/11630-11648/ISSM-11631-11632.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11631-11632.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11631-11632.diff (revision 11991) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11631) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/cronfiles/mac_cronfile (revision 11632) +@@ -6,4 +6,4 @@ + MAILTO=eric.larour@jpl.nasa.gov,mathieu.morlighem@jpl.nasa.gov,helene.seroussi@jpl.nasa.gov,Christopher.P.Borstad@jpl.nasa.gov,Nicole-Jeanne.Schlegel@jpl.nasa.gov,Feras.A.Habbal@jpl.nasa.gov + + #cronjob: issm 9:00pm +-30 10 * * 1 cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel ++30 00 * * 1 cd /Users/schlegel/issmuci/trunk-jpl/cron/ && ./nightlyrun.sh configs/macosx64_schlegel Index: /issm/oecreview/Archive/11630-11648/ISSM-11632-11633.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11632-11633.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11632-11633.diff (revision 11991) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11632) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11633) +@@ -182,6 +182,16 @@ + make distclean + ./scripts/automakererun.sh + source ./configs/$COMPILE_CONFIG_FILE ++ ++ #4: compile and install ISSM ++ if [ $NUMCPUS_INSTALL -gt 1 ] ++ then ++ echo "Making with " $NUMCPUS_INSTALL "cpus" ++ make -j $NUMCPUS_INSTALL install ++ else ++ make install ++ fi ++ + make install + + elif [ "$ISSM_COMPILATION" == "no" ] Index: /issm/oecreview/Archive/11630-11648/ISSM-11633-11634.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11633-11634.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11633-11634.diff (revision 11991) @@ -0,0 +1,75 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11633) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_validation (revision 11634) +@@ -83,6 +83,10 @@ + # 6: Nightly run options # + #------------------------# + ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily (revision 11633) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_daily (revision 11634) +@@ -84,6 +84,10 @@ + # 6: Nightly run options # + #------------------------# + ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=8 ++ + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_ucitrunk +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_ucitrunk (revision 11633) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_ucitrunk (revision 11634) +@@ -84,6 +84,10 @@ + # 6: Nightly run options # + #------------------------# + ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11633) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11634) +@@ -82,6 +82,10 @@ + # 6: Nightly run options # + #------------------------# + ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ + #number of cpus used in the nightly runs. + NUMCPUS_RUN=4 + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly (revision 11633) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_schlegel_nightly (revision 11634) +@@ -84,6 +84,10 @@ + # 6: Nightly run options # + #------------------------# + ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ + #number of cpus used in the nightly runs. + NUMCPUS_RUN=7 + Index: /issm/oecreview/Archive/11630-11648/ISSM-11634-11635.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11634-11635.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11634-11635.diff (revision 11991) @@ -0,0 +1,184 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour (revision 11634) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour (revision 11635) +@@ -47,7 +47,7 @@ + # - "copy" copy existing directories (EXTERNALPACKAGESDIR) + # - "none" leave external packages as is + # ->skip to section 4 +-ISSM_EXTERNALPACKAGES="install" ++ISSM_EXTERNALPACKAGES="copy" + EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" + + #List of external pakages to be installed +@@ -72,10 +72,10 @@ + + #Mail delivery. If SKIPMAIL="no", the html nightly run report will be + #sent to the adresses present in $ISSM_TIER/cron/mailinglist. +-SKIPMAIL="no" ++SKIPMAIL="yes" + + #Sender email address +-EMAIL_ADRESS="schlegel@jpl.nasa.gov" ++EMAIL_ADRESS="eric.larour@jpl.nasa.gov" + + #------------------------# + # 6: Nightly run options # +@@ -83,10 +83,10 @@ + + #number of cpus used in ISSM installation and compilation (one is usually + #safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=1 ++NUMCPUS_INSTALL=4 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=7 ++NUMCPUS_RUN=1 + + #Nightly run options. The matlab routine nightlyrun.m will be called + #as follows: nightlyrun($NROPTIONS). The options must be understandable +@@ -101,6 +101,6 @@ + #------------------------# + + #MATLAB path +-MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++MATLAB_PATH="/Applications/MATLAB_R2010a.app/" + +-MATLABBIN="/usr/local/pkgs/matlab-7.6/bin/matlab" ++MATLABBIN="/Applications/MATLAB_R2010a.app/bin/matlab" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11635) +@@ -0,0 +1,106 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/Users/larour/issm-uci" ++ISSM_TIER="/Users/larour/issm-uci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="macosx-gnu" ++ ++#Machine configuration ++MACHINE="macosx-gil" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-macosx64-mathieu.sh" ++ ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/Users/larour/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="link" ++EXTERNALPACKAGESDIR="/Users/larour/issm-uci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++EXTERNALPACKAGES_NUMCPUS=" 1 1 1 1 1 1" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="yes" ++ ++#Sender email address ++EMAIL_ADRESS="eric.larour@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=4 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=1 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="id,401:499" ++ ++ ++#------------------------# ++# 7: Matlab# ++#------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/Applications/MATLAB_R2010a.app/" ++ ++MATLABBIN="/Applications/MATLAB_R2010a.app/bin/matlab" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11634) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11635) +@@ -159,6 +159,14 @@ + rm -rf externalpackages + cp -Rf $EXTERNALPACKAGESDIR ./ + ++elif [ "$ISSM_EXTERNALPACKAGES" == "link" ] ++then ++ ++ #erase externapackages, and link with externalpackages_dir ++ cd $ISSM_TIER ++ rm -rf externalpackages ++ ln -s -Rf $EXTERNALPACKAGESDIR ++ + elif [ "$ISSM_EXTERNALPACKAGES" == "none" ] + then + Index: /issm/oecreview/Archive/11630-11648/ISSM-11635-11636.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11635-11636.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11635-11636.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11635) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11636) +@@ -165,7 +165,7 @@ + #erase externapackages, and link with externalpackages_dir + cd $ISSM_TIER + rm -rf externalpackages +- ln -s -Rf $EXTERNALPACKAGESDIR ++ ln -s $EXTERNALPACKAGESDIR . + + elif [ "$ISSM_EXTERNALPACKAGES" == "none" ] + then Index: /issm/oecreview/Archive/11630-11648/ISSM-11636-11637.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11636-11637.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11636-11637.diff (revision 11991) @@ -0,0 +1,11 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11636) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11637) +@@ -104,3 +104,6 @@ + MATLAB_PATH="/Applications/MATLAB_R2010a.app/" + + MATLABBIN="/Applications/MATLAB_R2010a.app/bin/matlab" ++ ++#Specialty one: ++export FC=gfortran Index: /issm/oecreview/Archive/11630-11648/ISSM-11637-11638.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11637-11638.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11637-11638.diff (revision 11991) @@ -0,0 +1,33 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11637) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11638) +@@ -30,7 +30,7 @@ + # ->skip to section 3 + # - "none" leave ISSM as is in its directory + # ->skip to section 3 +-ISSM_INSTALLATION="checkout" ++ISSM_INSTALLATION="none" + + #SVN repository + REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +@@ -64,7 +64,7 @@ + #ISSM_COMPILATION can have 2 values: + # - "yes" compile ISSM + # - "no" do not compile ISSM +-ISSM_COMPILATION="yes" ++ISSM_COMPILATION="no" + + #----------------------# + # 5: Mail notification # +@@ -93,9 +93,8 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="id,401:499" ++NROPTIONS="'id',401:499" + +- + #------------------------# + # 7: Matlab# + #------------------------# Index: /issm/oecreview/Archive/11630-11648/ISSM-11638-11639.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11638-11639.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11638-11639.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11638) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11639) +@@ -30,7 +30,7 @@ + # ->skip to section 3 + # - "none" leave ISSM as is in its directory + # ->skip to section 3 +-ISSM_INSTALLATION="none" ++ISSM_INSTALLATION="checkout" + + #SVN repository + REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" +@@ -64,7 +64,7 @@ + #ISSM_COMPILATION can have 2 values: + # - "yes" compile ISSM + # - "no" do not compile ISSM +-ISSM_COMPILATION="no" ++ISSM_COMPILATION="yes" + + #----------------------# + # 5: Mail notification # Index: /issm/oecreview/Archive/11630-11648/ISSM-11639-11640.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11639-11640.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11639-11640.diff (revision 11991) @@ -0,0 +1,38 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11640) +@@ -0,0 +1,27 @@ ++#!/bin/sh ++ ++#petsc 3.2 ++#mpich 1.4 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-numthreads=8 ++ #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11630-11648/ISSM-11640-11641.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11640-11641.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11640-11641.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11640) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11641) +@@ -20,8 +20,8 @@ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ ++ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ + --with-numthreads=8 +- #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ Index: /issm/oecreview/Archive/11630-11648/ISSM-11641-11642.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11641-11642.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11641-11642.diff (revision 11991) @@ -0,0 +1,33 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_write.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_write.m (revision 11641) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_write.m (revision 11642) +@@ -233,11 +233,11 @@ + param_write(fidi,'\t ','analysis_driver',' = ''','''\n',params); + param_write(fidi,'\t ','evaluation_static_scheduling','','\n',params); + if ~isempty(params.analysis_components) +- [pathstr,name,ext,versn] = fileparts(params.analysis_components); ++ [pathstr,name,ext] = fileparts(params.analysis_components); + if isempty(ext) + ext='.m'; + end +- params.analysis_components=fullfile(pathstr,[name ext versn]); ++ params.analysis_components=fullfile(pathstr,[name ext]); + param_write(fidi,'\t ','analysis_components',' = ''','''\n',params); + end + if ~isempty(params.input_filter) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_data.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_data.m (revision 11641) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/qmu/dakota_in_data.m (revision 11642) +@@ -79,8 +79,8 @@ + + if strcmpi(params.analysis_driver,'matlab') && ... + isempty(params.analysis_components) +- [pathstr,name,ext,versn] = fileparts(filei); +- params.analysis_components=fullfile(pathstr,[name '.m' versn]); ++ [pathstr,name,ext] = fileparts(filei); ++ params.analysis_components=fullfile(pathstr,[name '.m']); + end + + % merge method parameters, though they shouldn't be in dparams Index: /issm/oecreview/Archive/11630-11648/ISSM-11642-11643.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11642-11643.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11642-11643.diff (revision 11991) @@ -0,0 +1,170 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumToModelField.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumToModelField.cpp (revision 11642) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumToModelField.cpp (revision 11643) +@@ -1,28 +0,0 @@ +-/*\file EnumToModelField.cpp: +-* \brief: output string associated with enum, that corresponds to a model field +-* for example: ThicknessEnum corresponds to model field thickness +-* FrictionCoefficientEnum corresponds to model field drag +-*/ +- +-#include "../shared/shared.h" +-#include "../include/include.h" +-#include "./EnumDefinitions.h" +- +-const char* EnumToModelField(int en){ +- +- switch(en){ +- +- case ThicknessEnum : return "thickness"; +- case FrictionCoefficientEnum : return "drag_coefficient"; +- case MaterialsRheologyBEnum : return "rheology_B"; +- case MaterialsRheologyBbarEnum : return "rheology_B"; +- case BalancethicknessThickeningRateEnum: return "dhdt"; +- case VxEnum : return "vx"; +- case InversionVxObsEnum : return "vx_obs"; +- case VyEnum : return "vy"; +- case InversionVyObsEnum : return "vy_obs"; +- case BasalforcingsMeltingRateEnum : return "basal_melting_rate"; +- case SurfaceforcingsMassBalanceEnum : return "surface_mass_balance"; +- default : _error_("No model field is associated to enum %s",EnumToStringx(en)); +- } +-} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 11642) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh (revision 11643) +@@ -12,31 +12,6 @@ + #Get number of enums + NUMENUMS=$(wc -l temp | awk '{printf("%s",$1);}'); + +-#Take care of EnumToModelField.m first (easy) +-#Build EnumToModelField.m {{{1 +-cat < $ISSM_TIER/src/m/enum/EnumToModelField.m +-function string=EnumToModelField(enum) +-%ENUMTOMODELFIELD - output string of model field associated to enum +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% string=EnumToModelField(enum) +- +-switch enum, +- +-END +- +-cat EnumToModelField.cpp | grep "case" | sed -e "s/Enum :/Enum(),/g" -e "s/\"/'/g" -e "s/return /string=/g" -e "s/;/; return/g" >> $ISSM_TIER/src/m/enum/EnumToModelField.m +- +-cat <> $ISSM_TIER/src/m/enum/EnumToModelField.m +- otherwise, error(['Enum ' num2str(enum) ' not found associated to any model field']); +- +-end +-END +-#}}} + #Build EnumToStringx.cpp {{{1 + #Header + cat < $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 11642) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 11643) +@@ -479,7 +479,4 @@ + MaximumNumberOfEnums + }; + +-/*Functions on enums: */ +-const char *EnumToModelField(int en); +- + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/README (revision 11642) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/README (revision 11643) +@@ -3,7 +3,7 @@ + - StringToEnumx.cpp + - EnumToStringx.cpp + - src/m/enum/* +-all these files are automatically synchronized with EnumDefinitions.h and EnumToModelField.cpp ++all these files are automatically synchronized with EnumDefinitions.h + + TO ADD AN ENUM: + add the corresponding lines to EnumDefinitions.h +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11642) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11643) +@@ -252,7 +252,6 @@ + ./io/Disk/pfclose.cpp\ + ./io/PrintfFunction.cpp\ + ./EnumDefinitions/EnumDefinitions.h\ +- ./EnumDefinitions/EnumToModelField.cpp\ + ./modules/ModelProcessorx/ModelProcessorx.h\ + ./modules/ModelProcessorx/ModelProcessorx.cpp\ + ./modules/ModelProcessorx/DistributeNumDofs.cpp\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/EnumToModelField.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/EnumToModelField.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/EnumToModelField.m (revision 11643) +@@ -0,0 +1,26 @@ ++function string=EnumToModelField(enum) ++%ENUMTOMODELFIELD - output string of model field associated to enum ++% ++% Usage: ++% string=EnumToModelField(enum) ++ ++disp('Warning: EnumToModelField is deprecated, it cannot work with new model definition. This function will be removed in the future'); ++ ++switch enum, ++ ++ case ThicknessEnum(), string='thickness'; return ++ case FrictionCoefficientEnum(), string='drag_coefficient'; return ++ case MaterialsRheologyBEnum(), string='rheology_B'; return ++ case MaterialsRheologyBbarEnum(), string='rheology_B'; return ++ case BalancethicknessThickeningRateEnum: string='dhdt'; return ++ case VxEnum(), string='vx'; return ++ case InversionVxObsEnum(), string='vx_obs'; return ++ case VyEnum(), string='vy'; return ++ case InversionVyObsEnum(), string='vy_obs'; return ++ case BasalforcingsMeltingRateEnum(), string='basal_melting_rate'; return ++ case SurfaceforcingsAccumulationRateEnum(), string='surface_accumulation_rate'; return ++ case SurfaceforcingsAblationRateEnum(), string='surface_ablation_rate'; return ++ case SurfaceforcingsMassBalanceEnum(), string='surface_mass_balance'; return ++ otherwise, error(['Enum ' num2str(enum) ' not found associated to any model field']); ++ ++end +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/EnumToModelField.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/EnumToModelField.m (revision 11642) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/EnumToModelField.m (revision 11643) +@@ -1,28 +0,0 @@ +-function string=EnumToModelField(enum) +-%ENUMTOMODELFIELD - output string of model field associated to enum +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% string=EnumToModelField(enum) +- +-switch enum, +- +- case ThicknessEnum(), string='thickness'; return +- case FrictionCoefficientEnum(), string='drag_coefficient'; return +- case MaterialsRheologyBEnum(), string='rheology_B'; return +- case MaterialsRheologyBbarEnum(), string='rheology_B'; return +- case BalancethicknessThickeningRateEnum: string='dhdt'; return +- case VxEnum(), string='vx'; return +- case InversionVxObsEnum(), string='vx_obs'; return +- case VyEnum(), string='vy'; return +- case InversionVyObsEnum(), string='vy_obs'; return +- case BasalforcingsMeltingRateEnum(), string='basal_melting_rate'; return +- case SurfaceforcingsAccumulationRateEnum(), string='surface_accumulation_rate'; return +- case SurfaceforcingsAblationRateEnum(), string='surface_ablation_rate'; return +- case SurfaceforcingsMassBalanceEnum(), string='surface_mass_balance'; return +- otherwise, error(['Enum ' num2str(enum) ' not found associated to any model field']); +- +-end Index: /issm/oecreview/Archive/11630-11648/ISSM-11643-11644.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11643-11644.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11643-11644.diff (revision 11991) @@ -0,0 +1,31 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11643) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/nightlyrun.sh (revision 11644) +@@ -336,15 +336,14 @@ + + if [ "$MACHINE" = "win7" ] + then +- echo $i +- email -html -s "Nightly runs of $ISSM_RELEASE , configuration: $MACHINE, host: $HOST_NAME, user: $USER. " $i < $ISSM_TIER/nightlylog/report.html ++ email -html -s "Nightly runs on $HOST_NAME (version: $ISSM_RELEASE)" $i < $ISSM_TIER/nightlylog/report.html + else + if [ "$MACHINE" = "astrid" ] + then + cat - $ISSM_TIER/nightlylog/report.html < + To: $i +-Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. ++Subject: Nightly runs on $HOST_NAME (version: $ISSM_RELEASE) + Mime-Version: 1.0 + Content-Type: text/html + HERE +@@ -352,7 +351,7 @@ + cat - $ISSM_TIER/nightlylog/report.html < + To: $i +-Subject: Nightly runs of $ISSM_RELEASE, configuration: $MACHINE, host: $HOST_NAME, user: $USER. ++Subject: Nightly runs on $HOST_NAME (version: $ISSM_RELEASE) + Mime-Version: 1.0 + Content-Type: text/html + HERE Index: /issm/oecreview/Archive/11630-11648/ISSM-11644-11645.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11644-11645.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11644-11645.diff (revision 11991) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Analysis/setcluster.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Analysis/setcluster.m (revision 11644) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Analysis/setcluster.m (revision 11645) +@@ -4,4 +4,5 @@ + % Usage: + % md=setcluster(md,cluster); + ++disp('Warning: setcluster is deprecated, use md.cluster=cluster instead'); + md.cluster=cluster; Index: /issm/oecreview/Archive/11630-11648/ISSM-11645-11646.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11645-11646.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11645-11646.diff (revision 11991) @@ -0,0 +1,10 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/dakota_njs_notes_macos64.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/dakota_njs_notes_macos64.txt (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/dakota/dakota_njs_notes_macos64.txt (revision 11646) +@@ -0,0 +1,5 @@ ++Matlab might try to use its local /Applications/MATLAB_R2011b.app/sys/os/maci64/ fortran libraries ++instead of the gfortran package libraries. Matlab library is missing some symbols, so you might ++need to link to the actual gfortran library ++sudo cp /Applications/MATLAB_R2011b.app/sys/os/maci64/libgfortran.3.dynlib /Applications/MATLAB_R2011b.app/sys/os/maci64/libgfortran.3.dynlib.matlab ++sudo ln -s /usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.3.dylib libgfortran.3.dylib Index: /issm/oecreview/Archive/11630-11648/ISSM-11646-11647.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11646-11647.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11646-11647.diff (revision 11991) @@ -0,0 +1,65 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/install.sh (revision 11647) +@@ -0,0 +1,10 @@ ++# Remove prior installations. ++rm -rf android-ndk-r7b ++rm -rf android-sdk-macosx ++rm -rf apache-ant-1.8.2-bin.zip ++ ++echo "Directories/Files Removed!" ++ ++# Install Android SDK and NDK. ++tar -zxvf android-ndk-r7b-darwin-x86.tar.bz2 ++unzip android-sdk_r16-macosx.zip + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk_r16-macosx.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-sdk_r16-macosx.zip +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk-r7b-darwin-x86.tar.bz2 +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/android-ndk-r7b-darwin-x86.tar.bz2 +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/README (revision 11646) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android/README (revision 11647) +@@ -3,17 +3,6 @@ + /* + * This is a temporary readme file for the installation of the Android emulator. + */ +-1) Download the Android SDK . +-2) Add to your PATH the following: +- ANDROID_HOME=~/android-sdk-macosx +- PATH=${PATH}:ANDROID_HOME/platforms/android-15/:~ANDROID_HOME/platform-tools/:ANDROID_HOME/tools/ +-3) Run Android and install the newest Android distribution(as of the last update: android-15) +-4) Navigate to the project directory and run Android update project ./ +-5) Run ant debug. +-6) Initiate an emulator by entering: +- 1) android list targets (this will produce a list of available of system image targets) +- 2) android create avd -n -t (Choose targetID to match android-15) +-7) Start up the emulator by entering: emulator -avd +-8) Install the app by entering: adb install .apk + +-The app should be installed and ready to run from the virtual device! ++1) Ensure a the Java SDK and JRE are properly installed. ++2) Run the install script to set up the Android SDK(Software Development Kit) and NDK(Native Development Kit). Index: /issm/oecreview/Archive/11630-11648/ISSM-11647-11648.diff =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-11647-11648.diff (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-11647-11648.diff (revision 11991) @@ -0,0 +1,24 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install-macosx-feras.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install-macosx-feras.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install-macosx-feras.sh (revision 11648) +@@ -0,0 +1,13 @@ ++#!/bin/bash ++ ++#Erase symlink ++rm -rf install ++ ++#Generic Matlab softlink for Macintosh (OSX) directory structure ++ ++#ln -s /Applications/MATLAB_R2008a/ install ++#ln -s /Applications/MATLAB_R2009a.app/ install ++#ln -s /Applications/MATLAB_R2010a.app/ install ++#ln -s /Applications/MATLAB_R2011b.app/ install ++ ++ln -s /Applications/MATLAB*.app/ install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install-macosx-feras.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11630-11648/ISSM-DocReview-11630-11648.tex =================================================================== --- /issm/oecreview/Archive/11630-11648/ISSM-DocReview-11630-11648.tex (revision 11991) +++ /issm/oecreview/Archive/11630-11648/ISSM-DocReview-11630-11648.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11630-11648/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11630-11648/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11630-11648/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11630-11648 Index: /issm/oecreview/Archive/11630-11648/Makefile =================================================================== --- /issm/oecreview/Archive/11630-11648/Makefile (revision 11991) +++ /issm/oecreview/Archive/11630-11648/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11630-11648 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11630-11648/log.tex =================================================================== --- /issm/oecreview/Archive/11630-11648/log.tex (revision 11991) +++ /issm/oecreview/Archive/11630-11648/log.tex (revision 11991) @@ -0,0 +1,36 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11630-11631.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/qmu/dakota\_in\_write.m \\ Export determination: 6. \\Rationale: matlab no longer allows fullfile version argument +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel run dakota too \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11631-11632.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: run dakota too +M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile run monday morning \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11632-11633.diff: \\ Function name: \\M /issm/trunk-jpl/cron/cronfiles/mac\_cronfile \\ Export determination: 6. \\Rationale: run monday morning +M /issm/trunk-jpl/cron/nightlyrun.sh daily runs compile with more cpus \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11633-11634.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: daily runs compile with more cpus +M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_daily M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_nightly M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_ucitrunk M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation M /issm/trunk-jpl/cron/configs/macosx64\_schlegel daily runs compile with more cpus \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11634-11635.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_daily M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_nightly M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_ucitrunk M /issm/trunk-jpl/cron/configs/linux64\_schlegel\_validation M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: daily runs compile with more cpus +M /issm/trunk-jpl/cron/configs/macosx64\_larour A /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation M /issm/trunk-jpl/cron/nightlyrun.sh Added link target during nightly runs \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11635-11636.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_larour A /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: Added link target during nightly runs +M /issm/trunk-jpl/cron/nightlyrun.sh Corrected misuse of ln command \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11636-11637.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: Corrected misuse of ln command +M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation Trying to prevent blowup of nightly run on mac \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11637-11638.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation \\ Export determination: 6. \\Rationale: Trying to prevent blowup of nightly run on mac +M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation Some tweaks to get mac runs to validate \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11638-11639.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation \\ Export determination: 6. \\Rationale: Some tweaks to get mac runs to validate +M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation Some tweaks to get mac runs to validate \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11639-11640.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation \\ Export determination: 6. \\Rationale: Some tweaks to get mac runs to validate +A /issm/trunk-jpl/configs/config-macosx64-larour.sh config macosx64 larour, including chaco \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11640-11641.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-macosx64-larour.sh \\ Export determination: 6. \\Rationale: config macosx64 larour, including chaco +M /issm/trunk-jpl/configs/config-macosx64-larour.sh Dakota support \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11641-11642.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-macosx64-larour.sh \\ Export determination: 6. \\Rationale: Dakota support +M /issm/trunk-jpl/src/m/qmu/dakota\_in\_data.m M /issm/trunk-jpl/src/m/qmu/dakota\_in\_write.m remove version from file info calls, not supported by new matlab \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11642-11643.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/qmu/dakota\_in\_data.m M /issm/trunk-jpl/src/m/qmu/dakota\_in\_write.m \\ Export determination: 6. \\Rationale: remove version from file info calls, not supported by new matlab +M /issm/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h D /issm/trunk-jpl/src/c/EnumDefinitions/EnumToModelField.cpp M /issm/trunk-jpl/src/c/EnumDefinitions/README M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh M /issm/trunk-jpl/src/c/Makefile.am D /issm/trunk-jpl/src/m/enum/EnumToModelField.m A /issm/trunk-jpl/src/m/model/EnumToModelField.m (from /issm/trunk-jpl/src/m/enum/EnumToModelField.m:11639) Trying to get rid of EnumToModelField (does not work anymore) \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11643-11644.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h D /issm/trunk-jpl/src/c/EnumDefinitions/EnumToModelField.cpp M /issm/trunk-jpl/src/c/EnumDefinitions/README M /issm/trunk-jpl/src/c/EnumDefinitions/Synchronize.sh M /issm/trunk-jpl/src/c/Makefile.am D /issm/trunk-jpl/src/m/enum/EnumToModelField.m A /issm/trunk-jpl/src/m/model/EnumToModelField.m (from /issm/trunk-jpl/src/m/enum/EnumToModelField.m:11639) \\ Export determination: 6. \\Rationale: Trying to get rid of EnumToModelField (does not work anymore) +M /issm/trunk-jpl/cron/nightlyrun.sh simplified email title \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11644-11645.diff: \\ Function name: \\M /issm/trunk-jpl/cron/nightlyrun.sh \\ Export determination: 6. \\Rationale: simplified email title +M /issm/trunk-jpl/src/m/utils/Analysis/setcluster.m Added deprecated warning: setcluster will be removed shortly \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11645-11646.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/Analysis/setcluster.m \\ Export determination: 6. \\Rationale: Added deprecated warning: setcluster will be removed shortly +A /issm/trunk-jpl/externalpackages/dakota/dakota\_njs\_notes\_macos64.txt some notes about gfortran \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11646-11647.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/dakota/dakota\_njs\_notes\_macos64.txt \\ Export determination: 6. \\Rationale: some notes about gfortran +D /issm/trunk-jpl/externalpackages/android/HelloWorldAppProject M /issm/trunk-jpl/externalpackages/android/README A /issm/trunk-jpl/externalpackages/android/android-ndk-r7b-darwin-x86.tar.bz2 A /issm/trunk-jpl/externalpackages/android/android-sdk\_r16-macosx.zip A /issm/trunk-jpl/externalpackages/android/install.sh Added appropriate development kits. \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-11647-11648.diff: \\ Function name: \\D /issm/trunk-jpl/externalpackages/android/HelloWorldAppProject M /issm/trunk-jpl/externalpackages/android/README A /issm/trunk-jpl/externalpackages/android/android-ndk-r7b-darwin-x86.tar.bz2 A /issm/trunk-jpl/externalpackages/android/android-sdk\_r16-macosx.zip A /issm/trunk-jpl/externalpackages/android/install.sh \\ Export determination: 6. \\Rationale: Added appropriate development kits. +A /issm/trunk-jpl/externalpackages/matlab/install-macosx-feras.sh Added generic Mac softlink for Matlab \\\\ Index: /issm/oecreview/Archive/11630-11648/r1.tex =================================================================== --- /issm/oecreview/Archive/11630-11648/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11630-11648/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11630 Index: /issm/oecreview/Archive/11630-11648/r2.tex =================================================================== --- /issm/oecreview/Archive/11630-11648/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11630-11648/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11648 Index: /issm/oecreview/Archive/11648-11666/Date.tex =================================================================== --- /issm/oecreview/Archive/11648-11666/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11648-11666/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11648-11666/ISSM-11648-11649.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11648-11649.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11648-11649.diff (revision 11991) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11648) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11649) +@@ -9,7 +9,10 @@ + #ln -s /usr/local/matlab711/ install + #ln -s /usr/local/matlab712/ install + #ln -s /usr/local/pkgs/matlab-7.6/ install ++ ++# Macintosh (OSX) simlink + #ln -s /Applications/MATLAB_R2008a/ install + #ln -s /Applications/MATLAB_R2009a.app/ install + #ln -s /Applications/MATLAB_R2010a.app/ install + #ln -s /Applications/MATLAB_R2011b.app/ install ++#ln -s /Applications/MATLAB*.app/ install Index: /issm/oecreview/Archive/11648-11666/ISSM-11649-11650.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11649-11650.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11649-11650.diff (revision 11991) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m (revision 11649) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m (revision 11650) +@@ -10,14 +10,14 @@ + % - hminVertices: minimum edge length for each vertex (mesh) + % - hmaxVertices: maximum edge length for each vertex (mesh) + % +-% - anisomax : maximum ration between the smallest and largest edges (default is 10^30) ++% - anisomax : maximum ratio between the smallest and largest edges (default is 10^30) + % - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) + % - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied + % - err : error used to generate the metric from a field + % - errg : geometrical error (default is 0.1) + % - field : field of the model that will be used to compute the metric + % to apply several fields, use one column per field +-% - gradation : maximum ration between two adjacent edges ++% - gradation : maximum ratio between two adjacent edges + % - Hessiantype : 0 -> use double P2 projection (default) + % 1 -> use Green formula + % - KeepVertices: try to keep initial vertices when adaptation is done on an existing mesh (default 1) Index: /issm/oecreview/Archive/11648-11666/ISSM-11650-11651.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11650-11651.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11650-11651.diff (revision 11991) @@ -0,0 +1,39 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m (revision 11650) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m (revision 11651) +@@ -5,7 +5,7 @@ + % + % - domain: followed by an ARGUS file that prescribes the domain outline + % - hmin : minimum edge length (default is 10^-100) +-% - hmax : maximum esge length (default is 10^100) ++% - hmax : maximum edge length (default is 10^100) + % - hVertices : imposed edge length for each vertex (geometry or mesh) + % - hminVertices: minimum edge length for each vertex (mesh) + % - hmaxVertices: maximum edge length for each vertex (mesh) +@@ -14,14 +14,14 @@ + % - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) + % - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied + % - err : error used to generate the metric from a field +-% - errg : geometrical error (default is 0.1) ++% - errg : geometric error (default is 0.1) + % - field : field of the model that will be used to compute the metric + % to apply several fields, use one column per field + % - gradation : maximum ratio between two adjacent edges + % - Hessiantype : 0 -> use double P2 projection (default) + % 1 -> use Green formula + % - KeepVertices: try to keep initial vertices when adaptation is done on an existing mesh (default 1) +-% - MaxCornerAngle: maximal angle of corners in degree (default is 10) ++% - MaxCornerAngle: maximum angle of corners in degree (default is 10) + % - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) + % - maxsubdiv : maximum subdivision of exisiting elements (default is 10) + % - metric : matrix (numberofnodes x 3) used as a metric +@@ -33,7 +33,7 @@ + % - omega : relaxation parameter of the smoothing procedure (default is 1.8) + % - power : power applied to the metric (default is 1) + % - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) +-% - geometricalmetric : Take the geometry into account to generate the metric (default is 0) ++% - geometricalmetric : take the geometry into account to generate the metric (default is 0) + % - verbose : level of verbosity (default is 1) + % + % - rifts : followed by an ARGUS file that prescribes the rifts Index: /issm/oecreview/Archive/11648-11666/ISSM-11651-11652.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11651-11652.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11651-11652.diff (revision 11991) @@ -0,0 +1,86 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m (revision 11651) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/mesh/bamg.m (revision 11652) +@@ -3,45 +3,45 @@ + % + % Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): + % +-% - domain: followed by an ARGUS file that prescribes the domain outline +-% - hmin : minimum edge length (default is 10^-100) +-% - hmax : maximum edge length (default is 10^100) +-% - hVertices : imposed edge length for each vertex (geometry or mesh) +-% - hminVertices: minimum edge length for each vertex (mesh) +-% - hmaxVertices: maximum edge length for each vertex (mesh) ++% - domain : followed by an ARGUS file that prescribes the domain outline ++% - hmin : minimum edge length (default is 10^-100) ++% - hmax : maximum edge length (default is 10^100) ++% - hVertices : imposed edge length for each vertex (geometry or mesh) ++% - hminVertices : minimum edge length for each vertex (mesh) ++% - hmaxVertices : maximum edge length for each vertex (mesh) + % +-% - anisomax : maximum ratio between the smallest and largest edges (default is 10^30) +-% - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) +-% - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied +-% - err : error used to generate the metric from a field +-% - errg : geometric error (default is 0.1) +-% - field : field of the model that will be used to compute the metric +-% to apply several fields, use one column per field +-% - gradation : maximum ratio between two adjacent edges +-% - Hessiantype : 0 -> use double P2 projection (default) +-% 1 -> use Green formula +-% - KeepVertices: try to keep initial vertices when adaptation is done on an existing mesh (default 1) +-% - MaxCornerAngle: maximum angle of corners in degree (default is 10) +-% - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) +-% - maxsubdiv : maximum subdivision of exisiting elements (default is 10) +-% - metric : matrix (numberofnodes x 3) used as a metric +-% - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) +-% 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) +-% 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) +-% - nbjacoby : correction used by Hessiantype=1 (default is 1) +-% - nbsmooth : number of metric smoothing procedure (default is 3) +-% - omega : relaxation parameter of the smoothing procedure (default is 1.8) +-% - power : power applied to the metric (default is 1) +-% - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) ++% - anisomax : maximum ratio between the smallest and largest edges (default is 10^30) ++% - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) ++% - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied ++% - err : error used to generate the metric from a field ++% - errg : geometric error (default is 0.1) ++% - field : field of the model that will be used to compute the metric ++% to apply several fields, use one column per field ++% - gradation : maximum ratio between two adjacent edges ++% - Hessiantype : 0 -> use double P2 projection (default) ++% 1 -> use Green formula ++% - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) ++% - MaxCornerAngle : maximum angle of corners in degree (default is 10) ++% - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) ++% - maxsubdiv : maximum subdivision of exisiting elements (default is 10) ++% - metric : matrix (numberofnodes x 3) used as a metric ++% - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) ++% 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) ++% 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) ++% - nbjacoby : correction used by Hessiantype=1 (default is 1) ++% - nbsmooth : number of metric smoothing procedure (default is 3) ++% - omega : relaxation parameter of the smoothing procedure (default is 1.8) ++% - power : power applied to the metric (default is 1) ++% - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) + % - geometricalmetric : take the geometry into account to generate the metric (default is 0) +-% - verbose : level of verbosity (default is 1) ++% - verbose : level of verbosity (default is 1) + % +-% - rifts : followed by an ARGUS file that prescribes the rifts +-% - toltip: tolerance to move tip on an existing point of the domain outline +-% - tracks: followed by an ARGUS file that prescribes the tracks that the mesh will stick to +-% - RequiredVertices: mesh vertices that are required. [x,y,ref]; ref is optional +-% - tol: if the distance between 2 points of the domain outline is less than tol, they +-% will be merged ++% - rifts : followed by an ARGUS file that prescribes the rifts ++% - toltip : tolerance to move tip on an existing point of the domain outline ++% - tracks : followed by an ARGUS file that prescribes the tracks that the mesh will stick to ++% - RequiredVertices : mesh vertices that are required. [x,y,ref]; ref is optional ++% - tol : if the distance between 2 points of the domain outline is less than tol, they ++% will be merged + % + % Examples: + % md=bamg(md,'domain','DomainOutline.exp','hmax',3000); Index: /issm/oecreview/Archive/11648-11666/ISSM-11652-11653.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11652-11653.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11652-11653.diff (revision 11991) @@ -0,0 +1,11 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11652) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11653) +@@ -94,5 +94,5 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'exclude',[137 527]" ++NROPTIONS="'exclude',[137 425 434 527]" + Index: /issm/oecreview/Archive/11648-11666/ISSM-11653-11654.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11653-11654.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11653-11654.diff (revision 11991) @@ -0,0 +1,109 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily (revision 11654) +@@ -0,0 +1,98 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/Users/schlegel/issmuci" ++ISSM_TIER="/Users/schlegel/issmuci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="macosx-gnu" ++ ++#Machine configuration ++MACHINE="macosx-gil" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" ++ ++#MATLAB path ++MATLAB_PATH="/Applications/MATLAB_R2011b.app/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="update" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/Users/schlegel/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="none" ++EXTERNALPACKAGESDIR="/Users/schlegel/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="schlegel@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=4 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=4 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="'exclude',[137 425 434 527]" ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11648-11666/ISSM-11654-11655.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11654-11655.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11654-11655.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily (revision 11654) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel_daily (revision 11655) +@@ -94,5 +94,5 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'exclude',[137 425 434 527]" ++NROPTIONS="'exclude',[137 425:434 527]" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11654) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_schlegel (revision 11655) +@@ -94,5 +94,5 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'exclude',[137 425 434 527]" ++NROPTIONS="'exclude',[137 425:434 527]" + Index: /issm/oecreview/Archive/11648-11666/ISSM-11655-11656.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11655-11656.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11655-11656.diff (revision 11991) @@ -0,0 +1,342 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Elements/elements.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Elements/elements.h (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Elements/elements.h (revision 11656) +@@ -16,8 +16,8 @@ + int GetNumberOfDofs( Node** nodes,int numnodes,int setenum,int approximation_enum); + int* GetLocalDofList( Node** nodes,int numnodes,int setenum,int approximation_enum); + int* GetGlobalDofList(Node** nodes,int numnodes,int setenum,int approximation_enum); ++#ifdef _HAVE_DIAGNOSTIC_ + void CoordinateSystemTransform(double** ptransform,Node** nodes,int numnodes,int* cs_array); +-#ifdef _HAVE_DIAGNOSTIC_ + void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); + void TransformInvStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int* cs_array); + void TransformStiffnessMatrixCoord(ElementMatrix* Ke,Node** nodes,int numnodes,int cs_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11656) +@@ -203,7 +203,6 @@ + ./shared/Elements/GetLocalDofList.cpp\ + ./shared/Elements/GetGlobalDofList.cpp\ + ./shared/Elements/GetNumberOfDofs.cpp\ +- ./shared/Elements/CoordinateSystemTransform.cpp\ + ./shared/String/sharedstring.h\ + ./toolkits/petsc\ + ./toolkits/petsc/patches\ +@@ -501,6 +500,7 @@ + ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ + ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ + ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ ++ ./shared/Elements/CoordinateSystemTransform.cpp\ + ./shared/Elements/TransformLoadVectorCoord.cpp \ + ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp (revision 11656) +@@ -318,15 +318,19 @@ + this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); + + switch(analysis_type){ ++ #ifdef _HAVE_DIAGNOSTIC_ + case DiagnosticHorizAnalysisEnum: case AdjointHorizAnalysisEnum: + Ke=PenaltyCreateKMatrixDiagnosticStokes(kmax); + break; ++ #endif ++ #ifdef _HAVE_THERMAL_ + case ThermalAnalysisEnum: + Ke=PenaltyCreateKMatrixThermal(kmax); + break; + case MeltingAnalysisEnum: + Ke=PenaltyCreateKMatrixMelting(kmax); + break; ++ #endif + default: + _error_("analysis %i (%s) not supported yet",analysis_type,EnumToStringx(analysis_type)); + } +@@ -347,14 +351,18 @@ + this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); + + switch(analysis_type){ ++ #ifdef _HAVE_DIAGNOSTIC_ + case ThermalAnalysisEnum: + pe=PenaltyCreatePVectorThermal(kmax); + break; ++ #endif ++ #ifdef _HAVE_THERMAL_ + case MeltingAnalysisEnum: + pe=PenaltyCreatePVectorMelting(kmax); + break; + case DiagnosticHorizAnalysisEnum: case AdjointHorizAnalysisEnum: + break; ++ #endif + default: + _error_("analysis %i (%s) not supported yet",analysis_type,EnumToStringx(analysis_type)); + } +@@ -538,6 +546,7 @@ + *punstable=unstable; + } + /*}}}1*/ ++#ifdef _HAVE_DIAGNOSTIC_ + /*FUNCTION Pengrid::PenaltyCreateKMatrixDiagnosticStokes {{{1*/ + ElementMatrix* Pengrid::PenaltyCreateKMatrixDiagnosticStokes(double kmax){ + +@@ -570,6 +579,8 @@ + return Ke; + } + /*}}}1*/ ++#endif ++#ifdef _HAVE_THERMAL_ + /*FUNCTION Pengrid::PenaltyCreateKMatrixMelting {{{1*/ + ElementMatrix* Pengrid::PenaltyCreateKMatrixMelting(double kmax){ + +@@ -689,6 +700,7 @@ + return pe; + } + /*}}}1*/ ++#endif + /*FUNCTION Pengrid::ResetConstraint {{{1*/ + void Pengrid::ResetConstraint(void){ + active=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h (revision 11656) +@@ -83,11 +83,15 @@ + bool InAnalysis(int analysis_type); + /*}}}*/ + /*Pengrid management {{{1*/ ++ #ifdef _HAVE_DIAGNOSTIC_ + ElementMatrix* PenaltyCreateKMatrixDiagnosticStokes(double kmax); ++ #endif ++ #ifdef _HAVE_THERMAL_ + ElementMatrix* PenaltyCreateKMatrixThermal(double kmax); + ElementMatrix* PenaltyCreateKMatrixMelting(double kmax); + ElementVector* PenaltyCreatePVectorThermal(double kmax); + ElementVector* PenaltyCreatePVectorMelting(double kmax); ++ #endif + void ConstraintActivate(int* punstable); + void ConstraintActivateThermal(int* punstable); + void UpdateInputs(double* solution); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11656) +@@ -57,6 +57,7 @@ + virtual void ProcessResultsUnits(void)=0; + virtual void RequestedOutput(int output_enum,int step,double time)=0; + ++ virtual int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units)=0; + virtual void InputScale(int enum_type,double scale_factor)=0; + virtual void GetVectorFromInputs(Vec vector, int name_enum)=0; + virtual void GetVectorFromResults(Vec vector,int id,int interp)=0; +@@ -87,7 +88,6 @@ + virtual double MassFlux(double* segment,bool process_units)=0; + virtual void ElementResponse(double* presponse,int response_enum,bool process_units)=0; + virtual double IceVolume(void)=0; +- virtual int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units)=0; + #endif + + #ifdef _HAVE_CONTROL_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11656) +@@ -2122,6 +2122,37 @@ + return my_rank; + } + /*}}}*/ ++/*FUNCTION Tria::NodalValue {{{1*/ ++int Tria::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ ++ ++ int i; ++ int found=0; ++ double value; ++ Input* data=NULL; ++ GaussTria *gauss = NULL; ++ ++ /*First, serarch the input: */ ++ data=inputs->GetInput(natureofdataenum); ++ ++ /*figure out if we have the vertex id: */ ++ found=0; ++ for(i=0;iGetVertexId()){ ++ /*Do we have natureofdataenum in our inputs? :*/ ++ if(data){ ++ /*ok, we are good. retrieve value of input at vertex :*/ ++ gauss=new GaussTria(); gauss->GaussVertex(i); ++ data->GetInputValue(&value,gauss); ++ found=1; ++ break; ++ } ++ } ++ } ++ ++ if(found)*pvalue=value; ++ return found; ++} ++/*}}}*/ + /*FUNCTION Tria::PatchFill{{{1*/ + void Tria::PatchFill(int* prow, Patch* patch){ + +@@ -2738,37 +2769,6 @@ + *pminvz=minvz; + } + /*}}}*/ +-/*FUNCTION Tria::NodalValue {{{1*/ +-int Tria::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ +- +- int i; +- int found=0; +- double value; +- Input* data=NULL; +- GaussTria *gauss = NULL; +- +- /*First, serarch the input: */ +- data=inputs->GetInput(natureofdataenum); +- +- /*figure out if we have the vertex id: */ +- found=0; +- for(i=0;iGetVertexId()){ +- /*Do we have natureofdataenum in our inputs? :*/ +- if(data){ +- /*ok, we are good. retrieve value of input at vertex :*/ +- gauss=new GaussTria(); gauss->GaussVertex(i); +- data->GetInputValue(&value,gauss); +- found=1; +- break; +- } +- } +- } +- +- if(found)*pvalue=value; +- return found; +-} +-/*}}}*/ + /*FUNCTION Tria::ElementResponse{{{1*/ + void Tria::ElementResponse(double* presponse,int response_enum,bool process_units){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11656) +@@ -105,6 +105,7 @@ + void DeleteResults(void); + void MaterialUpdateFromTemperature(void){_error_("not implemented yet");}; + void MigrateGroundingLine(double* oldfloating,double* sheet_ungrounding); ++ int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); + void PotentialSheetUngrounding(Vec potential_sheet_ungrounding); + void PositiveDegreeDay(void); + void RequestedOutput(int output_enum,int step,double time); +@@ -126,7 +127,6 @@ + void MinVx(double* pminvx, bool process_units); + void MinVy(double* pminvy, bool process_units); + void MinVz(double* pminvz, bool process_units); +- int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); + double MassFlux(double* segment,bool process_units); + void MaxAbsVx(double* pmaxabsvx, bool process_units); + void MaxAbsVy(double* pmaxabsvy, bool process_units); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11656) +@@ -2326,6 +2326,37 @@ + return my_rank; + } + /*}}}*/ ++/*FUNCTION Penta::NodalValue {{{1*/ ++int Penta::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ ++ ++ int i; ++ int found=0; ++ double value; ++ Input* data=NULL; ++ GaussPenta* gauss=NULL; ++ ++ /*First, serarch the input: */ ++ data=inputs->GetInput(natureofdataenum); ++ ++ /*figure out if we have the vertex id: */ ++ found=0; ++ for(i=0;iGetVertexId()){ ++ /*Do we have natureofdataenum in our inputs? :*/ ++ if(data){ ++ /*ok, we are good. retrieve value of input at vertex :*/ ++ gauss=new GaussPenta(); gauss->GaussVertex(i); ++ data->GetInputValue(&value,gauss); ++ found=1; ++ break; ++ } ++ } ++ } ++ ++ if(found)*pvalue=value; ++ return found; ++} ++/*}}}*/ + /*FUNCTION Penta::PatchFill{{{1*/ + void Penta::PatchFill(int* pcount, Patch* patch){ + +@@ -3001,37 +3032,6 @@ + return base*height; + } + /*}}}*/ +-/*FUNCTION Penta::NodalValue {{{1*/ +-int Penta::NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units){ +- +- int i; +- int found=0; +- double value; +- Input* data=NULL; +- GaussPenta* gauss=NULL; +- +- /*First, serarch the input: */ +- data=inputs->GetInput(natureofdataenum); +- +- /*figure out if we have the vertex id: */ +- found=0; +- for(i=0;iGetVertexId()){ +- /*Do we have natureofdataenum in our inputs? :*/ +- if(data){ +- /*ok, we are good. retrieve value of input at vertex :*/ +- gauss=new GaussPenta(); gauss->GaussVertex(i); +- data->GetInputValue(&value,gauss); +- found=1; +- break; +- } +- } +- } +- +- if(found)*pvalue=value; +- return found; +-} +-/*}}}*/ + /*FUNCTION Penta::MinVel{{{1*/ + void Penta::MinVel(double* pminvel, bool process_units){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11655) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11656) +@@ -117,6 +117,7 @@ + double SurfaceArea(void); + void Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type); + int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf); ++ int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); + double TimeAdapt(); + int* GetHorizontalNeighboorSids(void); + void ViscousHeatingCreateInput(void); +@@ -128,7 +129,6 @@ + void MinVx(double* pminvx, bool process_units); + void MinVy(double* pminvy, bool process_units); + void MinVz(double* pminvz, bool process_units); +- int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); + double MassFlux(double* segment,bool process_units); + void MaxAbsVx(double* pmaxabsvx, bool process_units); + void MaxAbsVy(double* pmaxabsvy, bool process_units); Index: /issm/oecreview/Archive/11648-11666/ISSM-11656-11657.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11656-11657.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11656-11657.diff (revision 11991) @@ -0,0 +1,14 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/manipulation +___________________________________________________________________ +Added: svn:ignore + + Makefile + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/Exp/readwrite +___________________________________________________________________ +Added: svn:ignore + + Makefile + + Index: /issm/oecreview/Archive/11648-11666/ISSM-11657-11658.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11657-11658.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11657-11658.diff (revision 11991) @@ -0,0 +1,918 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/Makefile.am (revision 11657) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/Makefile.am (revision 11658) +@@ -1,29 +1,26 @@ +-INCLUDES = @DAKOTAINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ ++INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ ++EXEEXT=$(ISSMEXT) + +-#This Makefile.am is for automatic differentiation of the parallel version of ISSM. +-#We do not compile in serial mode +-#If user requests no parallel compilation, we compile an empty ISSM. +-#Compilation can still be blocked if user has not activated --with-adic compilation +- + #Library declaration {{{1 +- ++#Compile serial library, and then try and compile parallel library ++if NOSERIAL + if NOPARALLEL + lib_LIBRARIES = + else +-lib_LIBRARIES = libpISSM.a libOverload.a ++lib_LIBRARIES = libpISSM.a libOverload.a + endif +- +-if ADIC2 +-lib_LIBRARIES += libAD.a libpISSMRose.a ++else ++if NOPARALLEL ++lib_LIBRARIES = libISSM.a libOverload.a ++else ++lib_LIBRARIES = libISSM.a libpISSM.a libOverload.a + endif ++endif ++#}}} + +-#}}} +-#Overload library, to overload any non-standard symbols. {{{1 +-libOverload_a_SOURCES = ./shared/String/stricmp.c +-libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) +-#}}} +-#ISSM library {{{1 +-libpISSM_a_SOURCES = ./include/macros.h\ ++#sources ++#Core sources{{{1 ++core_sources = ./include/macros.h\ + ./include/typedefs.h\ + ./include/types.h\ + ./include/include.h\ +@@ -37,6 +34,10 @@ + ./objects/FemModel.cpp\ + ./objects/Material.h\ + ./objects/Load.h\ ++ ./objects/Contour.h\ ++ ./objects/Contour.cpp\ ++ ./objects/OptArgs.h\ ++ ./objects/OptPars.h\ + ./objects/Loads/Friction.h\ + ./objects/Loads/Friction.cpp\ + ./objects/Inputs/TransientInput.h\ +@@ -60,8 +61,8 @@ + ./objects/ElementResults/ElementResultLocal.h\ + ./objects/ElementResults/DoubleElementResult.h\ + ./objects/ElementResults/DoubleElementResult.cpp\ +- ./objects/ElementResults/TriaVertexElementResult.h\ +- ./objects/ElementResults/TriaVertexElementResult.cpp\ ++ ./objects/ElementResults/TriaP1ElementResult.h\ ++ ./objects/ElementResults/TriaP1ElementResult.cpp\ + ./objects/ElementResults/BoolElementResult.h\ + ./objects/ElementResults/BoolElementResult.cpp\ + ./objects/ExternalResults/ExternalResult.h\ +@@ -87,8 +88,8 @@ + ./objects/Elements/TriaRef.cpp\ + ./objects/Inputs/Input.h\ + ./objects/Inputs/InputLocal.h\ +- ./objects/Inputs/TriaVertexInput.h\ +- ./objects/Inputs/TriaVertexInput.cpp\ ++ ./objects/Inputs/TriaP1Input.h\ ++ ./objects/Inputs/TriaP1Input.cpp\ + ./objects/Inputs/BoolInput.h\ + ./objects/Inputs/BoolInput.cpp\ + ./objects/Inputs/IntInput.h\ +@@ -137,6 +138,8 @@ + ./objects/Params/StringArrayParam.h\ + ./objects/Params/DoubleMatParam.cpp\ + ./objects/Params/DoubleMatParam.h\ ++ ./objects/Params/DoubleTransientMatParam.cpp\ ++ ./objects/Params/DoubleTransientMatParam.h\ + ./objects/Params/DoubleMatArrayParam.cpp\ + ./objects/Params/DoubleMatArrayParam.h\ + ./objects/Params/DoubleVecParam.cpp\ +@@ -160,6 +163,8 @@ + ./Container/Materials.cpp\ + ./Container/Nodes.h\ + ./Container/Nodes.cpp\ ++ ./Container/Options.h\ ++ ./Container/Options.cpp\ + ./Container/Parameters.h\ + ./Container/Parameters.cpp\ + ./Container/Results.h\ +@@ -180,7 +185,10 @@ + ./shared/Numerics/GaussPoints.h\ + ./shared/Numerics/GaussPoints.cpp\ + ./shared/Numerics/cross.cpp\ ++ ./shared/Numerics/isnan.h\ ++ ./shared/Numerics/isnan.cpp\ + ./shared/Numerics/extrema.cpp\ ++ ./shared/Numerics/XZvectorsToCoordinateSystem.cpp\ + ./shared/Numerics/UnitConversion.cpp\ + ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ + ./shared/Exceptions/exceptions.h\ +@@ -243,7 +251,6 @@ + ./io/Disk/pfclose.cpp\ + ./io/PrintfFunction.cpp\ + ./EnumDefinitions/EnumDefinitions.h\ +- ./EnumDefinitions/EnumToModelField.cpp\ + ./modules/ModelProcessorx/ModelProcessorx.h\ + ./modules/ModelProcessorx/ModelProcessorx.cpp\ + ./modules/ModelProcessorx/DistributeNumDofs.cpp\ +@@ -260,6 +267,8 @@ + ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ + ./modules/NodesDofx/NodesDofx.h\ + ./modules/NodesDofx/NodesDofx.cpp\ ++ ./modules/NodalValuex/NodalValuex.h\ ++ ./modules/NodalValuex/NodalValuex.cpp\ + ./modules/VerticesDofx/VerticesDofx.h\ + ./modules/VerticesDofx/VerticesDofx.cpp\ + ./modules/OutputResultsx/OutputResultsx.h\ +@@ -268,6 +277,8 @@ + ./modules/InputDuplicatex/InputDuplicatex.cpp\ + ./modules/InputScalex/InputScalex.h\ + ./modules/InputScalex/InputScalex.cpp\ ++ ./modules/SurfaceAreax/SurfaceAreax.h\ ++ ./modules/SurfaceAreax/SurfaceAreax.cpp\ + ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h\ + ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp\ + ./modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h\ +@@ -298,6 +309,8 @@ + ./modules/ComputeStrainRatex/ComputeStrainRatex.cpp\ + ./modules/SpcNodesx/SpcNodesx.h\ + ./modules/SpcNodesx/SpcNodesx.cpp\ ++ ./modules/PositiveDegreeDayx/PositiveDegreeDayx.h\ ++ ./modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp\ + ./modules/UpdateConstraintsx/UpdateConstraintsx.h\ + ./modules/UpdateConstraintsx/UpdateConstraintsx.cpp\ + ./modules/MeshPartitionx/MeshPartitionx.cpp\ +@@ -312,13 +325,19 @@ + ./modules/StringToEnumx/StringToEnumx.h\ + ./modules/SystemMatricesx/SystemMatricesx.cpp\ + ./modules/SystemMatricesx/SystemMatricesx.h\ ++ ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp\ ++ ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h\ + ./modules/ConstraintsStatex/ConstraintsStatex.cpp\ + ./modules/ConstraintsStatex/ConstraintsStatex.h\ + ./modules/ConstraintsStatex/ConstraintsStateLocal.h\ ++ ./modules/Responsex/Responsex.h\ ++ ./modules/Responsex/Responsex.cpp\ + ./modules/RequestedOutputsx/RequestedOutputsx.h\ + ./modules/RequestedOutputsx/RequestedOutputsx.cpp\ + ./modules/ResetConstraintsx/ResetConstraintsx.h\ + ./modules/ResetConstraintsx/ResetConstraintsx.cpp\ ++ ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h\ ++ ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ + ./modules/Solverx/Solverx.cpp\ + ./modules/Solverx/Solverx.h\ + ./modules/Solverx/DofTypesToIndexSet.cpp\ +@@ -331,19 +350,17 @@ + ./modules/InputConvergencex/InputConvergencex.cpp\ + ./modules/InputConvergencex/InputConvergencex.h\ + ./solutions/convergence.cpp\ ++ ./solutions/ProcessArguments.cpp\ + ./solutions/WriteLockFile.cpp\ + ./solutions/ResetBoundaryConditions.cpp\ + ./solutions/AnalysisConfiguration.cpp\ + ./solutions/CorePointerFromSolutionEnum.cpp\ + ./solvers/solver_linear.cpp\ +- ./solvers/solver_nonlinear.cpp +- +- +-libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) ++ ./solvers/solver_nonlinear.cpp\ ++ ./solvers/solver_newton.cpp + #}}} + #DAKOTA sources {{{1 +-if DAKOTA +-libpISSM_a_SOURCES += ./objects/DakotaPlugin.h\ ++dakota_sources = ./objects/DakotaPlugin.h\ + ./objects/DakotaPlugin.cpp\ + ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\ + ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp\ +@@ -351,6 +368,8 @@ + ./modules/DakotaResponsesx/DakotaResponsesx.cpp\ + ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h\ + ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp\ ++ ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.h\ ++ ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ + ./modules/Dakotax/Dakotax.h\ +@@ -358,42 +377,29 @@ + ./modules/Dakotax/DakotaMPI_Bcast.cpp\ + ./modules/Dakotax/DakotaFree.cpp\ + ./modules/Dakotax/SpawnCore.cpp\ +- ./modules/Dakotax/SpawnCoreParallel.cpp\ + ./modules/Dakotax/DescriptorIndex.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ +- ./modules/ModelProcessorx/Qmu/CreateParametersQmu.cpp\ ++ ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h +-endif ++dakota_psources= ./modules/Dakotax/SpawnCoreParallel.cpp + #}}} + #Transient sources {{{1 +-if TRANSIENT +-libpISSM_a_SOURCES += ./solutions/transient_core.cpp\ +- ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp +-endif ++transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp ++transient_psources = ./solutions/transient_core.cpp + #}}} + #Steadystate sources {{{1 +-if STEADYSTATE +-libpISSM_a_SOURCES += ./solutions/steadystate_core.cpp\ +- ./solutions/steadystateconvergence.cpp +-endif ++steadystate_psources = ./solutions/steadystate_core.cpp\ ++ ./solutions/steadystateconvergence.cpp + #}}} + #Prognostic sources {{{1 +-if PROGNOSTIC +-libpISSM_a_SOURCES += ./solutions/prognostic_core.cpp\ +- ./modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp\ +- ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ +- ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ +- ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp +- +-endif ++prognostic_sources = ./modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp\ ++ ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ ++ ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ ++ ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp ++prognostic_psources = ./solutions/prognostic_core.cpp + #}}} + #Thermal sources {{{1 +-if THERMAL +-libpISSM_a_SOURCES += ./solutions/thermal_core.cpp\ +- ./solutions/thermal_core_step.cpp\ +- ./solutions/enthalpy_core.cpp\ +- ./solvers/solver_thermal_nonlinear.cpp\ +- ./modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp\ ++thermal_sources = ./modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp\ + ./modules/ModelProcessorx/Thermal/CreateNodesThermal.cpp\ + ./modules/ModelProcessorx/Thermal/CreateConstraintsThermal.cpp\ + ./modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp\ +@@ -408,26 +414,24 @@ + ./modules/ConstraintsStatex/ThermalConstraintsState.cpp\ + ./modules/ConstraintsStatex/ThermalIsPresent.cpp\ + ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp +-endif ++ ++thermal_psources = ./solutions/thermal_core.cpp\ ++ ./solutions/thermal_core_step.cpp\ ++ ./solutions/enthalpy_core.cpp\ ++ ./solutions/enthalpy_core_step.cpp\ ++ ./solvers/solver_thermal_nonlinear.cpp + #}}} + #Control sources {{{1 +-if CONTROL +-libpISSM_a_SOURCES += ./solutions/control_core.cpp\ +- ./solutions/controltao_core.cpp\ +- ./solutions/controlrestart.cpp\ +- ./solutions/controlconvergence.cpp\ +- ./solutions/objectivefunctionC.cpp\ +- ./solutions/gradient_core.cpp\ +- ./solutions/adjointdiagnostic_core.cpp\ +- ./solutions/adjointbalancethickness_core.cpp\ +- ./solutions/AdjointCorePointerFromSolutionEnum.cpp\ +- ./solvers/solver_adjoint_linear.cpp\ +- ./modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp\ ++control_sources= ./modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp\ + ./modules/ControlInputGetGradientx/ControlInputGetGradientx.h\ + ./modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp\ + ./modules/ControlInputSetGradientx/ControlInputSetGradientx.h\ + ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.cpp\ + ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.h\ ++ ./modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp\ ++ ./modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h\ ++ ./modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp\ ++ ./modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h\ + ./modules/ModelProcessorx/Control/CreateParametersControl.cpp\ + ./modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp\ + ./modules/InputControlUpdatex/InputControlUpdatex.h\ +@@ -460,171 +464,502 @@ + ./objects/Inputs/ControlInput.cpp\ + ./shared/Numerics/BrentSearch.cpp\ + ./shared/Numerics/OptimalSearch.cpp\ +- ./shared/Numerics/OptFunc.cpp\ +- ./objects/OptArgs.h\ +- ./objects/OptPars.h ++ ./shared/Numerics/OptFunc.cpp + +-endif ++control_psources=./solutions/control_core.cpp\ ++ ./solutions/controltao_core.cpp\ ++ ./solutions/controlrestart.cpp\ ++ ./solutions/controlconvergence.cpp\ ++ ./solutions/objectivefunctionC.cpp\ ++ ./solutions/gradient_core.cpp\ ++ ./solutions/adjointdiagnostic_core.cpp\ ++ ./solutions/adjointbalancethickness_core.cpp\ ++ ./solutions/AdjointCorePointerFromSolutionEnum.cpp\ ++ ./solvers/solver_adjoint_linear.cpp ++ + #}}} + #Hydrology sources {{{1 +-if HYDROLOGY +-libpISSM_a_SOURCES += ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\ +- ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ +- ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ +- ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp\ +- ./solutions/hydrology_core.cpp\ +- ./solutions/hydrology_core_step.cpp +-endif ++hydrology_sources = ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\ ++ ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ ++ ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ ++ ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp ++ ++hydrology_psources = ./solutions/hydrology_core.cpp\ ++ ./solutions/hydrology_core_step.cpp + #}}} + #Diagnostic sources {{{1 +-if DIAGNOSTIC +-libpISSM_a_SOURCES += ./modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp\ +- ./modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp \ +- ./modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp \ +- ./modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp\ +- ./modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp\ +- ./modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp \ +- ./modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp \ +- ./modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp\ +- ./modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp\ +- ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ +- ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ +- ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp\ +- ./solutions/diagnostic_core.cpp\ +- ./solvers/solver_stokescoupling_nonlinear.cpp +-endif ++diagnostic_sources = ./modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp\ ++ ./modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp \ ++ ./modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp \ ++ ./modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp\ ++ ./modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp\ ++ ./modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp \ ++ ./modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp \ ++ ./modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp\ ++ ./modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp\ ++ ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ ++ ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ ++ ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ ++ ./shared/Elements/CoordinateSystemTransform.cpp\ ++ ./shared/Elements/TransformLoadVectorCoord.cpp \ ++ ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ ++ ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ ++ ./shared/Elements/TransformSolutionCoord.cpp ++diagnostic_psources =./solutions/diagnostic_core.cpp\ ++ ./solvers/solver_stokescoupling_nonlinear.cpp + #}}} + #Balanced sources {{{1 +-if BALANCED +-libpISSM_a_SOURCES += ./modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp\ +- ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ +- ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ +- ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ +- ./solutions/balancethickness_core.cpp +-endif ++balanced_sources = ./modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp\ ++ ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ ++ ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ ++ ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp ++balanced_psources = ./solutions/balancethickness_core.cpp + #}}} + #Responses sources {{{1 +-if RESPONSES +-libpISSM_a_SOURCES += ./modules/MinVelx/MinVelx.h\ +- ./modules/MinVelx/MinVelx.cpp\ +- ./modules/MaxVelx/MaxVelx.h\ +- ./modules/MaxVelx/MaxVelx.cpp\ +- ./modules/MaxAbsVxx/MaxAbsVxx.h\ +- ./modules/MaxAbsVxx/MaxAbsVxx.cpp\ +- ./modules/MaxAbsVyx/MaxAbsVyx.h\ +- ./modules/MaxAbsVyx/MaxAbsVyx.cpp\ +- ./modules/MaxAbsVzx/MaxAbsVzx.h\ +- ./modules/MaxAbsVzx/MaxAbsVzx.cpp\ +- ./modules/MaxVxx/MaxVxx.h\ +- ./modules/MaxVxx/MaxVxx.cpp\ +- ./modules/MaxVyx/MaxVyx.h\ +- ./modules/MaxVyx/MaxVyx.cpp\ +- ./modules/MaxVzx/MaxVzx.h\ +- ./modules/MaxVzx/MaxVzx.cpp\ +- ./modules/MinVxx/MinVxx.h\ +- ./modules/MinVxx/MinVxx.cpp\ +- ./modules/MinVyx/MinVyx.h\ +- ./modules/MinVyx/MinVyx.cpp\ +- ./modules/MinVzx/MinVzx.h\ +- ./modules/MinVzx/MinVzx.cpp\ +- ./modules/RheologyBbarx/RheologyBbarx.cpp\ +- ./modules/RheologyBbarx/RheologyBbarx.h\ +- ./modules/MassFluxx/MassFluxx.cpp\ +- ./modules/MassFluxx/MassFluxx.h\ +- ./modules/NodalValuex/NodalValuex.h\ +- ./modules/NodalValuex/NodalValuex.cpp\ +- ./modules/SurfaceAreax/SurfaceAreax.h\ +- ./modules/SurfaceAreax/SurfaceAreax.cpp\ +- ./modules/Responsex/Responsex.h\ +- ./modules/Responsex/Responsex.cpp +-endif ++responses_sources = ./modules/MinVelx/MinVelx.h\ ++ ./modules/MinVelx/MinVelx.cpp\ ++ ./modules/MaxVelx/MaxVelx.h\ ++ ./modules/MaxVelx/MaxVelx.cpp\ ++ ./modules/MaxAbsVxx/MaxAbsVxx.h\ ++ ./modules/MaxAbsVxx/MaxAbsVxx.cpp\ ++ ./modules/MaxAbsVyx/MaxAbsVyx.h\ ++ ./modules/MaxAbsVyx/MaxAbsVyx.cpp\ ++ ./modules/MaxAbsVzx/MaxAbsVzx.h\ ++ ./modules/MaxAbsVzx/MaxAbsVzx.cpp\ ++ ./modules/MaxVxx/MaxVxx.h\ ++ ./modules/MaxVxx/MaxVxx.cpp\ ++ ./modules/MaxVyx/MaxVyx.h\ ++ ./modules/MaxVyx/MaxVyx.cpp\ ++ ./modules/MaxVzx/MaxVzx.h\ ++ ./modules/MaxVzx/MaxVzx.cpp\ ++ ./modules/MinVxx/MinVxx.h\ ++ ./modules/MinVxx/MinVxx.cpp\ ++ ./modules/MinVyx/MinVyx.h\ ++ ./modules/MinVyx/MinVyx.cpp\ ++ ./modules/MinVzx/MinVzx.h\ ++ ./modules/MinVzx/MinVzx.cpp\ ++ ./modules/IceVolumex/IceVolumex.h\ ++ ./modules/IceVolumex/IceVolumex.cpp\ ++ ./modules/ElementResponsex/ElementResponsex.h\ ++ ./modules/ElementResponsex/ElementResponsex.cpp\ ++ ./modules/MassFluxx/MassFluxx.cpp\ ++ ./modules/MassFluxx/MassFluxx.h + #}}} + #Slope sources {{{1 +-if SLOPE +-libpISSM_a_SOURCES += ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ ++slope_sources = ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ + ./modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp \ + ./modules/ModelProcessorx/BedSlope/CreateConstraintsBedSlope.cpp\ + ./modules/ModelProcessorx/BedSlope/CreateLoadsBedSlope.cpp\ + ./modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp\ + ./modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp \ + ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\ +- ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp\ +- ./solutions/surfaceslope_core.cpp\ ++ ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp ++slope_psources = ./solutions/surfaceslope_core.cpp\ + ./solutions/bedslope_core.cpp ++#}}} ++#Groundingline sources {{{1 ++groundingline_sources= ./modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp\ ++ ./modules/GroundinglineMigrationx/GroundinglineMigrationx.h ++#}}} ++#Rifts sources {{{1 ++rifts_sources = ./objects/Loads/Riftfront.cpp\ ++ ./objects/Loads/Riftfront.h\ ++ ./modules/ConstraintsStatex/RiftConstraintsState.cpp ++#}}} ++#3D sources {{{1 ++threed_sources = ./objects/Gauss/GaussPenta.h\ ++ ./objects/Gauss/GaussPenta.cpp\ ++ ./objects/ElementResults/PentaP1ElementResult.h\ ++ ./objects/ElementResults/PentaP1ElementResult.cpp\ ++ ./objects/Inputs/PentaP1Input.h\ ++ ./objects/Inputs/PentaP1Input.cpp\ ++ ./objects/Elements/Penta.h\ ++ ./objects/Elements/Penta.cpp\ ++ ./objects/Elements/PentaHook.h\ ++ ./objects/Elements/PentaHook.cpp\ ++ ./objects/Elements/PentaRef.h\ ++ ./objects/Elements/PentaRef.cpp ++#}}} ++#Bamg sources {{{1 ++bamg_sources = ./objects/Bamg/BamgGeom.h\ ++ ./objects/Bamg/BamgGeom.cpp\ ++ ./objects/Bamg/BamgMesh.h\ ++ ./objects/Bamg/BamgMesh.cpp\ ++ ./objects/Bamg/BamgOpts.h\ ++ ./objects/Bamg/BamgOpts.cpp\ ++ ./objects/Bamg/CrackedEdge.h\ ++ ./objects/Bamg/CrackedEdge.cpp\ ++ ./objects/Bamg/Curve.h\ ++ ./objects/Bamg/Curve.cpp\ ++ ./objects/Bamg/Direction.h\ ++ ./objects/Bamg/Direction.cpp\ ++ ./objects/Bamg/DoubleAndInt.h\ ++ ./objects/Bamg/Edge.h\ ++ ./objects/Bamg/Edge.cpp\ ++ ./objects/Bamg/GeomEdge.h\ ++ ./objects/Bamg/GeomEdge.cpp\ ++ ./objects/Bamg/GeomSubDomain.h\ ++ ./objects/Bamg/GeomSubDomain.cpp\ ++ ./objects/Bamg/GeomVertex.h\ ++ ./objects/Bamg/GeomVertex.cpp\ ++ ./objects/Bamg/Geometry.cpp\ ++ ./objects/Bamg/Geometry.h\ ++ ./objects/Bamg/ListofIntersectionTriangles.cpp\ ++ ./objects/Bamg/ListofIntersectionTriangles.h\ ++ ./objects/Bamg/EigenMetric.cpp\ ++ ./objects/Bamg/Metric.cpp\ ++ ./objects/Bamg/Metric.h\ ++ ./objects/Bamg/QuadTree.cpp\ ++ ./objects/Bamg/QuadTree.h\ ++ ./objects/Bamg/R2.h\ ++ ./objects/Bamg/SetOfE4.cpp\ ++ ./objects/Bamg/SetOfE4.h\ ++ ./objects/Bamg/SubDomain.h\ ++ ./objects/Bamg/SubDomain.cpp\ ++ ./objects/Bamg/AdjacentTriangle.h\ ++ ./objects/Bamg/AdjacentTriangle.cpp\ ++ ./objects/Bamg/Triangle.cpp\ ++ ./objects/Bamg/Triangle.h\ ++ ./objects/Bamg/BamgVertex.cpp\ ++ ./objects/Bamg/BamgVertex.h\ ++ ./objects/Bamg/VertexOnEdge.h\ ++ ./objects/Bamg/VertexOnEdge.cpp\ ++ ./objects/Bamg/VertexOnGeom.h\ ++ ./objects/Bamg/VertexOnGeom.cpp\ ++ ./objects/Bamg/VertexOnVertex.h\ ++ ./objects/Bamg/VertexOnVertex.cpp\ ++ ./objects/Bamg/Mesh.cpp\ ++ ./objects/Bamg/Mesh.h\ ++ ./shared/Bamg/Abs.h \ ++ ./shared/Bamg/BigPrimeNumber.h\ ++ ./shared/Bamg/BigPrimeNumber.cpp\ ++ ./shared/Bamg/BinaryRand.h \ ++ ./shared/Bamg/det.h \ ++ ./shared/Bamg/Exchange.h \ ++ ./shared/Bamg/extrema.h \ ++ ./shared/Bamg/HeapSort.h \ ++ ./shared/Bamg/OppositeAngle.h \ ++ ./modules/Bamgx/Bamgx.cpp\ ++ ./modules/Bamgx/Bamgx.h\ ++ ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ ++ ./modules/BamgConvertMeshx/BamgConvertMeshx.h\ ++ ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ ++ ./modules/BamgTriangulatex/BamgTriangulatex.h ++#}}} ++#Kml sources {{{1 ++kml_sources = ./modules/Exp2Kmlx/Exp2Kmlx.h\ ++ ./modules/Exp2Kmlx/Exp2Kmlx.cpp\ ++ ./modules/Kml2Expx/Kml2Expx.h\ ++ ./modules/Kml2Expx/Kml2Expx.cpp\ ++ ./modules/Shp2Kmlx/Shp2Kmlx.h\ ++ ./modules/Shp2Kmlx/Shp2Kmlx.cpp\ ++ ./modules/KMLFileReadx/KMLFileReadx.h\ ++ ./modules/KMLFileReadx/KMLFileReadx.cpp\ ++ ./modules/KMLMeshWritex/KMLMeshWritex.h\ ++ ./modules/KMLMeshWritex/KMLMeshWritex.cpp\ ++ ./modules/KMLOverlayx/KMLOverlayx.h\ ++ ./modules/KMLOverlayx/KMLOverlayx.cpp\ ++ ./objects/KML/KML_Attribute.cpp\ ++ ./objects/KML/KML_Attribute.h\ ++ ./objects/KML/KML_Comment.cpp\ ++ ./objects/KML/KML_Comment.h\ ++ ./objects/KML/KML_ColorStyle.cpp\ ++ ./objects/KML/KML_ColorStyle.h\ ++ ./objects/KML/KML_Container.cpp\ ++ ./objects/KML/KML_Container.h\ ++ ./objects/KML/KML_Document.cpp\ ++ ./objects/KML/KML_Document.h\ ++ ./objects/KML/KML_Feature.cpp\ ++ ./objects/KML/KML_Feature.h\ ++ ./objects/KML/KML_File.cpp\ ++ ./objects/KML/KML_File.h\ ++ ./objects/KML/KML_Folder.cpp\ ++ ./objects/KML/KML_Folder.h\ ++ ./objects/KML/KML_Geometry.cpp\ ++ ./objects/KML/KML_Geometry.h\ ++ ./objects/KML/KML_GroundOverlay.cpp\ ++ ./objects/KML/KML_GroundOverlay.h\ ++ ./objects/KML/KML_Icon.cpp\ ++ ./objects/KML/KML_Icon.h\ ++ ./objects/KML/KML_LatLonBox.cpp\ ++ ./objects/KML/KML_LatLonBox.h\ ++ ./objects/KML/KML_LinearRing.cpp\ ++ ./objects/KML/KML_LinearRing.h\ ++ ./objects/KML/KML_LineString.cpp\ ++ ./objects/KML/KML_LineString.h\ ++ ./objects/KML/KML_LineStyle.cpp\ ++ ./objects/KML/KML_LineStyle.h\ ++ ./objects/KML/KML_MultiGeometry.cpp\ ++ ./objects/KML/KML_MultiGeometry.h\ ++ ./objects/KML/KML_Object.cpp\ ++ ./objects/KML/KML_Object.h\ ++ ./objects/KML/KML_Overlay.cpp\ ++ ./objects/KML/KML_Overlay.h\ ++ ./objects/KML/KML_Point.cpp\ ++ ./objects/KML/KML_Point.h\ ++ ./objects/KML/KML_Placemark.cpp\ ++ ./objects/KML/KML_Placemark.h\ ++ ./objects/KML/KML_Polygon.cpp\ ++ ./objects/KML/KML_Polygon.h\ ++ ./objects/KML/KML_PolyStyle.cpp\ ++ ./objects/KML/KML_PolyStyle.h\ ++ ./objects/KML/KML_Style.cpp\ ++ ./objects/KML/KML_Style.h\ ++ ./objects/KML/KML_StyleSelector.cpp\ ++ ./objects/KML/KML_StyleSelector.h\ ++ ./objects/KML/KML_SubStyle.cpp\ ++ ./objects/KML/KML_SubStyle.h\ ++ ./objects/KML/KML_Unknown.cpp\ ++ ./objects/KML/KML_Unknown.h\ ++ ./objects/KML/KMLFileReadUtils.cpp\ ++ ./objects/KML/KMLFileReadUtils.h ++#}}} ++#Matlab sources {{{1 ++matlab_sources= ./shared/Matlab/matlabshared.h\ ++ ./shared/Matlab/ModuleBoot.cpp\ ++ ./shared/Matlab/ModuleEnd.cpp\ ++ ./shared/Matlab/mxGetAssignedField.cpp\ ++ ./shared/Matlab/mxGetField.cpp\ ++ ./shared/Matlab/CheckNumMatlabArguments.cpp\ ++ ./toolkits/matlab/matlabincludes.h\ ++ ./toolkits/matlab/MatlabNArrayToNArray.cpp\ ++ ./io/Matlab/matlabio.h\ ++ ./io/Matlab/WriteMatlabData.cpp\ ++ ./io/Matlab/FetchMatlabData.cpp\ ++ ./io/Matlab/OptionParse.cpp ++#}}} ++#Serialsources {{{1 ++serial_sources= ./objects/Options/Option.cpp\ ++ ./objects/Options/Option.h\ ++ ./objects/Options/OptionDouble.cpp\ ++ ./objects/Options/OptionDouble.h\ ++ ./objects/Options/OptionLogical.cpp\ ++ ./objects/Options/OptionLogical.h\ ++ ./objects/Options/OptionChar.cpp\ ++ ./objects/Options/OptionChar.h\ ++ ./objects/Options/OptionStruct.cpp\ ++ ./objects/Options/OptionStruct.h\ ++ ./objects/Options/OptionCell.cpp\ ++ ./objects/Options/OptionCell.h\ ++ ./objects/Options/OptionUtilities.cpp\ ++ ./objects/Options/OptionUtilities.h\ ++ ./shared/Threads/issm_threads.h\ ++ ./shared/Threads/LaunchThread.cpp\ ++ ./shared/Threads/PartitionRange.cpp\ ++ ./shared/Exp/exp.h\ ++ ./shared/Exp/IsInPoly.cpp\ ++ ./shared/Exp/IsInPolySerial.cpp\ ++ ./shared/Exp/DomainOutlineRead.cpp\ ++ ./shared/Exp/DomainOutlineWrite.cpp\ ++ ./shared/TriMesh/trimesh.h\ ++ ./shared/TriMesh/AssociateSegmentToElement.cpp\ ++ ./shared/TriMesh/GridInsideHole.cpp\ ++ ./shared/TriMesh/OrderSegments.cpp\ ++ ./shared/TriMesh/SplitMeshForRifts.cpp\ ++ ./shared/TriMesh/TriMeshUtils.cpp\ ++ ./modules/AddExternalResultx/AddExternalResultx.h\ ++ ./modules/AddExternalResultx/AddExternalResultx.cpp\ ++ ./modules/Chacox/Chacox.h\ ++ ./modules/Chacox/Chacox.cpp\ ++ ./modules/Chacox/input_parse.cpp\ ++ ./modules/Chacox/chaco_seconds.cpp\ ++ ./modules/Chacox/user_params.cpp\ ++ ./modules/Dakotax/SpawnCoreSerial.cpp\ ++ ./modules/TriaSearchx/TriaSearchx.h\ ++ ./modules/TriaSearchx/TriaSearchx.cpp\ ++ ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h\ ++ ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp\ ++ ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp\ ++ ./modules/Xy2llx/Xy2llx.h\ ++ ./modules/Xy2llx/Xy2llx.cpp\ ++ ./modules/Ll2xyx/Ll2xyx.h\ ++ ./modules/Ll2xyx/Ll2xyx.cpp\ ++ ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp\ ++ ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h\ ++ ./modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp\ ++ ./modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp\ ++ ./modules/InterpFromMesh2dx/InterpFromMesh2dx.h\ ++ ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp\ ++ ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h\ ++ ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp\ ++ ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h\ ++ ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp\ ++ ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.h\ ++ ./modules/HoleFillerx/HoleFillerx.cpp\ ++ ./modules/HoleFillerx/HoleFillerx.h\ ++ ./modules/AverageFilterx/AverageFilterx.cpp\ ++ ./modules/AverageFilterx/AverageFilterx.h\ ++ ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp\ ++ ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h\ ++ ./modules/MeshProfileIntersectionx/MeshSegmentsIntersection.cpp\ ++ ./modules/MeshProfileIntersectionx/ElementSegmentsIntersection.cpp\ ++ ./modules/MeshProfileIntersectionx/ElementSegment.cpp\ ++ ./modules/MeshProfileIntersectionx/SegmentIntersect.cpp\ ++ ./modules/MeshProfileIntersectionx/NodeInElement.cpp\ ++ ./modules/ContourToMeshx/ContourToMeshx.cpp\ ++ ./modules/ContourToMeshx/ContourToMeshxt.cpp\ ++ ./modules/ContourToMeshx/ContourToMeshx.h\ ++ ./modules/ContourToNodesx/ContourToNodesx.cpp\ ++ ./modules/ContourToNodesx/ContourToNodesx.h\ ++ ./modules/Reducevectorgtosx/Reducevectorgtosx.cpp\ ++ ./modules/Reducevectorgtosx/Reducevectorgtosx.h\ ++ ./modules/NodeConnectivityx/NodeConnectivityx.cpp\ ++ ./modules/NodeConnectivityx/NodeConnectivityx.h\ ++ ./modules/ElementConnectivityx/ElementConnectivityx.cpp\ ++ ./modules/ElementConnectivityx/ElementConnectivityx.h\ ++ ./modules/Scotchx/Scotchx.cpp\ ++ ./modules/Scotchx/Scotchx.h\ ++ ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.cpp\ ++ ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.h ++#}}} ++ ++#ISSM sources are a combination of core sources and sources related to specific capabilities (which can ++#be activated by autotools conditionals ++#{{{1 ++ ++#First the core ++issm_sources = $(core_sources) ++issm_psources = ++ ++#Now the optional source ++if DAKOTA ++issm_sources += $(dakota_sources) ++issm_psources += $(dakota_psources) + endif +-#}}} +-#GroundingLine sources {{{1 ++ ++if TRANSIENT ++issm_sources += $(transient_sources) ++issm_psources += $(transient_psources) ++endif ++ ++if STEADYSTATE ++issm_sources += $(steadystate_sources) ++issm_psources += $(steadystate_psources) ++endif ++ ++if PROGNOSTIC ++issm_sources += $(prognostic_sources) ++issm_psources += $(prognostic_psources) ++endif ++ ++if THERMAL ++issm_sources += $(thermal_sources) ++issm_psources += $(thermal_psources) ++endif ++ ++if CONTROL ++issm_sources += $(control_sources) ++issm_psources += $(control_psources) ++endif ++ ++if HYDROLOGY ++issm_sources += $(hydrology_sources) ++issm_psources += $(hydrology_psources) ++endif ++ ++if DIAGNOSTIC ++issm_sources += $(diagnostic_sources) ++issm_psources += $(diagnostic_psources) ++endif ++ ++if BALANCED ++issm_sources += $(balanced_sources) ++issm_psources += $(balanced_psources) ++endif ++ ++if RESPONSES ++issm_sources += $(responses_sources) ++endif ++ ++if SLOPE ++issm_sources += $(slope_sources) ++issm_psources += $(slope_psources) ++endif ++ + if GROUNDINGLINE +-libpISSM_a_SOURCES += ./modules/GroundingLineMigrationx/GroundingLineMigrationx.cpp\ +- ./modules/GroundingLineMigrationx/GroundingLineMigrationx.h\ +- ./modules/GroundingLineMigrationx/GroundingLineMigrationxLocal.h\ +- ./modules/GroundingLineMigrationx/GroundingLineMigrationxUtils.cpp\ +- ./solutions/groundinglinemigration2d_core.cpp ++issm_sources += $(groundingline_sources) + endif +-#}}} +-#Rifts sources {{{1 ++ + if RIFTS +-libpISSM_a_SOURCES += ./objects/Loads/Riftfront.cpp\ +- ./objects/Loads/Riftfront.h\ +- ./modules/ConstraintsStatex/RiftConstraintsState.cpp ++issm_sources += $(rifts_sources) + endif +-#}}} +-#3D sources {{{1 ++ + if THREED +-libpISSM_a_SOURCES += ./objects/Gauss/GaussPenta.h\ +- ./objects/Gauss/GaussPenta.cpp\ +- ./objects/ElementResults/PentaVertexElementResult.h\ +- ./objects/ElementResults/PentaVertexElementResult.cpp\ +- ./objects/Inputs/PentaVertexInput.h\ +- ./objects/Inputs/PentaVertexInput.cpp\ +- ./objects/Elements/Penta.h\ +- ./objects/Elements/Penta.cpp\ +- ./objects/Elements/PentaHook.h\ +- ./objects/Elements/PentaHook.cpp\ +- ./objects/Elements/PentaRef.h\ +- ./objects/Elements/PentaRef.cpp ++issm_sources += $(threed_sources) + endif + #}}} + +-#ADIC2 library, for automatic differentiation {{{1 +-if ADIC2 ++#ISSM serial library {{{1 ++libISSM_a_SOURCES = $(issm_sources) ++libISSM_a_SOURCES += $(serial_sources) ++libISSM_a_SOURCES += $(bamg_sources) ++libISSM_a_SOURCES += $(kml_sources) ++libISSM_a_SOURCES += $(matlab_sources) ++ ++libISSM_a_CXXFLAGS = -fPIC -DMATLAB -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) ++if LARGEARRAYS ++libISSM_a_CXXFLAGS += -D__GCC4BUILD__ ++else ++libISSM_a_CXXFLAGS += -DMX_COMPAT_32 ++endif ++#}}} ++#ISSM parallel library {{{1 ++libpISSM_a_SOURCES = $(issm_sources) ++libpISSM_a_SOURCES += $(issm_psources) ++libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) ++#}}} ++#Overload library, to overload any non-standard symbols. {{{1 ++libOverload_a_SOURCES = ./shared/String/stricmp.c ++libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) $(CFLAGS) ++#}}} ++ ++#Executable {{{1 ++if NOPARALLEL ++bin_PROGRAMS = ++else ++bin_PROGRAMS = issm ++endif ++ ++#Standard libraries ++LDADD = ./libpISSM.a ./libOverload.a ++ ++#External packages ++LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) ++ ++issm_SOURCES = solutions/issm.cpp ++issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) ++#}}} ++ ++#Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ ++if ADIC2 ++lib_LIBRARIES += libAD.a libpISSMRose.a ++ ++#ADIC2 library, for automatic differentiation + #libAD_a_SOURCES = ./mini1.ad.c + libAD_a_SOURCES = + libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) + ++ ++ + #test rose preprocessing + %.r2cpp.cpp : %.cpp + testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< +- + libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) + libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) ++ ++ ++ + #Automatic differentiation rules: + %.ad.c: %.c + adic2 -mforward $< --nary +-endif +-#}}} +-#Executable {{{1 + +-if NOPARALLEL +-bin_PROGRAMS = +-else +-bin_PROGRAMS = issm.exe issmRose.exe +-endif + +-#Standard libraries +-LDADD = ./libOverload.a +-issm_exe_LDADD = ./libpISSM.a $(LDADD) +-if ADIC2 ++ ++#Executable ++bin_PROGRAMS += issmRose.exe + issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) +-endif +- +-#External packages +-LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(ADIC2LIB) +- +- +-issm_exe_SOURCES = solutions/issm.cpp +-issm_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) + issmRose_exe_SOURCES = solutions/issm.cpp + issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) ++LDADD += $(ADIC2LIB) + +-#}}} ++endif #}}} Index: /issm/oecreview/Archive/11648-11666/ISSM-11658-11659.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11658-11659.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11658-11659.diff (revision 11991) @@ -0,0 +1,24 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m (revision 11658) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m (revision 11659) +@@ -270,8 +270,10 @@ + if isfield(structmd,'x'), md.mesh.x=structmd.x; end + if isfield(structmd,'z'), md.mesh.z=structmd.z; end + if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end +- if isfield(structmd,'pressureload'), md.diagnostic.icefront=structmd.pressureload; end ++ if isfield(structmd,'pressureload'), md.diagnostic.icefront=structmd.pressureload; end + if isfield(structmd,'diagnostic_ref'), md.diagnostic.referential=structmd.diagnostic_ref; end ++ if isfield(structmd,'rifts'), md.rifts.riftstruct=structmd.rifts; end ++ if isfield(structmd,'riftsinfo'), md.rifts.riftproperties=structmd.riftinfo; end + + %Field changes + if (isfield(structmd,'type') & ischar(structmd.type)), +@@ -356,6 +358,7 @@ + pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502; + pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503; + end ++ + if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2, + md.thermal.stabilization=2; + md.prognostic.stabilization=1; Index: /issm/oecreview/Archive/11648-11666/ISSM-11659-11660.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11659-11660.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11659-11660.diff (revision 11991) @@ -0,0 +1,23 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11659) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11660) +@@ -814,7 +814,8 @@ + #}}} + + #ISSM sources are a combination of core sources and sources related to specific capabilities (which can +-#be activated by autotools conditionals {{{1 ++#be activated by autotools conditionals ++#{{{1 + + #First the core + issm_sources = $(core_sources) +@@ -923,7 +924,7 @@ + LDADD = ./libpISSM.a ./libOverload.a + + #External packages +-LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(ADIC2LIB) $(OSLIBS) ++LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) + + issm_SOURCES = solutions/issm.cpp + issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) Index: /issm/oecreview/Archive/11648-11666/ISSM-11660-11661.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11660-11661.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11660-11661.diff (revision 11991) @@ -0,0 +1,36 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml (revision 11660) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml (revision 11661) +@@ -1 +1 @@ +- +\ No newline at end of file ++modegroupowner +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11660) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml (revision 11661) +@@ -1 +1 @@ +- +\ No newline at end of file ++modemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodegroupmode +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml (revision 11660) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml (revision 11661) +@@ -1 +1 @@ +-issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/bin/ISSM/bininstallTo.pathincludeRootinstallFrom.pathidentifierinstallToparent02bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file ++issm.bin.pkg1.0/Users/larour/issm-uci/trunk-jpl/packagers/macosx/bin/ISSM/bininstallTo.pathparentinstallFrom.pathincludeRootidentifierinstallTo02bin-contents.xml/CVS$/\.svn$/\.cvsignore$/\.cvspass$/\.DS_Store$ +\ No newline at end of file +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml (revision 11660) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml (revision 11661) +@@ -1 +1 @@ +- +\ No newline at end of file ++modemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodemodegroupowner +\ No newline at end of file Index: /issm/oecreview/Archive/11648-11666/ISSM-11661-11662.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11661-11662.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11661-11662.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11661) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11662) +@@ -168,3 +168,6 @@ + + #cccl + CCCL_DIR="$ISSM_TIER/externalpackages/cccl/install" ++ ++#packagemaker ++PACKAGEMAKER_DIR="$ISSM_TIER/externalpackages/packagemaker/install" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11661) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11662) +@@ -232,3 +232,6 @@ + + #CCCL + export PATH="$PATH:$CCCL_DIR/bin" ++ ++#PACKAGEMAKER ++export PATH="$PATH:$PACKAGEMAKER_DIR" Index: /issm/oecreview/Archive/11648-11666/ISSM-11662-11663.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11662-11663.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11662-11663.diff (revision 11991) @@ -0,0 +1,86 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh (revision 11663) +@@ -0,0 +1,44 @@ ++#!/bin/sh ++ ++#petsc 3.2 ++#mpich 1.4 ++ ++./configure \ ++ --with-serial=no\ ++ --prefix=$ISSM_TIER \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++ --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ ++ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-adic2-dir=$ISSM_TIER/externalpackages/adic/install/ \ ++ --with-adolc-dir=$ISSM_TIER/externalpackages/adolc/install/ \ ++ --with-numthreads=8 \ ++ --without-thermal \ ++ --without-control \ ++ --without-hydrology \ ++ --without-diagnostic \ ++ --without-balanced \ ++ --without-responses \ ++ --without-slope \ ++ --without-rifts \ ++ --without-steadystate \ ++ --without-transient \ ++ --without-3d \ ++ --without-groundingline ++ ++#--without-prognostic \ ++ ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11662) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11663) +@@ -16,7 +16,7 @@ + MACHINE="macosx-gil" + + #COMPILATION CONFIGURATION FILE +-COMPILE_CONFIG_FILE="config-macosx64-mathieu.sh" ++COMPILE_CONFIG_FILE="config-macosx64-larour.sh" + + + #----------------------# +@@ -83,7 +83,7 @@ + + #number of cpus used in ISSM installation and compilation (one is usually + #safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=4 ++NUMCPUS_INSTALL=8 + + #number of cpus used in the nightly runs. + NUMCPUS_RUN=1 +@@ -93,7 +93,7 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'id',401:499" ++NROPTIONS="'id',101:151" + + #------------------------# + # 7: Matlab# Index: /issm/oecreview/Archive/11648-11666/ISSM-11663-11664.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11663-11664.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11663-11664.diff (revision 11991) @@ -0,0 +1,29 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m (revision 11663) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/model/model.m (revision 11664) +@@ -157,9 +157,11 @@ + if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end + if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end + if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end +- if isfield(structmd,'riftproperties'), +- md.rifts=rifts; ++ if isfield(structmd,'riftproperties'), %old implementation ++ md.rifts=rifts(); + md.rifts.riftproperties=structmd.riftproperties; ++ md.rifts.riftstruct=structmd.rifts; ++ md.rifts.riftproperties=structmd.riftinfo; + end + if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end + if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end +@@ -272,9 +274,8 @@ + if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end + if isfield(structmd,'pressureload'), md.diagnostic.icefront=structmd.pressureload; end + if isfield(structmd,'diagnostic_ref'), md.diagnostic.referential=structmd.diagnostic_ref; end +- if isfield(structmd,'rifts'), md.rifts.riftstruct=structmd.rifts; end +- if isfield(structmd,'riftsinfo'), md.rifts.riftproperties=structmd.riftinfo; end + ++ + %Field changes + if (isfield(structmd,'type') & ischar(structmd.type)), + if strcmpi(structmd.type,'2d'), md.mesh.dimension=2; end Index: /issm/oecreview/Archive/11648-11666/ISSM-11664-11665.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11664-11665.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11664-11665.diff (revision 11991) @@ -0,0 +1,1062 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11664) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11665) +@@ -929,3 +929,36 @@ + issm_SOURCES = solutions/issm.cpp + issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) + #}}} ++#Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ ++if ADIC2 ++lib_LIBRARIES += libAD.a libpISSMRose.a ++ ++#ADIC2 library, for automatic differentiation ++#libAD_a_SOURCES = ./mini1.ad.c ++libAD_a_SOURCES = ++libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) ++ ++ ++ ++#test rose preprocessing ++%.r2cpp.cpp : %.cpp ++ testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< ++libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) ++libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) ++ ++ ++ ++#Automatic differentiation rules: ++%.ad.c: %.c ++ adic2 -mforward $< --nary ++ ++ ++ ++#Executable ++bin_PROGRAMS += issmRose.exe ++issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) ++issmRose_exe_SOURCES = solutions/issm.cpp ++issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) ++LDADD += $(ADIC2LIB) ++ ++endif #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/softlink.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/softlink.sh (revision 11664) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/softlink.sh (revision 11665) +@@ -1,14 +0,0 @@ +-#/bin/bash +-#This script soflinks all files in trunk/src/c/ directory necessary for compilation +-#of trunk/src/ad/ +-ln -s ../c/include +-ln -s ../c/objects +-ln -s ../c/Container +-ln -s ../c/shared +-ln -s ../c/toolkits +-ln -s ../c/io +-ln -s ../c/EnumDefinitions +-ln -s ../c/modules +-ln -s ../c/solutions +-ln -s ../c/solvers +-ln -s ../c/issm.h +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/Makefile.am (revision 11664) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/Makefile.am (revision 11665) +@@ -1,965 +0,0 @@ +-INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ +-EXEEXT=$(ISSMEXT) +- +-#Library declaration {{{1 +-#Compile serial library, and then try and compile parallel library +-if NOSERIAL +-if NOPARALLEL +-lib_LIBRARIES = +-else +-lib_LIBRARIES = libpISSM.a libOverload.a +-endif +-else +-if NOPARALLEL +-lib_LIBRARIES = libISSM.a libOverload.a +-else +-lib_LIBRARIES = libISSM.a libpISSM.a libOverload.a +-endif +-endif +-#}}} +- +-#sources +-#Core sources{{{1 +-core_sources = ./include/macros.h\ +- ./include/typedefs.h\ +- ./include/types.h\ +- ./include/include.h\ +- ./objects/objects.h\ +- ./objects/Object.h\ +- ./objects/Gauss/GaussTria.h\ +- ./objects/Gauss/GaussTria.cpp\ +- ./objects/Update.h\ +- ./objects/Element.h\ +- ./objects/FemModel.h\ +- ./objects/FemModel.cpp\ +- ./objects/Material.h\ +- ./objects/Load.h\ +- ./objects/Contour.h\ +- ./objects/Contour.cpp\ +- ./objects/OptArgs.h\ +- ./objects/OptPars.h\ +- ./objects/Loads/Friction.h\ +- ./objects/Loads/Friction.cpp\ +- ./objects/Inputs/TransientInput.h\ +- ./objects/Inputs/TransientInput.cpp\ +- ./objects/Constraints/SpcTransient.cpp\ +- ./objects/Constraints/SpcTransient.h\ +- ./objects/DofIndexing.h\ +- ./objects/DofIndexing.cpp\ +- ./objects/IoModel.h\ +- ./objects/IoModel.cpp\ +- ./objects/Node.h\ +- ./objects/Node.cpp\ +- ./objects/Segment.h\ +- ./objects/Segment.cpp\ +- ./objects/Vertex.h\ +- ./objects/Vertex.cpp\ +- ./objects/Hook.h\ +- ./objects/Hook.cpp\ +- ./objects/Patch.h\ +- ./objects/Patch.cpp\ +- ./objects/ElementResults/ElementResultLocal.h\ +- ./objects/ElementResults/DoubleElementResult.h\ +- ./objects/ElementResults/DoubleElementResult.cpp\ +- ./objects/ElementResults/TriaP1ElementResult.h\ +- ./objects/ElementResults/TriaP1ElementResult.cpp\ +- ./objects/ElementResults/BoolElementResult.h\ +- ./objects/ElementResults/BoolElementResult.cpp\ +- ./objects/ExternalResults/ExternalResult.h\ +- ./objects/ExternalResults/BoolExternalResult.h\ +- ./objects/ExternalResults/BoolExternalResult.cpp\ +- ./objects/ExternalResults/DoubleExternalResult.h\ +- ./objects/ExternalResults/DoubleExternalResult.cpp\ +- ./objects/ExternalResults/DoubleVecExternalResult.h\ +- ./objects/ExternalResults/DoubleVecExternalResult.cpp\ +- ./objects/ExternalResults/DoubleMatExternalResult.h\ +- ./objects/ExternalResults/DoubleMatExternalResult.cpp\ +- ./objects/ExternalResults/IntExternalResult.h\ +- ./objects/ExternalResults/IntExternalResult.cpp\ +- ./objects/ExternalResults/StringExternalResult.h\ +- ./objects/ExternalResults/StringExternalResult.cpp\ +- ./objects/ExternalResults/PetscVecExternalResult.h\ +- ./objects/ExternalResults/PetscVecExternalResult.cpp\ +- ./objects/Elements/Tria.h\ +- ./objects/Elements/Tria.cpp\ +- ./objects/Elements/TriaHook.h\ +- ./objects/Elements/TriaHook.cpp\ +- ./objects/Elements/TriaRef.h\ +- ./objects/Elements/TriaRef.cpp\ +- ./objects/Inputs/Input.h\ +- ./objects/Inputs/InputLocal.h\ +- ./objects/Inputs/TriaP1Input.h\ +- ./objects/Inputs/TriaP1Input.cpp\ +- ./objects/Inputs/BoolInput.h\ +- ./objects/Inputs/BoolInput.cpp\ +- ./objects/Inputs/IntInput.h\ +- ./objects/Inputs/IntInput.cpp\ +- ./objects/Inputs/DoubleInput.h\ +- ./objects/Inputs/DoubleInput.cpp\ +- ./objects/Inputs/DatasetInput.h\ +- ./objects/Inputs/DatasetInput.cpp\ +- ./objects/Materials/Matice.h\ +- ./objects/Materials/Matice.cpp\ +- ./objects/Materials/Matpar.h\ +- ./objects/Materials/Matpar.cpp\ +- ./objects/Constraints/Constraint.h\ +- ./objects/Constraints/SpcStatic.cpp\ +- ./objects/Constraints/SpcStatic.h\ +- ./objects/Constraints/SpcDynamic.cpp\ +- ./objects/Constraints/SpcDynamic.h\ +- ./objects/Loads/Penpair.cpp\ +- ./objects/Loads/Penpair.h\ +- ./objects/Loads/Pengrid.cpp\ +- ./objects/Loads/Pengrid.h\ +- ./objects/Loads/Icefront.cpp\ +- ./objects/Loads/Icefront.h\ +- ./objects/Loads/Numericalflux.cpp\ +- ./objects/Loads/Numericalflux.h\ +- ./objects/Numerics/ElementMatrix.h\ +- ./objects/Numerics/ElementMatrix.cpp\ +- ./objects/Numerics/ElementVector.h\ +- ./objects/Numerics/ElementVector.cpp\ +- ./objects/Params/Param.h\ +- ./objects/Params/BoolParam.cpp\ +- ./objects/Params/BoolParam.h\ +- ./objects/Params/IntParam.cpp\ +- ./objects/Params/IntParam.h\ +- ./objects/Params/IntVecParam.cpp\ +- ./objects/Params/IntVecParam.h\ +- ./objects/Params/IntMatParam.cpp\ +- ./objects/Params/IntMatParam.h\ +- ./objects/Params/DoubleParam.cpp\ +- ./objects/Params/DoubleParam.h\ +- ./objects/Params/FileParam.cpp\ +- ./objects/Params/FileParam.h\ +- ./objects/Params/PetscMatParam.cpp\ +- ./objects/Params/PetscMatParam.h\ +- ./objects/Params/StringArrayParam.cpp\ +- ./objects/Params/StringArrayParam.h\ +- ./objects/Params/DoubleMatParam.cpp\ +- ./objects/Params/DoubleMatParam.h\ +- ./objects/Params/DoubleTransientMatParam.cpp\ +- ./objects/Params/DoubleTransientMatParam.h\ +- ./objects/Params/DoubleMatArrayParam.cpp\ +- ./objects/Params/DoubleMatArrayParam.h\ +- ./objects/Params/DoubleVecParam.cpp\ +- ./objects/Params/DoubleVecParam.h\ +- ./objects/Params/PetscVecParam.cpp\ +- ./objects/Params/PetscVecParam.h\ +- ./objects/Params/StringParam.cpp\ +- ./objects/Params/StringParam.h\ +- ./Container/Container.h\ +- ./Container/Constraints.h\ +- ./Container/Constraints.cpp\ +- ./Container/DataSet.h\ +- ./Container/DataSet.cpp\ +- ./Container/Elements.h\ +- ./Container/Elements.cpp\ +- ./Container/Inputs.h\ +- ./Container/Inputs.cpp\ +- ./Container/Loads.h\ +- ./Container/Loads.cpp\ +- ./Container/Materials.h\ +- ./Container/Materials.cpp\ +- ./Container/Nodes.h\ +- ./Container/Nodes.cpp\ +- ./Container/Options.h\ +- ./Container/Options.cpp\ +- ./Container/Parameters.h\ +- ./Container/Parameters.cpp\ +- ./Container/Results.h\ +- ./Container/Results.cpp\ +- ./Container/Vertices.h\ +- ./Container/Vertices.cpp\ +- ./shared/shared.h\ +- ./shared/Alloc/alloc.h\ +- ./shared/Alloc/alloc.cpp\ +- ./shared/Matrix/matrix.h\ +- ./shared/Matrix/MatrixUtils.cpp\ +- ./shared/Dofs/dofs.h\ +- ./shared/Dofs/dofsetgen.cpp\ +- ./shared/Numerics/numerics.h\ +- ./shared/Numerics/Verbosity.h\ +- ./shared/Numerics/Verbosity.cpp\ +- ./shared/Numerics/IsInputConverged.cpp\ +- ./shared/Numerics/GaussPoints.h\ +- ./shared/Numerics/GaussPoints.cpp\ +- ./shared/Numerics/cross.cpp\ +- ./shared/Numerics/isnan.h\ +- ./shared/Numerics/isnan.cpp\ +- ./shared/Numerics/extrema.cpp\ +- ./shared/Numerics/XZvectorsToCoordinateSystem.cpp\ +- ./shared/Numerics/UnitConversion.cpp\ +- ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ +- ./shared/Exceptions/exceptions.h\ +- ./shared/Exceptions/Exceptions.cpp\ +- ./shared/Exceptions/exprintf.cpp\ +- ./shared/Sorting/binary_search.cpp\ +- ./shared/Sorting/sorting.h\ +- ./shared/Elements/elements.h\ +- ./shared/Elements/Paterson.cpp\ +- ./shared/Elements/Arrhenius.cpp\ +- ./shared/Elements/GetVerticesCoordinates.cpp\ +- ./shared/Elements/GetLocalDofList.cpp\ +- ./shared/Elements/GetGlobalDofList.cpp\ +- ./shared/Elements/GetNumberOfDofs.cpp\ +- ./shared/String/sharedstring.h\ +- ./toolkits/petsc\ +- ./toolkits/petsc/patches\ +- ./toolkits/petsc/patches/SolverEnum.h\ +- ./toolkits/petsc/patches/petscpatches.h\ +- ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ +- ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ +- ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ +- ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ +- ./toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp\ +- ./toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp\ +- ./toolkits/petsc/patches/PetscDetermineLocalSize.cpp\ +- ./toolkits/petsc/patches/VecTranspose.cpp\ +- ./toolkits/petsc/patches/VecToMPISerial.cpp\ +- ./toolkits/petsc/patches/MatToSerial.cpp\ +- ./toolkits/petsc/patches/VecMerge.cpp\ +- ./toolkits/petsc/patches/NewVec.cpp\ +- ./toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp\ +- ./toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp\ +- ./toolkits/petsc/patches/NewMat.cpp\ +- ./toolkits/petsc/patches/SerialToVec.cpp\ +- ./toolkits/petsc/patches/VecFree.cpp\ +- ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ +- ./toolkits/petsc/patches/KSPFree.cpp\ +- ./toolkits/petsc/patches/ISFree.cpp\ +- ./toolkits/petsc/patches/MatFree.cpp\ +- ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ +- ./toolkits/petsc/patches/VecPartition.cpp\ +- ./toolkits/petsc/patches/MatPartition.cpp\ +- ./toolkits/petsc/patches/MatInvert.cpp\ +- ./toolkits/petsc/patches/MatMultPatch.cpp\ +- ./toolkits/petsc/petscincludes.h\ +- ./toolkits/mpi/mpiincludes.h\ +- ./toolkits/mpi/patches/mpipatches.h\ +- ./toolkits/mpi/patches/MPI_Upperrow.cpp\ +- ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ +- ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ +- ./toolkits/metis/metisincludes.h\ +- ./toolkits/metis/patches/metispatches.h\ +- ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ +- ./toolkits/triangle/triangleincludes.h\ +- ./toolkits.h\ +- ./io/io.h\ +- ./io/Disk/diskio.h\ +- ./io/Disk/pfopen.cpp\ +- ./io/Disk/pfclose.cpp\ +- ./io/PrintfFunction.cpp\ +- ./EnumDefinitions/EnumDefinitions.h\ +- ./modules/ModelProcessorx/ModelProcessorx.h\ +- ./modules/ModelProcessorx/ModelProcessorx.cpp\ +- ./modules/ModelProcessorx/DistributeNumDofs.cpp\ +- ./modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp\ +- ./modules/ModelProcessorx/NodesPartitioning.cpp\ +- ./modules/ModelProcessorx/SortDataSets.cpp\ +- ./modules/ModelProcessorx/UpdateCounters.cpp\ +- ./modules/ModelProcessorx/CreateDataSets.cpp\ +- ./modules/ModelProcessorx/CreateParameters.cpp\ +- ./modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp\ +- ./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\ +- ./modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp\ +- ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ +- ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ +- ./modules/NodesDofx/NodesDofx.h\ +- ./modules/NodesDofx/NodesDofx.cpp\ +- ./modules/NodalValuex/NodalValuex.h\ +- ./modules/NodalValuex/NodalValuex.cpp\ +- ./modules/VerticesDofx/VerticesDofx.h\ +- ./modules/VerticesDofx/VerticesDofx.cpp\ +- ./modules/OutputResultsx/OutputResultsx.h\ +- ./modules/OutputResultsx/OutputResultsx.cpp\ +- ./modules/InputDuplicatex/InputDuplicatex.h\ +- ./modules/InputDuplicatex/InputDuplicatex.cpp\ +- ./modules/InputScalex/InputScalex.h\ +- ./modules/InputScalex/InputScalex.cpp\ +- ./modules/SurfaceAreax/SurfaceAreax.h\ +- ./modules/SurfaceAreax/SurfaceAreax.cpp\ +- ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h\ +- ./modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp\ +- ./modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h\ +- ./modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp\ +- ./modules/IoModelToConstraintsx/IoModelToConstraintsx.h\ +- ./modules/IoModelToConstraintsx/IoModelToConstraintsx.cpp\ +- ./modules/InputUpdateFromConstantx/InputUpdateFromConstantx.h\ +- ./modules/InputUpdateFromConstantx/InputUpdateFromConstantx.cpp\ +- ./modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h\ +- ./modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp\ +- ./modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h\ +- ./modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp\ +- ./modules/GetVectorFromInputsx/GetVectorFromInputsx.h\ +- ./modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp\ +- ./modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h\ +- ./modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp\ +- ./modules/InputArtificialNoisex/InputArtificialNoisex.h\ +- ./modules/InputArtificialNoisex/InputArtificialNoisex.cpp\ +- ./modules/TimeAdaptx/TimeAdaptx.h\ +- ./modules/TimeAdaptx/TimeAdaptx.cpp\ +- ./modules/UpdateVertexPositionsx/UpdateVertexPositionsx.h\ +- ./modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp\ +- ./modules/ConfigureObjectsx/ConfigureObjectsx.h\ +- ./modules/ConfigureObjectsx/ConfigureObjectsx.cpp\ +- ./modules/ComputeBasalStressx/ComputeBasalStressx.h\ +- ./modules/ComputeBasalStressx/ComputeBasalStressx.cpp\ +- ./modules/ComputeStrainRatex/ComputeStrainRatex.h\ +- ./modules/ComputeStrainRatex/ComputeStrainRatex.cpp\ +- ./modules/SpcNodesx/SpcNodesx.h\ +- ./modules/SpcNodesx/SpcNodesx.cpp\ +- ./modules/PositiveDegreeDayx/PositiveDegreeDayx.h\ +- ./modules/PositiveDegreeDayx/PositiveDegreeDayx.cpp\ +- ./modules/UpdateConstraintsx/UpdateConstraintsx.h\ +- ./modules/UpdateConstraintsx/UpdateConstraintsx.cpp\ +- ./modules/MeshPartitionx/MeshPartitionx.cpp\ +- ./modules/MeshPartitionx/MeshPartitionx.h\ +- ./modules/Reducevectorgtofx/Reducevectorgtofx.cpp\ +- ./modules/Reducevectorgtofx/Reducevectorgtofx.h\ +- ./modules/Reduceloadx/Reduceloadx.h\ +- ./modules/Reduceloadx/Reduceloadx.cpp\ +- ./modules/EnumToStringx/EnumToStringx.cpp\ +- ./modules/EnumToStringx/EnumToStringx.h\ +- ./modules/StringToEnumx/StringToEnumx.cpp\ +- ./modules/StringToEnumx/StringToEnumx.h\ +- ./modules/SystemMatricesx/SystemMatricesx.cpp\ +- ./modules/SystemMatricesx/SystemMatricesx.h\ +- ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp\ +- ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h\ +- ./modules/ConstraintsStatex/ConstraintsStatex.cpp\ +- ./modules/ConstraintsStatex/ConstraintsStatex.h\ +- ./modules/ConstraintsStatex/ConstraintsStateLocal.h\ +- ./modules/Responsex/Responsex.h\ +- ./modules/Responsex/Responsex.cpp\ +- ./modules/RequestedOutputsx/RequestedOutputsx.h\ +- ./modules/RequestedOutputsx/RequestedOutputsx.cpp\ +- ./modules/ResetConstraintsx/ResetConstraintsx.h\ +- ./modules/ResetConstraintsx/ResetConstraintsx.cpp\ +- ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h\ +- ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ +- ./modules/Solverx/Solverx.cpp\ +- ./modules/Solverx/Solverx.h\ +- ./modules/Solverx/DofTypesToIndexSet.cpp\ +- ./modules/VecMergex/VecMergex.cpp\ +- ./modules/VecMergex/VecMergex.h\ +- ./modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp\ +- ./modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h\ +- ./modules/InputToResultx/InputToResultx.cpp\ +- ./modules/InputToResultx/InputToResultx.h\ +- ./modules/InputConvergencex/InputConvergencex.cpp\ +- ./modules/InputConvergencex/InputConvergencex.h\ +- ./solutions/convergence.cpp\ +- ./solutions/ProcessArguments.cpp\ +- ./solutions/WriteLockFile.cpp\ +- ./solutions/ResetBoundaryConditions.cpp\ +- ./solutions/AnalysisConfiguration.cpp\ +- ./solutions/CorePointerFromSolutionEnum.cpp\ +- ./solvers/solver_linear.cpp\ +- ./solvers/solver_nonlinear.cpp\ +- ./solvers/solver_newton.cpp +-#}}} +-#DAKOTA sources {{{1 +-dakota_sources = ./objects/DakotaPlugin.h\ +- ./objects/DakotaPlugin.cpp\ +- ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.h\ +- ./modules/InputUpdateFromDakotax/InputUpdateFromDakotax.cpp\ +- ./modules/DakotaResponsesx/DakotaResponsesx.h\ +- ./modules/DakotaResponsesx/DakotaResponsesx.cpp\ +- ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h\ +- ./modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp\ +- ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.h\ +- ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.cpp\ +- ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ +- ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ +- ./modules/Dakotax/Dakotax.h\ +- ./modules/Dakotax/Dakotax.cpp\ +- ./modules/Dakotax/DakotaMPI_Bcast.cpp\ +- ./modules/Dakotax/DakotaFree.cpp\ +- ./modules/Dakotax/SpawnCore.cpp\ +- ./modules/Dakotax/DescriptorIndex.cpp\ +- ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ +- ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ +- ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h +-dakota_psources= ./modules/Dakotax/SpawnCoreParallel.cpp +-#}}} +-#Transient sources {{{1 +-transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp +-transient_psources = ./solutions/transient_core.cpp +-#}}} +-#Steadystate sources {{{1 +-steadystate_psources = ./solutions/steadystate_core.cpp\ +- ./solutions/steadystateconvergence.cpp +-#}}} +-#Prognostic sources {{{1 +-prognostic_sources = ./modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp\ +- ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ +- ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ +- ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp +-prognostic_psources = ./solutions/prognostic_core.cpp +-#}}} +-#Thermal sources {{{1 +-thermal_sources = ./modules/ModelProcessorx/Thermal/UpdateElementsThermal.cpp\ +- ./modules/ModelProcessorx/Thermal/CreateNodesThermal.cpp\ +- ./modules/ModelProcessorx/Thermal/CreateConstraintsThermal.cpp\ +- ./modules/ModelProcessorx/Thermal/CreateLoadsThermal.cpp\ +- ./modules/ModelProcessorx/Enthalpy/UpdateElementsEnthalpy.cpp\ +- ./modules/ModelProcessorx/Enthalpy/CreateNodesEnthalpy.cpp\ +- ./modules/ModelProcessorx/Enthalpy/CreateConstraintsEnthalpy.cpp\ +- ./modules/ModelProcessorx/Enthalpy/CreateLoadsEnthalpy.cpp\ +- ./modules/ModelProcessorx/Melting/UpdateElementsMelting.cpp\ +- ./modules/ModelProcessorx/Melting/CreateNodesMelting.cpp\ +- ./modules/ModelProcessorx/Melting/CreateConstraintsMelting.cpp\ +- ./modules/ModelProcessorx/Melting/CreateLoadsMelting.cpp\ +- ./modules/ConstraintsStatex/ThermalConstraintsState.cpp\ +- ./modules/ConstraintsStatex/ThermalIsPresent.cpp\ +- ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp +- +-thermal_psources = ./solutions/thermal_core.cpp\ +- ./solutions/thermal_core_step.cpp\ +- ./solutions/enthalpy_core.cpp\ +- ./solutions/enthalpy_core_step.cpp\ +- ./solvers/solver_thermal_nonlinear.cpp +-#}}} +-#Control sources {{{1 +-control_sources= ./modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp\ +- ./modules/ControlInputGetGradientx/ControlInputGetGradientx.h\ +- ./modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp\ +- ./modules/ControlInputSetGradientx/ControlInputSetGradientx.h\ +- ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.cpp\ +- ./modules/ControlInputScaleGradientx/ControlInputScaleGradientx.h\ +- ./modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp\ +- ./modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h\ +- ./modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp\ +- ./modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h\ +- ./modules/ModelProcessorx/Control/CreateParametersControl.cpp\ +- ./modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp\ +- ./modules/InputControlUpdatex/InputControlUpdatex.h\ +- ./modules/InputControlUpdatex/InputControlUpdatex.cpp\ +- ./modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.h\ +- ./modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp\ +- ./modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.h\ +- ./modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp\ +- ./modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.h\ +- ./modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp\ +- ./modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.h\ +- ./modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp\ +- ./modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.h\ +- ./modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp\ +- ./modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.h\ +- ./modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp\ +- ./modules/CostFunctionx/CostFunctionx.h\ +- ./modules/CostFunctionx/CostFunctionx.cpp\ +- ./modules/Orthx/Orthx.h\ +- ./modules/Orthx/Orthx.cpp\ +- ./modules/Gradjx/Gradjx.h\ +- ./modules/Gradjx/Gradjx.cpp\ +- ./modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp\ +- ./modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.h\ +- ./modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp\ +- ./modules/ThicknessAbsGradientx/ThicknessAbsGradientx.h\ +- ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.cpp\ +- ./modules/RheologyBbarAbsGradientx/RheologyBbarAbsGradientx.h\ +- ./objects/Inputs/ControlInput.h\ +- ./objects/Inputs/ControlInput.cpp\ +- ./shared/Numerics/BrentSearch.cpp\ +- ./shared/Numerics/OptimalSearch.cpp\ +- ./shared/Numerics/OptFunc.cpp +- +-control_psources=./solutions/control_core.cpp\ +- ./solutions/controltao_core.cpp\ +- ./solutions/controlrestart.cpp\ +- ./solutions/controlconvergence.cpp\ +- ./solutions/objectivefunctionC.cpp\ +- ./solutions/gradient_core.cpp\ +- ./solutions/adjointdiagnostic_core.cpp\ +- ./solutions/adjointbalancethickness_core.cpp\ +- ./solutions/AdjointCorePointerFromSolutionEnum.cpp\ +- ./solvers/solver_adjoint_linear.cpp +- +-#}}} +-#Hydrology sources {{{1 +-hydrology_sources = ./modules/ModelProcessorx/Hydrology/UpdateElementsHydrology.cpp\ +- ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ +- ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ +- ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp +- +-hydrology_psources = ./solutions/hydrology_core.cpp\ +- ./solutions/hydrology_core_step.cpp +-#}}} +-#Diagnostic sources {{{1 +-diagnostic_sources = ./modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp\ +- ./modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp \ +- ./modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp \ +- ./modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp\ +- ./modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp\ +- ./modules/ModelProcessorx/DiagnosticVert/CreateNodesDiagnosticVert.cpp \ +- ./modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp \ +- ./modules/ModelProcessorx/DiagnosticVert/CreateLoadsDiagnosticVert.cpp\ +- ./modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp\ +- ./modules/ModelProcessorx/DiagnosticHutter/CreateNodesDiagnosticHutter.cpp \ +- ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ +- ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ +- ./shared/Elements/CoordinateSystemTransform.cpp\ +- ./shared/Elements/TransformLoadVectorCoord.cpp \ +- ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ +- ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ +- ./shared/Elements/TransformSolutionCoord.cpp +-diagnostic_psources =./solutions/diagnostic_core.cpp\ +- ./solvers/solver_stokescoupling_nonlinear.cpp +-#}}} +-#Balanced sources {{{1 +-balanced_sources = ./modules/ModelProcessorx/Balancethickness/UpdateElementsBalancethickness.cpp\ +- ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ +- ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ +- ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp +-balanced_psources = ./solutions/balancethickness_core.cpp +-#}}} +-#Responses sources {{{1 +-responses_sources = ./modules/MinVelx/MinVelx.h\ +- ./modules/MinVelx/MinVelx.cpp\ +- ./modules/MaxVelx/MaxVelx.h\ +- ./modules/MaxVelx/MaxVelx.cpp\ +- ./modules/MaxAbsVxx/MaxAbsVxx.h\ +- ./modules/MaxAbsVxx/MaxAbsVxx.cpp\ +- ./modules/MaxAbsVyx/MaxAbsVyx.h\ +- ./modules/MaxAbsVyx/MaxAbsVyx.cpp\ +- ./modules/MaxAbsVzx/MaxAbsVzx.h\ +- ./modules/MaxAbsVzx/MaxAbsVzx.cpp\ +- ./modules/MaxVxx/MaxVxx.h\ +- ./modules/MaxVxx/MaxVxx.cpp\ +- ./modules/MaxVyx/MaxVyx.h\ +- ./modules/MaxVyx/MaxVyx.cpp\ +- ./modules/MaxVzx/MaxVzx.h\ +- ./modules/MaxVzx/MaxVzx.cpp\ +- ./modules/MinVxx/MinVxx.h\ +- ./modules/MinVxx/MinVxx.cpp\ +- ./modules/MinVyx/MinVyx.h\ +- ./modules/MinVyx/MinVyx.cpp\ +- ./modules/MinVzx/MinVzx.h\ +- ./modules/MinVzx/MinVzx.cpp\ +- ./modules/IceVolumex/IceVolumex.h\ +- ./modules/IceVolumex/IceVolumex.cpp\ +- ./modules/ElementResponsex/ElementResponsex.h\ +- ./modules/ElementResponsex/ElementResponsex.cpp\ +- ./modules/MassFluxx/MassFluxx.cpp\ +- ./modules/MassFluxx/MassFluxx.h +-#}}} +-#Slope sources {{{1 +-slope_sources = ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ +- ./modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp \ +- ./modules/ModelProcessorx/BedSlope/CreateConstraintsBedSlope.cpp\ +- ./modules/ModelProcessorx/BedSlope/CreateLoadsBedSlope.cpp\ +- ./modules/ModelProcessorx/SurfaceSlope/UpdateElementsSurfaceSlope.cpp\ +- ./modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp \ +- ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\ +- ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp +-slope_psources = ./solutions/surfaceslope_core.cpp\ +- ./solutions/bedslope_core.cpp +-#}}} +-#Groundingline sources {{{1 +-groundingline_sources= ./modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp\ +- ./modules/GroundinglineMigrationx/GroundinglineMigrationx.h +-#}}} +-#Rifts sources {{{1 +-rifts_sources = ./objects/Loads/Riftfront.cpp\ +- ./objects/Loads/Riftfront.h\ +- ./modules/ConstraintsStatex/RiftConstraintsState.cpp +-#}}} +-#3D sources {{{1 +-threed_sources = ./objects/Gauss/GaussPenta.h\ +- ./objects/Gauss/GaussPenta.cpp\ +- ./objects/ElementResults/PentaP1ElementResult.h\ +- ./objects/ElementResults/PentaP1ElementResult.cpp\ +- ./objects/Inputs/PentaP1Input.h\ +- ./objects/Inputs/PentaP1Input.cpp\ +- ./objects/Elements/Penta.h\ +- ./objects/Elements/Penta.cpp\ +- ./objects/Elements/PentaHook.h\ +- ./objects/Elements/PentaHook.cpp\ +- ./objects/Elements/PentaRef.h\ +- ./objects/Elements/PentaRef.cpp +-#}}} +-#Bamg sources {{{1 +-bamg_sources = ./objects/Bamg/BamgGeom.h\ +- ./objects/Bamg/BamgGeom.cpp\ +- ./objects/Bamg/BamgMesh.h\ +- ./objects/Bamg/BamgMesh.cpp\ +- ./objects/Bamg/BamgOpts.h\ +- ./objects/Bamg/BamgOpts.cpp\ +- ./objects/Bamg/CrackedEdge.h\ +- ./objects/Bamg/CrackedEdge.cpp\ +- ./objects/Bamg/Curve.h\ +- ./objects/Bamg/Curve.cpp\ +- ./objects/Bamg/Direction.h\ +- ./objects/Bamg/Direction.cpp\ +- ./objects/Bamg/DoubleAndInt.h\ +- ./objects/Bamg/Edge.h\ +- ./objects/Bamg/Edge.cpp\ +- ./objects/Bamg/GeomEdge.h\ +- ./objects/Bamg/GeomEdge.cpp\ +- ./objects/Bamg/GeomSubDomain.h\ +- ./objects/Bamg/GeomSubDomain.cpp\ +- ./objects/Bamg/GeomVertex.h\ +- ./objects/Bamg/GeomVertex.cpp\ +- ./objects/Bamg/Geometry.cpp\ +- ./objects/Bamg/Geometry.h\ +- ./objects/Bamg/ListofIntersectionTriangles.cpp\ +- ./objects/Bamg/ListofIntersectionTriangles.h\ +- ./objects/Bamg/EigenMetric.cpp\ +- ./objects/Bamg/Metric.cpp\ +- ./objects/Bamg/Metric.h\ +- ./objects/Bamg/QuadTree.cpp\ +- ./objects/Bamg/QuadTree.h\ +- ./objects/Bamg/R2.h\ +- ./objects/Bamg/SetOfE4.cpp\ +- ./objects/Bamg/SetOfE4.h\ +- ./objects/Bamg/SubDomain.h\ +- ./objects/Bamg/SubDomain.cpp\ +- ./objects/Bamg/AdjacentTriangle.h\ +- ./objects/Bamg/AdjacentTriangle.cpp\ +- ./objects/Bamg/Triangle.cpp\ +- ./objects/Bamg/Triangle.h\ +- ./objects/Bamg/BamgVertex.cpp\ +- ./objects/Bamg/BamgVertex.h\ +- ./objects/Bamg/VertexOnEdge.h\ +- ./objects/Bamg/VertexOnEdge.cpp\ +- ./objects/Bamg/VertexOnGeom.h\ +- ./objects/Bamg/VertexOnGeom.cpp\ +- ./objects/Bamg/VertexOnVertex.h\ +- ./objects/Bamg/VertexOnVertex.cpp\ +- ./objects/Bamg/Mesh.cpp\ +- ./objects/Bamg/Mesh.h\ +- ./shared/Bamg/Abs.h \ +- ./shared/Bamg/BigPrimeNumber.h\ +- ./shared/Bamg/BigPrimeNumber.cpp\ +- ./shared/Bamg/BinaryRand.h \ +- ./shared/Bamg/det.h \ +- ./shared/Bamg/Exchange.h \ +- ./shared/Bamg/extrema.h \ +- ./shared/Bamg/HeapSort.h \ +- ./shared/Bamg/OppositeAngle.h \ +- ./modules/Bamgx/Bamgx.cpp\ +- ./modules/Bamgx/Bamgx.h\ +- ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ +- ./modules/BamgConvertMeshx/BamgConvertMeshx.h\ +- ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ +- ./modules/BamgTriangulatex/BamgTriangulatex.h +-#}}} +-#Kml sources {{{1 +-kml_sources = ./modules/Exp2Kmlx/Exp2Kmlx.h\ +- ./modules/Exp2Kmlx/Exp2Kmlx.cpp\ +- ./modules/Kml2Expx/Kml2Expx.h\ +- ./modules/Kml2Expx/Kml2Expx.cpp\ +- ./modules/Shp2Kmlx/Shp2Kmlx.h\ +- ./modules/Shp2Kmlx/Shp2Kmlx.cpp\ +- ./modules/KMLFileReadx/KMLFileReadx.h\ +- ./modules/KMLFileReadx/KMLFileReadx.cpp\ +- ./modules/KMLMeshWritex/KMLMeshWritex.h\ +- ./modules/KMLMeshWritex/KMLMeshWritex.cpp\ +- ./modules/KMLOverlayx/KMLOverlayx.h\ +- ./modules/KMLOverlayx/KMLOverlayx.cpp\ +- ./objects/KML/KML_Attribute.cpp\ +- ./objects/KML/KML_Attribute.h\ +- ./objects/KML/KML_Comment.cpp\ +- ./objects/KML/KML_Comment.h\ +- ./objects/KML/KML_ColorStyle.cpp\ +- ./objects/KML/KML_ColorStyle.h\ +- ./objects/KML/KML_Container.cpp\ +- ./objects/KML/KML_Container.h\ +- ./objects/KML/KML_Document.cpp\ +- ./objects/KML/KML_Document.h\ +- ./objects/KML/KML_Feature.cpp\ +- ./objects/KML/KML_Feature.h\ +- ./objects/KML/KML_File.cpp\ +- ./objects/KML/KML_File.h\ +- ./objects/KML/KML_Folder.cpp\ +- ./objects/KML/KML_Folder.h\ +- ./objects/KML/KML_Geometry.cpp\ +- ./objects/KML/KML_Geometry.h\ +- ./objects/KML/KML_GroundOverlay.cpp\ +- ./objects/KML/KML_GroundOverlay.h\ +- ./objects/KML/KML_Icon.cpp\ +- ./objects/KML/KML_Icon.h\ +- ./objects/KML/KML_LatLonBox.cpp\ +- ./objects/KML/KML_LatLonBox.h\ +- ./objects/KML/KML_LinearRing.cpp\ +- ./objects/KML/KML_LinearRing.h\ +- ./objects/KML/KML_LineString.cpp\ +- ./objects/KML/KML_LineString.h\ +- ./objects/KML/KML_LineStyle.cpp\ +- ./objects/KML/KML_LineStyle.h\ +- ./objects/KML/KML_MultiGeometry.cpp\ +- ./objects/KML/KML_MultiGeometry.h\ +- ./objects/KML/KML_Object.cpp\ +- ./objects/KML/KML_Object.h\ +- ./objects/KML/KML_Overlay.cpp\ +- ./objects/KML/KML_Overlay.h\ +- ./objects/KML/KML_Point.cpp\ +- ./objects/KML/KML_Point.h\ +- ./objects/KML/KML_Placemark.cpp\ +- ./objects/KML/KML_Placemark.h\ +- ./objects/KML/KML_Polygon.cpp\ +- ./objects/KML/KML_Polygon.h\ +- ./objects/KML/KML_PolyStyle.cpp\ +- ./objects/KML/KML_PolyStyle.h\ +- ./objects/KML/KML_Style.cpp\ +- ./objects/KML/KML_Style.h\ +- ./objects/KML/KML_StyleSelector.cpp\ +- ./objects/KML/KML_StyleSelector.h\ +- ./objects/KML/KML_SubStyle.cpp\ +- ./objects/KML/KML_SubStyle.h\ +- ./objects/KML/KML_Unknown.cpp\ +- ./objects/KML/KML_Unknown.h\ +- ./objects/KML/KMLFileReadUtils.cpp\ +- ./objects/KML/KMLFileReadUtils.h +-#}}} +-#Matlab sources {{{1 +-matlab_sources= ./shared/Matlab/matlabshared.h\ +- ./shared/Matlab/ModuleBoot.cpp\ +- ./shared/Matlab/ModuleEnd.cpp\ +- ./shared/Matlab/mxGetAssignedField.cpp\ +- ./shared/Matlab/mxGetField.cpp\ +- ./shared/Matlab/CheckNumMatlabArguments.cpp\ +- ./toolkits/matlab/matlabincludes.h\ +- ./toolkits/matlab/MatlabNArrayToNArray.cpp\ +- ./io/Matlab/matlabio.h\ +- ./io/Matlab/WriteMatlabData.cpp\ +- ./io/Matlab/FetchMatlabData.cpp\ +- ./io/Matlab/OptionParse.cpp +-#}}} +-#Serialsources {{{1 +-serial_sources= ./objects/Options/Option.cpp\ +- ./objects/Options/Option.h\ +- ./objects/Options/OptionDouble.cpp\ +- ./objects/Options/OptionDouble.h\ +- ./objects/Options/OptionLogical.cpp\ +- ./objects/Options/OptionLogical.h\ +- ./objects/Options/OptionChar.cpp\ +- ./objects/Options/OptionChar.h\ +- ./objects/Options/OptionStruct.cpp\ +- ./objects/Options/OptionStruct.h\ +- ./objects/Options/OptionCell.cpp\ +- ./objects/Options/OptionCell.h\ +- ./objects/Options/OptionUtilities.cpp\ +- ./objects/Options/OptionUtilities.h\ +- ./shared/Threads/issm_threads.h\ +- ./shared/Threads/LaunchThread.cpp\ +- ./shared/Threads/PartitionRange.cpp\ +- ./shared/Exp/exp.h\ +- ./shared/Exp/IsInPoly.cpp\ +- ./shared/Exp/IsInPolySerial.cpp\ +- ./shared/Exp/DomainOutlineRead.cpp\ +- ./shared/Exp/DomainOutlineWrite.cpp\ +- ./shared/TriMesh/trimesh.h\ +- ./shared/TriMesh/AssociateSegmentToElement.cpp\ +- ./shared/TriMesh/GridInsideHole.cpp\ +- ./shared/TriMesh/OrderSegments.cpp\ +- ./shared/TriMesh/SplitMeshForRifts.cpp\ +- ./shared/TriMesh/TriMeshUtils.cpp\ +- ./modules/AddExternalResultx/AddExternalResultx.h\ +- ./modules/AddExternalResultx/AddExternalResultx.cpp\ +- ./modules/Chacox/Chacox.h\ +- ./modules/Chacox/Chacox.cpp\ +- ./modules/Chacox/input_parse.cpp\ +- ./modules/Chacox/chaco_seconds.cpp\ +- ./modules/Chacox/user_params.cpp\ +- ./modules/Dakotax/SpawnCoreSerial.cpp\ +- ./modules/TriaSearchx/TriaSearchx.h\ +- ./modules/TriaSearchx/TriaSearchx.cpp\ +- ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h\ +- ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp\ +- ./modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp\ +- ./modules/Xy2llx/Xy2llx.h\ +- ./modules/Xy2llx/Xy2llx.cpp\ +- ./modules/Ll2xyx/Ll2xyx.h\ +- ./modules/Ll2xyx/Ll2xyx.cpp\ +- ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp\ +- ./modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h\ +- ./modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp\ +- ./modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp\ +- ./modules/InterpFromMesh2dx/InterpFromMesh2dx.h\ +- ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp\ +- ./modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h\ +- ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp\ +- ./modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h\ +- ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.cpp\ +- ./modules/InterpFromMeshToGridx/InterpFromMeshToGridx.h\ +- ./modules/HoleFillerx/HoleFillerx.cpp\ +- ./modules/HoleFillerx/HoleFillerx.h\ +- ./modules/AverageFilterx/AverageFilterx.cpp\ +- ./modules/AverageFilterx/AverageFilterx.h\ +- ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.cpp\ +- ./modules/MeshProfileIntersectionx/MeshProfileIntersectionx.h\ +- ./modules/MeshProfileIntersectionx/MeshSegmentsIntersection.cpp\ +- ./modules/MeshProfileIntersectionx/ElementSegmentsIntersection.cpp\ +- ./modules/MeshProfileIntersectionx/ElementSegment.cpp\ +- ./modules/MeshProfileIntersectionx/SegmentIntersect.cpp\ +- ./modules/MeshProfileIntersectionx/NodeInElement.cpp\ +- ./modules/ContourToMeshx/ContourToMeshx.cpp\ +- ./modules/ContourToMeshx/ContourToMeshxt.cpp\ +- ./modules/ContourToMeshx/ContourToMeshx.h\ +- ./modules/ContourToNodesx/ContourToNodesx.cpp\ +- ./modules/ContourToNodesx/ContourToNodesx.h\ +- ./modules/Reducevectorgtosx/Reducevectorgtosx.cpp\ +- ./modules/Reducevectorgtosx/Reducevectorgtosx.h\ +- ./modules/NodeConnectivityx/NodeConnectivityx.cpp\ +- ./modules/NodeConnectivityx/NodeConnectivityx.h\ +- ./modules/ElementConnectivityx/ElementConnectivityx.cpp\ +- ./modules/ElementConnectivityx/ElementConnectivityx.h\ +- ./modules/Scotchx/Scotchx.cpp\ +- ./modules/Scotchx/Scotchx.h\ +- ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.cpp\ +- ./modules/PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.h +-#}}} +- +-#ISSM sources are a combination of core sources and sources related to specific capabilities (which can +-#be activated by autotools conditionals +-#{{{1 +- +-#First the core +-issm_sources = $(core_sources) +-issm_psources = +- +-#Now the optional source +-if DAKOTA +-issm_sources += $(dakota_sources) +-issm_psources += $(dakota_psources) +-endif +- +-if TRANSIENT +-issm_sources += $(transient_sources) +-issm_psources += $(transient_psources) +-endif +- +-if STEADYSTATE +-issm_sources += $(steadystate_sources) +-issm_psources += $(steadystate_psources) +-endif +- +-if PROGNOSTIC +-issm_sources += $(prognostic_sources) +-issm_psources += $(prognostic_psources) +-endif +- +-if THERMAL +-issm_sources += $(thermal_sources) +-issm_psources += $(thermal_psources) +-endif +- +-if CONTROL +-issm_sources += $(control_sources) +-issm_psources += $(control_psources) +-endif +- +-if HYDROLOGY +-issm_sources += $(hydrology_sources) +-issm_psources += $(hydrology_psources) +-endif +- +-if DIAGNOSTIC +-issm_sources += $(diagnostic_sources) +-issm_psources += $(diagnostic_psources) +-endif +- +-if BALANCED +-issm_sources += $(balanced_sources) +-issm_psources += $(balanced_psources) +-endif +- +-if RESPONSES +-issm_sources += $(responses_sources) +-endif +- +-if SLOPE +-issm_sources += $(slope_sources) +-issm_psources += $(slope_psources) +-endif +- +-if GROUNDINGLINE +-issm_sources += $(groundingline_sources) +-endif +- +-if RIFTS +-issm_sources += $(rifts_sources) +-endif +- +-if THREED +-issm_sources += $(threed_sources) +-endif +-#}}} +- +-#ISSM serial library {{{1 +-libISSM_a_SOURCES = $(issm_sources) +-libISSM_a_SOURCES += $(serial_sources) +-libISSM_a_SOURCES += $(bamg_sources) +-libISSM_a_SOURCES += $(kml_sources) +-libISSM_a_SOURCES += $(matlab_sources) +- +-libISSM_a_CXXFLAGS = -fPIC -DMATLAB -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) +-if LARGEARRAYS +-libISSM_a_CXXFLAGS += -D__GCC4BUILD__ +-else +-libISSM_a_CXXFLAGS += -DMX_COMPAT_32 +-endif +-#}}} +-#ISSM parallel library {{{1 +-libpISSM_a_SOURCES = $(issm_sources) +-libpISSM_a_SOURCES += $(issm_psources) +-libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) +-#}}} +-#Overload library, to overload any non-standard symbols. {{{1 +-libOverload_a_SOURCES = ./shared/String/stricmp.c +-libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) $(CFLAGS) +-#}}} +- +-#Executable {{{1 +-if NOPARALLEL +-bin_PROGRAMS = +-else +-bin_PROGRAMS = issm +-endif +- +-#Standard libraries +-LDADD = ./libpISSM.a ./libOverload.a +- +-#External packages +-LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) +- +-issm_SOURCES = solutions/issm.cpp +-issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) +-#}}} +- +-#Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ +-if ADIC2 +-lib_LIBRARIES += libAD.a libpISSMRose.a +- +-#ADIC2 library, for automatic differentiation +-#libAD_a_SOURCES = ./mini1.ad.c +-libAD_a_SOURCES = +-libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) +- +- +- +-#test rose preprocessing +-%.r2cpp.cpp : %.cpp +- testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< +-libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) +-libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) +- +- +- +-#Automatic differentiation rules: +-%.ad.c: %.c +- adic2 -mforward $< --nary +- +- +- +-#Executable +-bin_PROGRAMS += issmRose.exe +-issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) +-issmRose_exe_SOURCES = solutions/issm.cpp +-issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) +-LDADD += $(ADIC2LIB) +- +-endif #}}} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/eraselinks.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/eraselinks.sh (revision 11664) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/ad/eraselinks.sh (revision 11665) +@@ -1,14 +0,0 @@ +-#/bin/bash +-#This script soflinks all files in trunk/src/c/ directory necessary for compilation +-#of trunk/src/ad/ +-rm include +-rm objects +-rm Container +-rm shared +-rm toolkits +-rm io +-rm EnumDefinitions +-rm modules +-rm solutions +-rm solvers +-rm issm.h +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am (revision 11664) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/Makefile.am (revision 11665) +@@ -1,8 +1,2 @@ + EXTRA_DIST = perl pro + SUBDIRS = c mex m +- +-if ADIC2 +-SUBDIRS += ad +-endif +- +- Index: /issm/oecreview/Archive/11648-11666/ISSM-11665-11666.diff =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-11665-11666.diff (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-11665-11666.diff (revision 11991) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 11665) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configure.ac (revision 11666) +@@ -18,7 +18,6 @@ + AC_CONFIG_FILES([Makefile + src/Makefile + src/c/Makefile +- src/ad/Makefile + src/mex/Makefile + src/m/Makefile + src/m/classes/Makefile Index: /issm/oecreview/Archive/11648-11666/ISSM-DocReview-11648-11666.tex =================================================================== --- /issm/oecreview/Archive/11648-11666/ISSM-DocReview-11648-11666.tex (revision 11991) +++ /issm/oecreview/Archive/11648-11666/ISSM-DocReview-11648-11666.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11648-11666/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11648-11666/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11648-11666/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11648-11666 Index: /issm/oecreview/Archive/11648-11666/Makefile =================================================================== --- /issm/oecreview/Archive/11648-11666/Makefile (revision 11991) +++ /issm/oecreview/Archive/11648-11666/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11648-11666 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11648-11666/log.tex =================================================================== --- /issm/oecreview/Archive/11648-11666/log.tex (revision 11991) +++ /issm/oecreview/Archive/11648-11666/log.tex (revision 11991) @@ -0,0 +1,36 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11648-11649.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/matlab/install-macosx-feras.sh \\ Export determination: 6. \\Rationale: Added generic Mac softlink for Matlab +M /issm/trunk-jpl/externalpackages/matlab/install.sh Added generic Matlab link for Mac (OSX) \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11649-11650.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/matlab/install.sh \\ Export determination: 6. \\Rationale: Added generic Matlab link for Mac (OSX) +M /issm/trunk-jpl/src/m/model/mesh/bamg.m fixed typo \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11650-11651.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/bamg.m \\ Export determination: 6. \\Rationale: fixed typo +M /issm/trunk-jpl/src/m/model/mesh/bamg.m fixed typo \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11651-11652.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/bamg.m \\ Export determination: 6. \\Rationale: fixed typo +M /issm/trunk-jpl/src/m/model/mesh/bamg.m fixed white space...will change back if you don't like it \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11652-11653.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/mesh/bamg.m \\ Export determination: 6. \\Rationale: fixed white space...will change back if you don't like it +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel remove crashing dakota tests \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11653-11654.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel \\ Export determination: 6. \\Rationale: remove crashing dakota tests +A /issm/trunk-jpl/cron/configs/macosx64\_schlegel\_daily remove crashing dakota tests \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11654-11655.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/macosx64\_schlegel\_daily \\ Export determination: 6. \\Rationale: remove crashing dakota tests +M /issm/trunk-jpl/cron/configs/macosx64\_schlegel M /issm/trunk-jpl/cron/configs/macosx64\_schlegel\_daily remove more dakota tests \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11655-11656.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_schlegel M /issm/trunk-jpl/cron/configs/macosx64\_schlegel\_daily \\ Export determination: 6. \\Rationale: remove more dakota tests +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.cpp M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.h M /issm/trunk-jpl/src/c/shared/Elements/elements.h updated compilation flag definition for ADIC \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11656-11657.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.cpp M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.h M /issm/trunk-jpl/src/c/shared/Elements/elements.h \\ Export determination: 6. \\Rationale: updated compilation flag definition for ADIC +M /issm/trunk-jpl/src/m/utils/Exp/manipulation M /issm/trunk-jpl/src/m/utils/Exp/readwrite Ignore Makefile \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11657-11658.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/utils/Exp/manipulation M /issm/trunk-jpl/src/m/utils/Exp/readwrite \\ Export determination: 6. \\Rationale: Ignore Makefile +M /issm/trunk-jpl/src/ad/Makefile.am Update of Makefile.am to match src/c/Makefile.am \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11658-11659.diff: \\ Function name: \\M /issm/trunk-jpl/src/ad/Makefile.am \\ Export determination: 6. \\Rationale: Update of Makefile.am to match src/c/Makefile.am +M /issm/trunk-jpl/src/m/classes/model/model.m Updated loading of old models that include rifts \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11659-11660.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/model/model.m \\ Export determination: 6. \\Rationale: Updated loading of old models that include rifts +M /issm/trunk-jpl/src/c/Makefile.am Minor comment \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11660-11661.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am \\ Export determination: 6. \\Rationale: Minor comment +M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml Some tweaking of permissions, not done yet \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11661-11662.diff: \\ Function name: \\M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/01issm-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin-contents.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/02bin.xml M /issm/trunk-jpl/packagers/macosx/ISSM.pmdoc/03test-contents.xml \\ Export determination: 6. \\Rationale: Some tweaking of permissions, not done yet +M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh Added PackageMaker \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11662-11663.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh \\ Export determination: 6. \\Rationale: Added PackageMaker +A /issm/trunk-jpl/configs/config-macosx64-larour-ad.sh M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation Added new configuration file + new validation test configuration file \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11663-11664.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-macosx64-larour-ad.sh M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation \\ Export determination: 6. \\Rationale: Added new configuration file + new validation test configuration file +M /issm/trunk-jpl/src/m/classes/model/model.m better recovery process \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11664-11665.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/model/model.m \\ Export determination: 6. \\Rationale: better recovery process +M /issm/trunk-jpl/src/Makefile.am D /issm/trunk-jpl/src/ad/Makefile.am D /issm/trunk-jpl/src/ad/eraselinks.sh D /issm/trunk-jpl/src/ad/softlink.sh M /issm/trunk-jpl/src/c/Makefile.am Took out Makefile.am in ad. Now resides in the main src/c/Makefile.am, shielded by the ADIC2 conditional. \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-11665-11666.diff: \\ Function name: \\M /issm/trunk-jpl/src/Makefile.am D /issm/trunk-jpl/src/ad/Makefile.am D /issm/trunk-jpl/src/ad/eraselinks.sh D /issm/trunk-jpl/src/ad/softlink.sh M /issm/trunk-jpl/src/c/Makefile.am \\ Export determination: 6. \\Rationale: Took out Makefile.am in ad. Now resides in the main src/c/Makefile.am, shielded by the ADIC2 conditional. +M /issm/trunk-jpl/configure.ac Took out ad/Makefile.am in configure.ac \\\\ Index: /issm/oecreview/Archive/11648-11666/r1.tex =================================================================== --- /issm/oecreview/Archive/11648-11666/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11648-11666/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11648 Index: /issm/oecreview/Archive/11648-11666/r2.tex =================================================================== --- /issm/oecreview/Archive/11648-11666/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11648-11666/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11666 Index: /issm/oecreview/Archive/11666-11680/Date.tex =================================================================== --- /issm/oecreview/Archive/11666-11680/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11666-11680/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11666-11680/ISSM-11666-11667.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11666-11667.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11666-11667.diff (revision 11991) @@ -0,0 +1,660 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad (revision 11667) +@@ -0,0 +1,98 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/Users/cborstad/issmuci" ++ISSM_TIER="/Users/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="macosx-gnu" ++ ++#Machine configuration ++MACHINE="macosx-gil" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-macosx64-chris.sh" ++ ++#MATLAB path ++MATLAB_PATH="/Applications/MATLAB_R2011b.app/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/Users/cborstad/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/Users/cborstad/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="cborstad@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=4 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="'exclude',[137 425:434 527]" ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_nightly +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_nightly (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_nightly (revision 11667) +@@ -0,0 +1,100 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" ++ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" ++#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" ++ ++#ISSM Architecture ++ISSM_ARCH="linux-gnu-amd64" ++ ++#Machine configuration ++MACHINE="astrid" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="cborstad@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=7 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="" ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_nightly +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_validation (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_validation (revision 11667) +@@ -0,0 +1,99 @@ ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" ++ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" ++#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" ++ ++#ISSM Architecture ++ISSM_ARCH="linux-gnu-amd64" ++ ++#Machine configuration ++MACHINE="astrid" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco yams" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="cborstad@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=7 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="'benchmark','all'" ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_validation +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad_daily (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad_daily (revision 11667) +@@ -0,0 +1,98 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/Users/cborstad/issmuci" ++ISSM_TIER="/Users/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" ++ ++#ISSM Architecture ++ISSM_ARCH="macosx-gnu" ++ ++#Machine configuration ++MACHINE="macosx-gil" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-macosx64-nicole.sh" ++ ++#MATLAB path ++MATLAB_PATH="/Applications/MATLAB_R2011b.app/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="update" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/Users/cborstad/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="none" ++EXTERNALPACKAGESDIR="/Users/cborstad/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.4-macosx64.sh install-3.2-macosx64.sh install-4.0-macosx64.sh install-macosx64.sh install-macosx64.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="cborstad@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=4 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=4 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="'exclude',[137 425:434 527]" ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_borstad_daily +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_daily +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_daily (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_daily (revision 11667) +@@ -0,0 +1,100 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full paths) ++ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" ++ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk-jpl" ++#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" ++ ++#ISSM Architecture ++ISSM_ARCH="linux-gnu-amd64" ++ ++#Machine configuration ++MACHINE="astrid" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="update" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk-jpl" ++#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="none" ++EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="cborstad@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=8 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=7 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="" ++ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_daily +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_ucitrunk +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_ucitrunk (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_ucitrunk (revision 11667) +@@ -0,0 +1,99 @@ ++# ++########### Configuration file for Mathieu Morlighem's nightly run on Linux ############ ++ ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#ISSM main directory (full path) ++ISSM_DIR="/u/astrid-r1b/cborstad/issmuci" ++ISSM_TIER="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/cron/trunk" ++#ISSM_TIER="/u/astrid-r1b/seroussi/svn/issm/trunk/cron/issm2.2" ++ ++#ISSM Architecture ++ISSM_ARCH="linux-gnu-amd64" ++ ++#Machine configuration ++MACHINE="astrid" ++ ++#COMPILATION CONFIGURATION FILE ++COMPILE_CONFIG_FILE="config-linux64-astrid.sh" ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/pkgs/matlab-7.6/" ++ ++#----------------------# ++# 2: ISSM Installation # ++#----------------------# ++ ++#ISSM_INSTALLATION can have 3 values: ++# - "checkout" the existing version of the code will be erased and ++# the latest version will be checked out ++# - "update" the directory won't be erased but ISSM will be updated ++# ->skip to section 3 ++# - "none" leave ISSM as is in its directory ++# ->skip to section 3 ++ISSM_INSTALLATION="checkout" ++ ++#SVN repository ++REPOSITORY="https://issm.ess.uci.edu/svn/issm/issm/trunk" ++#REPOSITORY="http://s383-rhat/issm/svn/issm/branches/issm2.2" ++ ++#execution path used for parallel runs ++EXECUTION_PATH="/u/astrid-r1b/cborstad/ExecutionNightlyRun" ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#ISSM_EXTERNALPACKAGES can have 3 values: ++# - "install" install all external packages listed below ++# - "copy" copy existing directories (EXTERNALPACKAGESDIR) ++# - "none" leave external packages as is ++# ->skip to section 4 ++ISSM_EXTERNALPACKAGES="install" ++EXTERNALPACKAGESDIR="/u/astrid-r1b/cborstad/issmuci/trunk-jpl/externalpackages" ++ ++#List of external pakages to be installed ++EXTERNALPACKAGES="autoconf automake matlab mpich2 petsc metis triangle dakota chaco" ++ ++#Corresponding list of installation files to use ++EXTERNALPACKAGES_CONFIGS=" install.sh install.sh install.sh install-1.0.2-linux64.sh install-3.2-linux64.sh install-4.0-linux64.sh install-linux64.sh install-linux64-astrid.sh install.sh" ++ ++#---------------------# ++# 4: ISSM Compilation # ++#---------------------# ++ ++#ISSM_COMPILATION can have 2 values: ++# - "yes" compile ISSM ++# - "no" do not compile ISSM ++ISSM_COMPILATION="yes" ++ ++#----------------------# ++# 5: Mail notification # ++#----------------------# ++ ++#Mail delivery. If SKIPMAIL="no", the html nightly run report will be ++#sent to the adresses present in $ISSM_TIER/cron/mailinglist. ++SKIPMAIL="no" ++ ++#Sender email address ++EMAIL_ADRESS="cborstad@jpl.nasa.gov" ++ ++#------------------------# ++# 6: Nightly run options # ++#------------------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=1 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=7 ++ ++#Nightly run options. The matlab routine nightlyrun.m will be called ++#as follows: nightlyrun($NROPTIONS). The options must be understandable ++#by Matlab and nightlyrun.m ++#ex: "'id',[101 102 103]" ++ ++NROPTIONS="" + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/linux64_borstad_ucitrunk +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11666-11680/ISSM-11667-11668.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11667-11668.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11667-11668.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11667) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/windows/InstallInstructions.txt (revision 11668) +@@ -73,7 +73,7 @@ + + In cygwin: + cd /cygdrive/c/ +-svn co http://issm.ess.uci.edi/svn/issm/issm ++svn co http://issm.ess.uci.edu/svn/issm/issm + + Once you download it, in your home directory, edit .bashrc: + and add the following lines: +@@ -102,7 +102,7 @@ + + If this does not work, do not go any further! The settings of your cl compiler are found + in externalpackages/windows/configs/ +-if there is a significant different between you sdk7.1.win7.64.sh file (see above section Compiler) ++if there is a significant different between your sdk7.1.win7.64.sh file (see above section Compiler) + and the file that is being sourced in the windows/configs directory, place your new file in + the configs directory. Relaunch bash, and try to run cl hello.cpp again. Beware, you might + have to erase some lines in your file, as cygwin might not like some of the stuff that your Index: /issm/oecreview/Archive/11666-11680/ISSM-11668-11669.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11668-11669.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11668-11669.diff (revision 11991) @@ -0,0 +1,39 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11668) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11669) +@@ -316,6 +316,34 @@ + fi + AC_MSG_RESULT($HAVE_SCOTCH) + dnl }}} ++ dnl adolc{{{1 ++ AC_ARG_WITH([adolc-dir], ++ AS_HELP_STRING([--with-adolc-dir = DIR], [adolc root directory.]), ++ [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) ++ AC_MSG_CHECKING(for ADOLC) ++ ++ if test "x$ADOLC_ROOT" = "xno"; then ++ HAVE_ADOLC=no ++ else ++ if test -d "$ADOLC_ROOT"; then ++ ++ dnl defaults ++ HAVE_ADOLC=yes ++ ADOLCINCL="-I$ADOLC_ROOT/include/adolc -I$ADOLC_ROOT/include" ++ ADOLCLIB="-L$ADOLC_ROOT/lib64 -ladolc" ++ ++ AC_DEFINE([_HAVE_ADOLC_],[1],[with adolc in ISSM src]) ++ AC_SUBST([ADOLCINCL]) ++ AC_SUBST([ADOLCLIB]) ++ ++ else ++ echo "Specified directory does not exist!" ++ exit 1 ++ fi ++ fi ++ AM_CONDITIONAL([ADOLC], [test x$HAVE_ADOLC = xyes]) ++ AC_MSG_RESULT($HAVE_ADOLC) ++ dnl }}} + dnl adic2{{{1 + AC_ARG_WITH([adic2-dir], + AS_HELP_STRING([--with-adic2-dir = DIR], [adic2 root directory.]), Index: /issm/oecreview/Archive/11666-11680/ISSM-11669-11670.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11669-11670.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11669-11670.diff (revision 11991) @@ -0,0 +1,681 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11669) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11670) +@@ -304,6 +304,33 @@ + *pmatrix=outmatrix; + } + /*}}}*/ ++/*FUNCTION FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){{{1*/ ++void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){ ++ ++ Matrix* outmatrix=NULL; ++ int dummy=0; ++ ++ if (mxIsClass(dataref,"double") ){ ++ ++ /*Check dataref is not pointing to NaN: */ ++ if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ ++ outmatrix=NULL; ++ } ++ else{ ++ ++ /*Convert matlab matrix to petsc matrix: */ ++ outmatrix=MatlabMatrixToMatrix(dataref); ++ } ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ ++ /*Assign output pointers:*/ ++ *pmatrix=outmatrix; ++} ++/*}}}*/ + /*FUNCTION FetchMatlabData(double** pvector,int* pM,const mxArray* dataref){{{1*/ + void FetchMatlabData(double** pvector,int* pM,const mxArray* dataref){ + +@@ -451,6 +478,30 @@ + *pvector=vector; + } + /*}}}*/ ++/*FUNCTION FetchMatlabData(Vector** pvector,const mxArray* dataref){{{1*/ ++void FetchMatlabData(Vector** pvector,const mxArray* dataref){ ++ ++ Vector* vector=NULL; ++ int dummy; ++ ++ if(mxIsEmpty(dataref)){ ++ /*Nothing to pick up. Just initialize matrix pointer to NULL: */ ++ vector=NULL; ++ } ++ else if (mxIsClass(dataref,"double") ){ ++ ++ /*Convert matlab vector to petsc vector: */ ++ vector=MatlabVectorToVector(dataref); ++ } ++ else{ ++ /*This is an error: we don't have the correct input!: */ ++ _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); ++ } ++ ++ /*Assign output pointers:*/ ++ *pvector=vector; ++} ++/*}}}*/ + /*FUNCTION FetchMatlabData(char** pstring,const mxArray* dataref){{{1*/ + void FetchMatlabData(char** pstring,const mxArray* dataref){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp (revision 11669) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp (revision 11670) +@@ -57,6 +57,23 @@ + *pdataref=dataref; + } + /*}}}*/ ++/*FUNCTION WriteMatlabData(mxArray** pdataref,Matrix* matrix){{{1*/ ++void WriteMatlabData(mxArray** pdataref,Matrix* matrix){ ++ ++ mxArray* dataref=NULL; ++ ++ if(matrix){ ++ ++ /*call toolkit routine: */ ++ dataref=matrix->ToMatlabMatrix(); ++ } ++ else{ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ } ++ ++ *pdataref=dataref; ++} ++/*}}}*/ + /*FUNCTION WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N){{{1*/ + void WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N){ + +@@ -124,6 +141,23 @@ + + } + /*}}}*/ ++/*FUNCTION WriteMatlabData(mxArray** pdataref,Vector* vector){{{1*/ ++void WriteMatlabData(mxArray** pdataref,Vector* vector){ ++ ++ mxArray* dataref=NULL; ++ ++ if(vector){ ++ ++ /*call toolkit routine: */ ++ dataref=vector->ToMatlabVector(); ++ } ++ else{ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ } ++ *pdataref=dataref; ++ ++} ++/*}}}*/ + /*FUNCTION WriteMatlabData(mxArray** pdataref,double* vector, int M){{{1*/ + void WriteMatlabData(mxArray** pdataref,double* vector, int M){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/matlabio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/matlabio.h (revision 11669) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/matlabio.h (revision 11670) +@@ -16,9 +16,11 @@ + #include + void WriteMatlabData(mxArray** pdataref,DataSet* dataset); + void WriteMatlabData(mxArray** pdataref,Mat matrix); ++void WriteMatlabData(mxArray** pdataref,Matrix* matrix); + void WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N); + void WriteMatlabData(mxArray** pdataref,int* matrix, int M,int N); + void WriteMatlabData(mxArray** pdataref,Vec vector); ++void WriteMatlabData(mxArray** pdataref,Vector* vector); + void WriteMatlabData(mxArray** pdataref,double* vector, int M); + void WriteMatlabData(mxArray** pdataref,int integer); + void WriteMatlabData(mxArray** pdataref,bool boolean); +@@ -33,11 +35,13 @@ + void FetchMatlabData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref); + void FetchMatlabData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); + void FetchMatlabData(Mat* pmatrix,const mxArray* dataref); ++void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref); + void FetchMatlabData(int** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(float** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(double** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(bool** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(Vec* pvector,const mxArray* dataref); ++void FetchMatlabData(Vector** pvector,const mxArray* dataref); + void FetchMatlabData(char** pstring,const mxArray* dataref); + void FetchMatlabData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); + void FetchMatlabData(double* pscalar,const mxArray* dataref); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp (revision 11670) +@@ -0,0 +1,36 @@ ++/* \file MatlabVectorToVector.cpp ++ * \brief: convert a sparse or dense matlab vector to a vector: ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#ifdef _SERIAL_ ++ ++/*Matlab includes: */ ++#include "mex.h" ++#include "../../objects/objects.h" ++ ++Vector* MatlabVectorToVector(const mxArray* mxvector){ ++ ++ Vector* vector=NULL; ++ ++ #ifdef _HAVE_PETSC_ ++ /*allocate vector object: */ ++ vector=new Vector(); ++ ++ /*Call Matlab to Petsc API: */ ++ MatlabVectorToPetscVector(&vector->vector,&vector->M,mxvector); ++ ++ #else ++ _error_("not supported yet!"); ++ #endif ++ ++ return vector; ++} ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h (revision 11669) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h (revision 11670) +@@ -7,9 +7,14 @@ + + #ifdef _SERIAL_ + #include ++class Matrix; ++class Vector; ++ + int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); ++Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); ++Vector* MatlabVectorToVector(const mxArray* mxvector); + #endif + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp (revision 11670) +@@ -0,0 +1,36 @@ ++/* \file MatlabMatrixToMatrix.cpp ++ * \brief: convert a sparse or dense matlab matrix to a matrix: ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#ifdef _SERIAL_ ++ ++/*Matlab includes: */ ++#include "mex.h" ++#include "../../objects/objects.h" ++ ++Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ ++ ++ Matrix* matrix=NULL; ++ ++ #ifdef _HAVE_PETSC_ ++ /*allocate matrix object: */ ++ matrix=new Matrix(); ++ ++ /*Call Matlab to Petsc API: */ ++ MatlabMatrixToPetscMatrix(&matrix->matrix,&matrix->M,&matrix->N,mxmatrix); ++ ++ #else ++ _error_("not supported yet!"); ++ #endif ++ ++ return matrix; ++} ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11669) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11670) +@@ -1,4 +1,4 @@ +-INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ ++INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ + EXEEXT=$(ISSMEXT) + + #Library declaration {{{1 +@@ -119,6 +119,10 @@ + ./objects/Numerics/ElementMatrix.cpp\ + ./objects/Numerics/ElementVector.h\ + ./objects/Numerics/ElementVector.cpp\ ++ ./objects/Numerics/Matrix.h\ ++ ./objects/Numerics/Matrix.cpp\ ++ ./objects/Numerics/Vector.h\ ++ ./objects/Numerics/Vector.cpp\ + ./objects/Params/Param.h\ + ./objects/Params/BoolParam.cpp\ + ./objects/Params/BoolParam.h\ +@@ -723,6 +727,8 @@ + ./shared/Matlab/CheckNumMatlabArguments.cpp\ + ./toolkits/matlab/matlabincludes.h\ + ./toolkits/matlab/MatlabNArrayToNArray.cpp\ ++ ./toolkits/matlab/MatlabMatrixToMatrix.cpp\ ++ ./toolkits/matlab/MatlabVectorToVector.cpp\ + ./io/Matlab/matlabio.h\ + ./io/Matlab/WriteMatlabData.cpp\ + ./io/Matlab/FetchMatlabData.cpp\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11670) +@@ -0,0 +1,103 @@ ++/*!\file Vector.cpp ++ * \brief: implementation of the Vector object ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++#include "./Vector.h" ++/*}}}*/ ++ ++/*Vector constructors and destructor*/ ++/*FUNCTION Vector::Vector(){{{1*/ ++Vector::Vector(){ ++ ++ #ifdef _HAVE_PETSC_ ++ this->vector=NULL; ++ #else ++ this->vector=NULL; ++ this->M=0; ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->avector=NULL; ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Vector::Vector(int M,bool fromlocalsize){{{1*/ ++Vector::Vector(int pM,bool fromlocalsize){ ++ ++ #ifdef _HAVE_PETSC_ ++ this->vector=NewVec(pM,fromlocalsize); ++ #else ++ this->M=pM; ++ this->vector=(double*)xcalloc(pM,sizeof(double)); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->avector=(adouble*)xmalloc(pM*sizeof(adouble)); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Vector::~Vector(){{{1*/ ++Vector::~Vector(){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecFree(&this->vector); ++ #else ++ xfree((void**)&this->vector); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ xfree((void**)&this->avector); ++ #endif ++} ++/*}}}*/ ++ ++/*Vector specific routines: */ ++/*FUNCTION Vector::Echo{{{1*/ ++void Vector::Echo(void){ ++ ++ int i; ++ ++ #ifdef _HAVE_PETSC_ ++ VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); ++ #else ++ printf("Vector size: %i\n",M); ++ for(i=0;i>?*/ ++ printf("ADOLC Vector equivalent:" ); ++ for(i=0;ivector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11670) +@@ -0,0 +1,145 @@ ++/*!\file Matrix.cpp ++ * \brief: implementation of the Matrix object ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++#include "./Matrix.h" ++/*}}}*/ ++ ++/*Matrix constructors and destructor*/ ++/*FUNCTION Matrix::Matrix(){{{1*/ ++Matrix::Matrix(){ ++ ++ this->M=0; ++ this->N=0; ++ ++ #ifdef _HAVE_PETSC_ ++ this->matrix=NULL; ++ #else ++ this->matrix=NULL; ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->amatrix=NULL; ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::Matrix(int M,int N){{{1*/ ++Matrix::Matrix(int pM,int pN){ ++ ++ this->M=pM; ++ this->N=pN; ++ ++ #ifdef _HAVE_PETSC_ ++ this->matrix=NewMat(pM,pN); ++ #else ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::Matrix(int M,int N,double sparsity){{{1*/ ++Matrix::Matrix(int pM,int pN,double sparsity){ ++ ++ this->M=pM; ++ this->N=pN; ++ ++ #ifdef _HAVE_PETSC_ ++ this->matrix=NewMat(pM,pN,sparsity); ++ #else ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::Matrix(int M,int N,int connectivity,int numberofdofspernode){{{1*/ ++Matrix::Matrix(int pM,int pN,int connectivity,int numberofdofspernode){ ++ ++ this->M=pM; ++ this->N=pN; ++ ++ #ifdef _HAVE_PETSC_ ++ this->matrix=NewMat(pM,pN,connectivity,numberofdofspernode); ++ #else ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::~Matrix(){{{1*/ ++Matrix::~Matrix(){ ++ ++ #ifdef _HAVE_PETSC_ ++ MatFree(&this->matrix); ++ #else ++ xfree((void**)&this->matrix); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ xfree((void**)&this->amatrix); ++ #endif ++} ++/*}}}*/ ++ ++/*Matrix specific routines: */ ++/*FUNCTION Matrix::Echo{{{1*/ ++void Matrix::Echo(void){ ++ ++ int i,j; ++ ++ #ifdef _HAVE_PETSC_ ++ MatView(this->matrix,PETSC_VIEWER_STDOUT_WORLD); ++ #else ++ printf("Matrix size: %i-%i\n",M,N); ++ for(i=0;i>?*/ ++ printf("ADOLC Matrix equivalent:" ); ++ for(i=0;imatrix); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11670) +@@ -0,0 +1,58 @@ ++/*!\file: Vector.h ++ * \brief wrapper to vector objects. The goal is to control which API (PETSC,Scalpack, Plapack?) ++ * implements our underlying vector format. ++ */ ++ ++#ifndef _VECTOR_H_ ++#define _VECTOR_H_ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++#include "../Object.h" ++#include "../../toolkits/toolkits.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++ ++#ifdef _HAVE_ADOLC_ ++#include "adolc.h" ++#endif ++ ++ ++#ifdef _SERIAL_ ++#include "mex.h" ++#endif ++ ++/*}}}*/ ++ ++class Vector{ ++ ++ public: ++ ++ int M; ++ ++ #ifdef _HAVE_PETSC_ ++ Vec vector; ++ #else ++ double* vector; ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ adouble* avector; ++ #endif ++ ++ /*Vector constructors, destructors {{{1*/ ++ Vector(); ++ Vector(int M,bool fromlocalsize=false); ++ ~Vector(); ++ /*}}}*/ ++ /*Vector specific routines {{{1*/ ++ void Echo(void); ++ #ifdef _SERIAL_ ++ mxArray* ToMatlabVector(void); ++ #endif ++ /*}}}*/ ++}; ++#endif //#ifndef _VECTOR_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11670) +@@ -0,0 +1,60 @@ ++/*!\file: Matrix.h ++ * \brief wrapper to matrix objects. The goal is to control which API (PETSC,Scalpack, Plapack?) ++ * implements our underlying matrix format. ++ */ ++ ++#ifndef _MATRIX_H_ ++#define _MATRIX_H_ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++#include "../Object.h" ++#include "../../toolkits/toolkits.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++ ++#ifdef _HAVE_ADOLC_ ++#include "adolc.h" ++#endif ++ ++#ifdef _SERIAL_ ++#include "mex.h" ++#endif ++ ++/*}}}*/ ++ ++class Matrix{ ++ ++ public: ++ ++ int M,N; ++ ++ #ifdef _HAVE_PETSC_ ++ Mat matrix; ++ #else ++ double* matrix; ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ adouble* amatrix; ++ #endif ++ ++ /*Matrix constructors, destructors {{{1*/ ++ Matrix(); ++ Matrix(int M,int N); ++ Matrix(int M,int N,double sparsity); ++ Matrix(int M,int N,int connectivity,int numberofdofspernode); ++ ~Matrix(); ++ /*}}}*/ ++ /*Matrix specific routines {{{1*/ ++ void Echo(void); ++ #ifdef _SERIAL_ ++ mxArray* ToMatlabMatrix(void); ++ #endif ++ /*}}}*/ ++ ++}; ++#endif //#ifndef _MATRIX_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 11669) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 11670) +@@ -119,6 +119,8 @@ + /*Numerics:*/ + #include "./Numerics/ElementMatrix.h" + #include "./Numerics/ElementVector.h" ++#include "./Numerics/Vector.h" ++#include "./Numerics/Matrix.h" + + /*Params: */ + #include "./Params/BoolParam.h" Index: /issm/oecreview/Archive/11666-11680/ISSM-11672-11673.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11672-11673.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11672-11673.diff (revision 11991) @@ -0,0 +1,164 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/install.sh (revision 11673) +@@ -0,0 +1,60 @@ ++#This installs the Android SDK (Software Development Kit) ++#which is needed for the compilation of the Java project. ++ ++step=1; ++ ++#Different steps here. ++#1: install sdk, ant and sdk tools ++#2: install an emulator. ++#3: test the emulator ++#4: cleanup ++ ++present_dir=`pwd`; ++ ++if [[ $step == "1" ]]; then ++ ++ #Cleanup the install ++ rm -rf install-sdk install-ant ++ ++ # Install Android SDK and NDK. ++ unzip -o android-sdk-r16-macosx.zip ++ unzip -o apache-ant-1.8.2-bin.zip ++ ++ #Move to install ++ mv android-sdk-macosx install-sdk ++ mv apache-ant-1.8.2 install-ant ++ ++ #Post_install configuration: ++ #We need specific settings for specific platforms, for the SDK to ++ #function properly ++ ++ #For now, we need to install: ++ #android sdk platform tools ++ #a specific android api: API 15 ++ ++ cd install-sdk/tools/ && source ./android ++fi ++ ++if [[ $step == "2" ]]; then ++ ++ #Once this is done, we need to install an emulator. Location will default to ~/.android/avd, ++ #which we will move to $ISSM_TIER/externalpackages/android-emulators. ++ #For now, it's called: Android-4.0.3 ++ ++ cd $present_dir/install-sdk/tools ++ ./android avd ++ mv ~/.android/avd/Android-4.0.3.* $ISSM_TIER/externalpackages/android-emulators ++ ++fi ++ ++ ++if [[ $step == "3" ]]; then ++ ++ cd $present_dir/install-sdk/platform-tools ++ ./adb -p "$ISSM_TIER/externalpackages/android-emulators" devices ++ ++fi ++ ++if [[ $step == "4" ]]; then ++ rm -rf install-sdk install-ant ++fi + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/apache-ant-1.8.2-bin.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/apache-ant-1.8.2-bin.zip +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/android-sdk-r16-macosx.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-sdk/android-sdk-r16-macosx.zip +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-ndk/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-ndk/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-ndk/install.sh (revision 11673) +@@ -0,0 +1,18 @@ ++#This installs the Android NDK (Native Development Kit) ++#which is needed for the compilation of C/C++ code into the ++#native architecture of the Android device. ++ ++#The android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 file was downloaded ++#from the android developer website: ++ ++#Cleanup the install ++rm -rf install ++ ++# Install Android SDK and NDK. ++cp android-ndk-r7b-darwin-x86.tar.bz2 dummy.tar.bz2 ++bunzip2 dummy.tar.bz2 ++tar -xvf dummy.tar ++rm -rf dummy.tar dummy.tar.bz2 ++ ++#Move to install ++mv android-ndk-r7b install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-ndk/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11672) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11673) +@@ -171,3 +171,12 @@ + + #packagemaker + PACKAGEMAKER_DIR="$ISSM_TIER/externalpackages/packagemaker/install" ++ ++#android-ndk ++ANDROID_NDK_DIR="$ISSM_TIER/externalpackages/android-ndk/install" ++ ++#android-sdk ++ANDROID_SDK_DIR="$ISSM_TIER/externalpackages/android-sdk/install-sdk" ++ ++#android-ant ++ANDROID_ANT_DIR="$ISSM_TIER/externalpackages/android-sdk/install-ant" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11672) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11673) +@@ -235,3 +235,12 @@ + + #PACKAGEMAKER + export PATH="$PATH:$PACKAGEMAKER_DIR" ++ ++#ANDROID_NDK: ++export PATH="$PATH:$ANDROID_NDK_DIR/" ++ ++#ANDROID_SDK ++export PATH="$PATH:$ANDROID_SDK_DIR/" ++ ++#ANDROID_ANT ++export PATH="$PATH:$ANDROID_ANT_DIR/" Index: /issm/oecreview/Archive/11666-11680/ISSM-11673-11674.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11673-11674.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11673-11674.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.m (revision 11673) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/classes/friction.m (revision 11674) +@@ -38,7 +38,7 @@ + checkfield(md,'friction.p','NaN',1,'size',[md.mesh.numberofelements 1]); + end % }}} + function disp(obj) % {{{ +- disp(sprintf('Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_ice*g*bed, r=q/p and s=1/p')); ++ disp(sprintf('Sigma= drag^2 * Neff ^r * u ^s, with Neff=rho_ice*g*thickness+rho_water*g*bed, r=q/p and s=1/p')); + fielddisplay(obj,'coefficient','friction coefficient [SI]'); + fielddisplay(obj,'p','p exponent'); + fielddisplay(obj,'q','q exponent'); Index: /issm/oecreview/Archive/11666-11680/ISSM-11674-11675.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11674-11675.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11674-11675.diff (revision 11991) @@ -0,0 +1,120 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11674) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11675) +@@ -59,8 +59,7 @@ + outmatrix_cols=0; + outmatrix=NULL; + } +- else if (mxIsClass(dataref,"double") ){ +- ++ else if(mxIsClass(dataref,"double") || mxIsClass(dataref,"single")){ + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ + outmatrix_rows=0; +@@ -68,7 +67,6 @@ + outmatrix=NULL; + } + else{ +- + /*Convert matlab matrix to double* matrix: */ + MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp (revision 11674) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp (revision 11675) +@@ -24,10 +24,9 @@ + + int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + +- int rows, cols; +- double* mxmatrix_ptr=NULL; +- int ierr; +- int i,j; ++ int i,j,count,rows,cols; ++ double *pmxdoublematrix = NULL; ++ float *pmxsinglematrix = NULL; + + /*output: */ + double* matrix=NULL; +@@ -35,25 +34,17 @@ + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; +- double* pr=NULL; +- int count; +- int nnz; +- int nz; + + /*Ok, first check if we are dealing with a sparse or full matrix: */ + if (mxIsSparse(mxmatrix)){ + + /*Dealing with sparse matrix: recover size first: */ +- mxmatrix_ptr=(double*)mxGetPr(mxmatrix); ++ pmxdoublematrix=(double*)mxGetPr(mxmatrix); + rows=mxGetM(mxmatrix); + cols=mxGetN(mxmatrix); +- nnz=mxGetNzmax(mxmatrix); +- nz=(int)((double)nnz/(double)rows); +- + matrix=(double*)xcalloc(rows*cols,sizeof(double)); + + /*Now, get ir,jc and pr: */ +- pr=mxGetPr(mxmatrix); + ir=mxGetIr(mxmatrix); + jc=mxGetJc(mxmatrix); + +@@ -61,31 +52,45 @@ + count=0; + for(i=0;iDuplicate(); Kff->MatMult(uf,KU); ++ KUF=KU->Duplicate(); KU->Copy(KUF); KUF->AYPX(pf,-1.0); + + //compute norm(KUF), norm(F) and residue +- VecNorm(KUF,NORM_2,&nKUF); +- VecNorm(pf,NORM_2,&nF); ++ nKUF=KUF->Norm(NORM_2); ++ nF=pf->Norm(NORM_2); + solver_residue=nKUF/nF; + _printf_(true,"\n%s%g\n"," solver residue: norm(KU-F)/norm(F)=",solver_residue); + + //clean up +- VecFree(&KU); +- VecFree(&KUF); ++ delete KU; ++ delete KUF; + } + + /*Force equilibrium (Mandatory)*/ + + //compute K[n]U[n-1]F = K[n]U[n-1] - F +- VecDuplicate(uf,&KUold); MatMultPatch(Kff,old_uf,KUold); +- VecDuplicate(KUold,&KUoldF);VecCopy(KUold,KUoldF); VecAYPX(KUoldF,-1.0,pf); +- VecNorm(KUoldF,NORM_2,&nKUoldF); +- VecNorm(pf,NORM_2,&nF); ++ KUold=uf->Duplicate(); Kff->MatMult(old_uf,KUold); ++ KUoldF=KUold->Duplicate();KUold->Copy(KUoldF); KUoldF->AYPX(pf,-1.0); ++ nKUoldF=KUoldF->Norm(NORM_2); ++ nF=pf->Norm(NORM_2); + res=nKUoldF/nF; + if (isnan(res)){ + _printf_(true,"norm nf = %lf and norm kuold = %lf\n",nF,nKUoldF); +@@ -75,8 +75,8 @@ + } + + //clean up +- VecFree(&KUold); +- VecFree(&KUoldF); ++ delete KUold; ++ delete KUoldF; + + //print + if(resDuplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); ++ ndu=duf->Norm(NORM_2); nu=old_uf->Norm(NORM_2); + + if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); + + //clean up +- VecFree(&duf); ++ delete duf; + + //print + if (!isnan(eps_rel)){ +@@ -118,12 +118,12 @@ + if (!isnan(eps_abs) || (VerboseConvergence())){ + + //compute max(du) +- VecDuplicate(old_uf,&duf);VecCopy(old_uf,duf); VecAYPX(duf,-1.0,uf); +- VecNorm(duf,NORM_2,&ndu); VecNorm(duf,NORM_INFINITY,&nduinf); ++ duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); ++ ndu=duf->Norm(NORM_2); nduinf=duf->Norm(NORM_INFINITY); + if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); + + //clean up +- VecFree(&duf); ++ delete duf; + + //print + if (!isnan(eps_abs)){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/solutions.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/solutions.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/solutions.h (revision 11679) +@@ -34,7 +34,7 @@ + double objectivefunctionC(double search_scalar,OptArgs* optargs); + + //convergence: +-void convergence(bool* pconverged, Mat K_ff,Vec p_f,Vec u_f,Vec u_f_old,Parameters* parameters); ++void convergence(bool* pconverged, Matrix* K_ff,Vector* p_f,Vector* u_f,Vector* u_f_old,Parameters* parameters); + bool controlconvergence(double J,double tol_cm); + bool steadystateconvergence(FemModel* femmodel); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/ResetBoundaryConditions.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/ResetBoundaryConditions.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/ResetBoundaryConditions.cpp (revision 11679) +@@ -10,7 +10,7 @@ + void ResetBoundaryConditions(FemModel* femmodel, int analysis_type){ + + /*variables: */ +- Vec yg = NULL; ++ Vector* yg = NULL; + Nodes *nodes = NULL; + int i; + +@@ -29,5 +29,5 @@ + UpdateDynamicConstraintsx(femmodel->constraints,femmodel->nodes,femmodel->parameters,yg); + + /*Free ressources:*/ +- VecFree(&yg); ++ delete yg; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.h (revision 11679) +@@ -4,10 +4,13 @@ + + #ifndef _ALLOC_H_ + #define _ALLOC_H_ +- ++class Matrix; ++class Vector; + void* xmalloc(int size); + void* xcalloc(int n,int size); + void xfree(void** pvptr); + void* xrealloc ( void* pv, int size); ++void xdelete(Matrix** pvptr); ++void xdelete(Vector** pvptr); + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11679) +@@ -28,6 +28,7 @@ + #include "./alloc.h" + #include "../Exceptions/exceptions.h" + #include "../../include/include.h" ++#include "../../objects/objects.h" + + void* xmalloc(int size){ + +@@ -79,6 +80,25 @@ + } + } + ++void xdelete( Matrix** pv){ ++ ++ if (pv && *pv) { ++ ++ delete *pv; ++ *pv=NULL; ++ } ++} ++ ++void xdelete( Vector** pv){ ++ ++ if (pv && *pv) { ++ ++ delete *pv; ++ *pv=NULL; ++ } ++} ++ ++ + void* xrealloc ( void* pv, int size){ + + register void* value=NULL; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp (revision 11679) +@@ -5,10 +5,10 @@ + + #include "./Reducevectorgtofx.h" + +-void Reducevectorgtofx(Vec* puf, Vec ug, Nodes* nodes,Parameters* parameters){ ++void Reducevectorgtofx(Vector** puf, Vector* ug, Nodes* nodes,Parameters* parameters){ + + /*output: */ +- Vec uf=NULL; ++ Vector* uf=NULL; + + /*variables: */ + int i; +@@ -25,12 +25,12 @@ + } + else{ + /*allocate: */ +- uf=NewVec(fsize); ++ uf=new Vector(fsize); + + if(nodes->NumberOfNodes(configuration_type)){ + + /*serialize ug, so nodes can index into it: */ +- VecToMPISerial(&ug_serial,ug); ++ ug_serial=ug->ToMPISerial(); + + /*Go through all nodes, and ask them to retrieve values from ug, and plug them into uf: */ + for(i=0;iSize();i++){ +@@ -46,8 +46,7 @@ + } + } + /*Assemble vector: */ +- VecAssemblyBegin(uf); +- VecAssemblyEnd(uf); ++ uf->Assemble(); + } + + /*Free ressources:*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void Reducevectorgtofx(Vec* puf, Vec ug, Nodes* nodes,Parameters* parameters); ++void Reducevectorgtofx(Vector** puf, Vector* ug, Nodes* nodes,Parameters* parameters); + + #endif /* _REDUCEVECTORGTOFX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void GetSolutionFromInputsx( Vec* psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); ++void GetSolutionFromInputsx( Vector** psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); + + #endif /* _GETSOLUTIONFROMINPUTSXX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp (revision 11679) +@@ -8,7 +8,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void GetSolutionFromInputsx( Vec* psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters){ ++void GetSolutionFromInputsx( Vector** psolution, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters){ + + /*intermediary: */ + int gsize; +@@ -18,7 +18,7 @@ + int configuration_type; + + /*output: */ +- Vec solution=NULL; ++ Vector* solution=NULL; + + /*retrive parameters: */ + parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +@@ -28,7 +28,7 @@ + if (gsize==0) _error_("Allocating a Vec of size 0 as gsize=0 for configuration: %s",EnumToStringx(configuration_type)); + + /*Initialize solution: */ +- solution=NewVec(gsize); ++ solution=new Vector(gsize); + + /*Go through elements and plug solution: */ + for (i=0;iSize();i++){ +@@ -37,8 +37,7 @@ + } + + /*Assemble vector: */ +- VecAssemblyBegin(solution); +- VecAssemblyEnd(solution); ++ solution->Assemble(); + + /*Assign output pointers:*/ + *psolution=solution; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11679) +@@ -11,49 +11,46 @@ + #include "./Reduceloadx.h" + #include "../../io/io.h" + +-void Reduceloadx( Vec pf, Mat Kfs, Vec y_s,bool flag_ys0){ ++void Reduceloadx( Vector* pf, Matrix* Kfs, Vector* y_s,bool flag_ys0){ + + /*intermediary*/ +- Vec y_s0 = NULL; +- Vec Kfsy_s = NULL; ++ Vector* y_s0 = NULL; ++ Vector* Kfsy_s = NULL; + int Kfsm,Kfsn; + int global_m,global_n; +- PetscScalar a; + bool fromlocalsize = true; + int verbose; + + _printf_(VerboseModule()," Dirichlet lifting applied to load vector\n"); + +- MatGetSize(Kfs,&global_m,&global_n); ++ Kfs->GetSize(&global_m,&global_n); + if(pf && global_m*global_n){ + + /*Some checks in debugging mode*/ + _assert_(y_s); + + /*pf = pf - Kfs * y_s;*/ +- MatGetLocalSize(Kfs,&Kfsm,&Kfsn); +- Kfsy_s=NewVec(Kfsm,fromlocalsize); ++ Kfs->GetLocalSize(&Kfsm,&Kfsn); ++ Kfsy_s=new Vector(Kfsm,fromlocalsize); + if (flag_ys0){ + + /*Create y_s0, full of 0: */ +- VecDuplicate(y_s,&y_s0); +- VecSet(y_s0,0.0); +- VecAssemblyBegin(y_s0); +- VecAssemblyEnd(y_s0); ++ y_s0=y_s->Duplicate(); ++ y_s0->Set(0.0); ++ y_s0->Assemble(); + +- MatMultPatch(Kfs,y_s0,Kfsy_s); ++ Kfs->MatMult(y_s0,Kfsy_s); + } + else{ +- MatMultPatch(Kfs,y_s,Kfsy_s); ++ Kfs->MatMult(y_s,Kfsy_s); + } + +- a=-1; +- VecAXPY(pf,a,Kfsy_s); ++ pf->AXPY(Kfsy_s,-1); + } + + + /*Free ressources and return*/ +- VecFree(&y_s0); +- VecFree(&Kfsy_s); ++ delete y_s0; ++ delete Kfsy_s; + + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.h (revision 11679) +@@ -8,6 +8,6 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void Reduceloadx( Vec pf, Mat Kfs, Vec ys,bool flag_ys0=false); ++void Reduceloadx( Vector* pf, Matrix* Kfs, Vector* ys,bool flag_ys0=false); + + #endif /* _REDUCELOADX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h (revision 11679) +@@ -9,11 +9,11 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec solution); ++void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* solution); + void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* solution); + + //with timestep +-void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec solution,int timestep); ++void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* solution,int timestep); + void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,double* solution, int timestep); + + #endif /* _UPDATEINPUTSFROMSOLUTIONXX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp (revision 11679) +@@ -8,12 +8,12 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec solution){ ++void InputUpdateFromSolutionx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* solution){ + + double* serial_solution=NULL; + + /*Serialize solution, so that elements can index into it on every CPU: */ +- VecToMPISerial(&serial_solution,solution); ++ serial_solution=solution->ToMPISerial(); + + /*Call overloaded form of InputUpdateFromSolutionx: */ + InputUpdateFromSolutionx( elements, nodes, vertices, loads, materials, parameters,serial_solution); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp (revision 11679) +@@ -5,10 +5,10 @@ + + #include "./Reducevectorgtosx.h" + +-void Reducevectorgtosx(Vec* pys, Vec yg, Nodes* nodes,Parameters* parameters){ ++void Reducevectorgtosx(Vector** pys, Vector* yg, Nodes* nodes,Parameters* parameters){ + + /*output: */ +- Vec ys=NULL; ++ Vector* ys=NULL; + + /*variables: */ + int i; +@@ -25,12 +25,12 @@ + } + else{ + /*allocate: */ +- ys=NewVec(ssize); ++ ys=new Vector(ssize); + + if(nodes->NumberOfNodes(configuration_type)){ + + /*serialize yg, so nodes can index into it: */ +- VecToMPISerial(&yg_serial,yg); ++ yg_serial=yg->ToMPISerial(); + + /*Go throygh all nodes, and ask them to retrieve values from yg, and plyg them into ys: */ + for(i=0;iSize();i++){ +@@ -46,8 +46,7 @@ + } + } + /*Assemble vector: */ +- VecAssemblyBegin(ys); +- VecAssemblyEnd(ys); ++ ys->Assemble(); + } + + /*Free ressources:*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void Reducevectorgtosx(Vec* pys, Vec yg, Nodes* nodes,Parameters* parameters); ++void Reducevectorgtosx(Vector** pys, Vector* yg, Nodes* nodes,Parameters* parameters); + + #endif /* _REDUCEVECTORGTOSX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp (revision 11679) +@@ -0,0 +1,180 @@ ++/*!\file SolverxPetsc ++ * \brief Petsc implementation of solver ++ */ ++ ++#include "./Solverx.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++#include "../../io/io.h" ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++void SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters){ ++ ++ /*Output: */ ++ Vec uf = NULL; ++ ++ /*Intermediary: */ ++ int local_m,local_n,global_m,global_n; ++ int analysis_type; ++ ++ /*Solver */ ++ KSP ksp = NULL; ++ PC pc = NULL; ++ int iteration_number; ++ int solver_type; ++ bool fromlocalsize = true; ++ #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) ++ PetscTruth flag,flg; ++ #else ++ PetscBool flag,flg; ++ #endif ++ ++ /*Stokes: */ ++ IS isv=NULL; ++ IS isp=NULL; ++ ++ #if _PETSC_MAJOR_ >= 3 ++ char ksp_type[50]; ++ #endif ++ ++ ++ /*Display message*/ ++ _printf_(VerboseModule()," Solving\n"); ++ #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) ++ if(VerboseSolver())PetscOptionsPrint(stdout); ++ #else ++ if(VerboseSolver())PetscOptionsView(PETSC_VIEWER_STDOUT_WORLD); ++ #endif ++ ++ /*First, check that f-set is not NULL, i.e. model is fully constrained: {{{*/ ++ _assert_(Kff); ++ MatGetSize(Kff,&global_m,&global_n); _assert_(global_m==global_m); ++ if(!global_n){ ++ *puf=NULL; return; ++ } ++ /*}}}*/ ++ /*Initial guess logic here: {{{1*/ ++ /*Now, check that we are not giving an initial guess to the solver, if we are running a direct solver: */ ++ #if _PETSC_MAJOR_ >= 3 ++ PetscOptionsGetString(PETSC_NULL,"-ksp_type",ksp_type,49,&flg); ++ if (strcmp(ksp_type,"preonly")==0)uf0=NULL; ++ #endif ++ ++ /*If initial guess for the solution exists, use it to create uf, otherwise, ++ * duplicate the right hand side so that the solution vector has the same structure*/ ++ if(uf0){ ++ VecDuplicate(uf0,&uf); VecCopy(uf0,uf); ++ } ++ else{ ++ MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); ++ } ++ /*}}}*/ ++ /*Process petsc options to see if we are using special types of external solvers: {{{1*/ ++ PetscOptionsDetermineSolverType(&solver_type); ++ ++ /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. ++ We need to convert them if we are going to run the solvers successfully: */ ++ #ifdef _SERIAL_ ++ #if _PETSC_MAJOR_ == 2 ++ if (solver_type==MUMPSPACKAGE_LU){ ++ /*Convert Kff to MATTAIJMUMPS: */ ++ MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); ++ } ++ if (solver_type==MUMPSPACKAGE_CHOL){ ++ /*Convert Kff to MATTSBAIJMUMPS: */ ++ MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); ++ } ++ if (solver_type==SPOOLESPACKAGE_LU){ ++ /*Convert Kff to MATTSBAIJMUMPS: */ ++ MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); ++ } ++ if (solver_type==SPOOLESPACKAGE_CHOL){ ++ /*Convert Kff to MATTSBAIJMUMPS: */ ++ MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); ++ } ++ if (solver_type==SUPERLUDISTPACKAGE){ ++ /*Convert Kff to MATTSBAIJMUMPS: */ ++ MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); ++ } ++ if (solver_type==StokesSolverEnum){ ++ _error_("Petsc 2 does not support multi-physics solvers"); ++ } ++ #endif ++ #endif ++ /*}}}*/ ++ /*Check the solver is available: {{{1*/ ++ if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ ++ #if _PETSC_MAJOR_ >=3 ++ #ifndef _HAVE_MUMPS_ ++ _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); ++ #endif ++ ++ #endif ++ } ++ /*}}}*/ ++ /*Prepare solver:{{{1*/ ++ KSPCreate(MPI_COMM_WORLD,&ksp); ++ KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); ++ KSPSetFromOptions(ksp); ++ ++ #if defined(_SERIAL_) && _PETSC_MAJOR_==3 ++ /*Specific solver?: */ ++ KSPGetPC(ksp,&pc); ++ if (solver_type==MUMPSPACKAGE_LU){ ++ #if _PETSC_MINOR_==1 ++ PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); ++ #else ++ PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS); ++ #endif ++ } ++ #endif ++ ++ #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 ++ /*Stokes: */ ++ if (solver_type==StokesSolverEnum){ ++ /*Make indices out of doftypes: */ ++ if(!df)_error_("need doftypes for Stokes solver!\n"); ++ DofTypesToIndexSet(&isv,&isp,df,StokesSolverEnum); ++ ++ /*Set field splits: */ ++ KSPGetPC(ksp,&pc); ++ #if _PETSC_MINOR_==1 ++ PCFieldSplitSetIS(pc,isv); ++ PCFieldSplitSetIS(pc,isp); ++ #else ++ PCFieldSplitSetIS(pc,PETSC_NULL,isv); ++ PCFieldSplitSetIS(pc,PETSC_NULL,isp); ++ #endif ++ ++ } ++ #endif ++ ++ /*}}}*/ ++ /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ ++ if (uf0){ ++ if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ ++ KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); ++ } ++ } ++ /*}}}*/ ++ ++ if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); ++ ++ /*Solve: */ ++ KSPSolve(ksp,pf,uf); ++ ++ /*Check convergence*/ ++ KSPGetIterationNumber(ksp,&iteration_number); ++ if (iteration_number<0) _error_("%s%i"," Solver diverged at iteration number: ",-iteration_number); ++ ++ /*Free resources:*/ ++ KSPFree(&ksp); ++ ++ /*Assign output pointers:*/ ++ *puf=uf; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11679) +@@ -13,168 +13,22 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-void Solverx(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters){ ++void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters){ + +- /*Output: */ +- Vec uf = NULL; ++ /*output: */ ++ Vector* uf=NULL; ++ uf=new Vector(); + +- /*Intermediary: */ +- int local_m,local_n,global_m,global_n; +- int analysis_type; ++ #ifdef _HAVE_PETSC_ ++ Vec uf0_vector=NULL; ++ if (uf0)uf0_vector=uf0->vector; + +- /*Solver */ +- KSP ksp = NULL; +- PC pc = NULL; +- int iteration_number; +- int solver_type; +- bool fromlocalsize = true; +- #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) +- PetscTruth flag,flg; ++ SolverxPetsc(&uf->vector, Kff->matrix, pf->vector, uf0_vector, df->vector, parameters); ++ VecGetSize(uf->vector,&uf->M); + #else +- PetscBool flag,flg; ++ _error_("not supported yet!"); + #endif + +- /*Stokes: */ +- IS isv=NULL; +- IS isp=NULL; +- +- #if _PETSC_MAJOR_ >= 3 +- char ksp_type[50]; +- #endif +- +- +- /*Display message*/ +- _printf_(VerboseModule()," Solving\n"); +- #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) +- if(VerboseSolver())PetscOptionsPrint(stdout); +- #else +- if(VerboseSolver())PetscOptionsView(PETSC_VIEWER_STDOUT_WORLD); +- #endif +- +- /*First, check that f-set is not NULL, i.e. model is fully constrained: {{{*/ +- _assert_(Kff); +- MatGetSize(Kff,&global_m,&global_n); _assert_(global_m==global_m); +- if(!global_n){ +- *puf=NULL; return; +- } +- /*}}}*/ +- /*Initial guess logic here: {{{1*/ +- /*Now, check that we are not giving an initial guess to the solver, if we are running a direct solver: */ +- #if _PETSC_MAJOR_ >= 3 +- PetscOptionsGetString(PETSC_NULL,"-ksp_type",ksp_type,49,&flg); +- if (strcmp(ksp_type,"preonly")==0)uf0=NULL; +- #endif +- +- /*If initial guess for the solution exists, use it to create uf, otherwise, +- * duplicate the right hand side so that the solution vector has the same structure*/ +- if(uf0){ +- VecDuplicate(uf0,&uf); VecCopy(uf0,uf); +- } +- else{ +- MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); +- } +- /*}}}*/ +- /*Process petsc options to see if we are using special types of external solvers: {{{1*/ +- PetscOptionsDetermineSolverType(&solver_type); +- +- /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. +- We need to convert them if we are going to run the solvers successfully: */ +- #ifdef _SERIAL_ +- #if _PETSC_MAJOR_ == 2 +- if (solver_type==MUMPSPACKAGE_LU){ +- /*Convert Kff to MATTAIJMUMPS: */ +- MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==MUMPSPACKAGE_CHOL){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==SPOOLESPACKAGE_LU){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==SPOOLESPACKAGE_CHOL){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==SUPERLUDISTPACKAGE){ +- /*Convert Kff to MATTSBAIJMUMPS: */ +- MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); +- } +- if (solver_type==StokesSolverEnum){ +- _error_("Petsc 2 does not support multi-physics solvers"); +- } +- #endif +- #endif +- /*}}}*/ +- /*Check the solver is available: {{{1*/ +- if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ +- #if _PETSC_MAJOR_ >=3 +- #ifndef _HAVE_MUMPS_ +- _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); +- #endif +- +- #endif +- } +- /*}}}*/ +- /*Prepare solver:{{{1*/ +- KSPCreate(MPI_COMM_WORLD,&ksp); +- KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); +- KSPSetFromOptions(ksp); +- +- #if defined(_SERIAL_) && _PETSC_MAJOR_==3 +- /*Specific solver?: */ +- KSPGetPC(ksp,&pc); +- if (solver_type==MUMPSPACKAGE_LU){ +- #if _PETSC_MINOR_==1 +- PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); +- #else +- PCFactorSetMatSolverPackage(pc,MATSOLVERMUMPS); +- #endif +- } +- #endif +- +- #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 +- /*Stokes: */ +- if (solver_type==StokesSolverEnum){ +- /*Make indices out of doftypes: */ +- if(!df)_error_("need doftypes for Stokes solver!\n"); +- DofTypesToIndexSet(&isv,&isp,df,StokesSolverEnum); +- +- /*Set field splits: */ +- KSPGetPC(ksp,&pc); +- #if _PETSC_MINOR_==1 +- PCFieldSplitSetIS(pc,isv); +- PCFieldSplitSetIS(pc,isp); +- #else +- PCFieldSplitSetIS(pc,PETSC_NULL,isv); +- PCFieldSplitSetIS(pc,PETSC_NULL,isp); +- #endif +- +- } +- #endif +- +- /*}}}*/ +- /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ +- if (uf0){ +- if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ +- KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); +- } +- } +- /*}}}*/ +- +- if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); +- +- /*Solve: */ +- KSPSolve(ksp,pf,uf); +- +- /*Check convergence*/ +- KSPGetIterationNumber(ksp,&iteration_number); +- if (iteration_number<0) _error_("%s%i"," Solver diverged at iteration number: ",-iteration_number); +- +- /*Free resources:*/ +- KSPFree(&ksp); +- +- /*Assign output pointers:*/ ++ /*Assign output pointers: */ + *puf=uf; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h (revision 11679) +@@ -8,7 +8,8 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void Solverx( Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df,Parameters* parameters); ++void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters); ++void SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters); + void DofTypesToIndexSet(IS* pisv, IS* pisp, Vec df,int typeenum); + #endif /* _SOLVERX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void SystemMatricesx(Mat* pKff, Mat* pKfs, Vec* ppf, Vec* pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,bool kflag,bool pflag,bool penalty_kflag,bool penalty_pflag){ ++void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,bool kflag,bool pflag,bool penalty_kflag,bool penalty_pflag){ + + /*intermediary: */ + int i,j; +@@ -20,10 +20,10 @@ + Load *load = NULL; + + /*output: */ +- Mat Kff = NULL; +- Mat Kfs = NULL; +- Vec pf = NULL; +- Vec df=NULL; ++ Matrix* Kff = NULL; ++ Matrix* Kfs = NULL; ++ Vector* pf = NULL; ++ Vector* df=NULL; + double kmax = 0; + + /*Display message*/ +@@ -48,9 +48,9 @@ + /*Compute penalty free mstiffness matrix and load vector*/ + if(kflag){ + +- Kff=NewMat(fsize,fsize,connectivity,numberofdofspernode); +- Kfs=NewMat(fsize,ssize,connectivity,numberofdofspernode); +- df=NewVec(fsize); ++ Kff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); ++ Kfs=new Matrix(fsize,ssize,connectivity,numberofdofspernode); ++ df=new Vector(fsize); + + /*Fill stiffness matrix from elements: */ + for (i=0;iSize();i++){ +@@ -65,25 +65,16 @@ + } + + /*Assemble matrix and doftypes and compress matrix to save memory: */ +- MatAssemblyBegin(Kff,MAT_FINAL_ASSEMBLY); +- MatAssemblyEnd(Kff,MAT_FINAL_ASSEMBLY); +- #if _PETSC_MAJOR_ == 2 +- MatCompress(Kff); +- #endif ++ Kff->Assemble(); ++ Kfs->Assemble(); ++ df->Assemble(); + +- MatAssemblyBegin(Kfs,MAT_FINAL_ASSEMBLY); +- MatAssemblyEnd(Kfs,MAT_FINAL_ASSEMBLY); +- #if _PETSC_MAJOR_ == 2 +- MatCompress(Kfs); +- #endif +- VecAssemblyBegin(df); +- VecAssemblyEnd(df); + + } + + if(pflag){ + +- pf=NewVec(fsize); ++ pf=new Vector(fsize); + + /*Fill right hand side vector, from elements: */ + for (i=0;iSize();i++){ +@@ -97,12 +88,11 @@ + if (load->InAnalysis(configuration_type)) load->CreatePVector(pf); + } + +- VecAssemblyBegin(pf); +- VecAssemblyEnd(pf); ++ pf->Assemble(); + } + + /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ +- MatNorm(Kff,NORM_INFINITY,&kmax); ++ kmax=Kff->Norm(NORM_INFINITY); + + /*Now, deal with penalties*/ + if(penalty_kflag){ +@@ -114,17 +104,8 @@ + } + + /*Assemble matrix and compress matrix to save memory: */ +- MatAssemblyBegin(Kff,MAT_FINAL_ASSEMBLY); +- MatAssemblyEnd(Kff,MAT_FINAL_ASSEMBLY); +- #if _PETSC_MAJOR_ == 2 +- MatCompress(Kff); +- #endif +- +- MatAssemblyBegin(Kfs,MAT_FINAL_ASSEMBLY); +- MatAssemblyEnd(Kfs,MAT_FINAL_ASSEMBLY); +- #if _PETSC_MAJOR_ == 2 +- MatCompress(Kfs); +- #endif ++ Kff->Assemble(); ++ Kfs->Assemble(); + } + + +@@ -136,18 +117,18 @@ + if (load->InAnalysis(configuration_type)) load->PenaltyCreatePVector(pf,kmax); + } + +- VecAssemblyBegin(pf); +- VecAssemblyEnd(pf); ++ pf->Assemble(); ++ pf->Assemble(); + } + + /*Assign output pointers: */ + if(pKff) *pKff=Kff; +- else MatFree(&Kff); ++ else delete Kff; + if(pKfs) *pKfs=Kfs; +- else MatFree(&Kfs); ++ else delete Kfs; + if(ppf) *ppf=pf; +- else VecFree(&pf); ++ else delete pf; + if(pdf) *pdf=df; +- else VecFree(&df); ++ else delete df; + if(pkmax) *pkmax=kmax; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void SystemMatricesx(Mat* pKff, Mat* pKfs, Vec* ppf, Vec* pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters, ++void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters, + bool kflag=true,bool pflag=true,bool penalty_kflag=true,bool penalty_pflag=true); + + #endif /* _SYSTEMMATRICESX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp (revision 11679) +@@ -9,14 +9,14 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void CreateJacobianMatrixx(Mat* pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax){ ++void CreateJacobianMatrixx(Matrix** pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax){ + + int i,connectivity; + int numberofdofspernode; + int fsize,configuration_type; + Element *element = NULL; + Load *load = NULL; +- Mat Jff = NULL; ++ Matrix* Jff = NULL; + + /*Checks*/ + _assert_(nodes && elements); +@@ -28,7 +28,7 @@ + numberofdofspernode=nodes->MaxNumDofs(configuration_type,GsetEnum); + + /*Initialize Jacobian Matrix*/ +- Jff=NewMat(fsize,fsize,connectivity,numberofdofspernode); ++ Jff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); + + /*Create and assemble matrix*/ + for(i=0;iSize();i++){ +@@ -40,8 +40,7 @@ + if(load->InAnalysis(configuration_type)) load->CreateJacobianMatrix(Jff); + if(load->InAnalysis(configuration_type)) load->PenaltyCreateJacobianMatrix(Jff,kmax); + } +- MatAssemblyBegin(Jff,MAT_FINAL_ASSEMBLY); +- MatAssemblyEnd(Jff,MAT_FINAL_ASSEMBLY); ++ Jff->Assemble(); + + /*Assign output pointer*/ + *pJff=Jff; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h (revision 11679) +@@ -9,6 +9,6 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void CreateJacobianMatrixx(Mat* pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax); ++void CreateJacobianMatrixx(Matrix** pJff,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,double kmax); + + #endif /* _CREATEJACOBIANMATRIXX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/VecMergex/VecMergex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/VecMergex/VecMergex.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/VecMergex/VecMergex.cpp (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void VecMergex(Vec ug, Vec uf, Nodes* nodes, Parameters* parameters, int SetEnum){ ++void VecMergex(Vector* ug, Vector* uf, Nodes* nodes, Parameters* parameters, int SetEnum){ + + /*variables: */ + int i; +@@ -20,8 +20,9 @@ + parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + + /*serialize uf: */ +- VecToMPISerial(&uf_serial,uf); ++ uf_serial=uf->ToMPISerial(); + ++ + /*Do we have any nodes for this configuration? :*/ + if(nodes->NumberOfNodes(configuration_type)){ + +@@ -42,7 +43,5 @@ + xfree((void**)&uf_serial); + + /*Assemble vector: */ +- VecAssemblyBegin(ug); +- VecAssemblyEnd(ug); +- ++ ug->Assemble(); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/VecMergex/VecMergex.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/VecMergex/VecMergex.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/VecMergex/VecMergex.h (revision 11679) +@@ -9,6 +9,6 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void VecMergex(Vec ug, Vec uf, Nodes* nodes, Parameters* parameters, int SetEnum); ++void VecMergex(Vector* ug, Vector* uf, Nodes* nodes, Parameters* parameters, int SetEnum); + + #endif /* _VECMERGEX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp (revision 11679) +@@ -6,10 +6,10 @@ + #include "../../io/io.h" + #include "./Mergesolutionfromftogx.h" + +-void Mergesolutionfromftogx( Vec* pug, Vec uf, Vec ys, Nodes* nodes, Parameters* parameters, bool flag_ys0){ ++void Mergesolutionfromftogx( Vector** pug, Vector* uf, Vector* ys, Nodes* nodes, Parameters* parameters, bool flag_ys0){ + + /*output: */ +- Vec ug=NULL; ++ Vector* ug=NULL; + + /*intermediary: */ + int configuration_type; +@@ -28,12 +28,12 @@ + *that know which values should be plugged into ug and where: */ + if(ssize){ + if(flag_ys0){ +- VecSet(ys,0.0); ++ ys->Set(0.0); + } + } + + /*initialize ug: */ +- ug=NewVec(gsize); ++ ug=new Vector(gsize); + + /*Merge f set back into g set: */ + if(fsize){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h (revision 11679) +@@ -8,7 +8,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void Mergesolutionfromftogx( Vec* pug, Vec uf, Vec ys, Nodes* nodes, Parameters* parameters, bool flag_ys0=false); ++void Mergesolutionfromftogx( Vector** pug, Vector* uf, Vector* ys, Nodes* nodes, Parameters* parameters, bool flag_ys0=false); + + #endif /* _MERGESOLUTIONFROMFTOGX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void CreateNodalConstraintsx( Vec* pys, Nodes* nodes,int configuration_type){ ++void CreateNodalConstraintsx( Vector** pys, Nodes* nodes,int configuration_type){ + + int i; + +@@ -17,13 +17,13 @@ + int numberofdofs; + + /*output: */ +- Vec ys=NULL; ++ Vector* ys=NULL; + + /*figure out how many dofs we have: */ + numberofdofs=nodes->NumberOfDofs(configuration_type,SsetEnum); + + /*allocate:*/ +- ys=NewVec(numberofdofs); ++ ys=new Vector(numberofdofs); + + /*go through all nodes, and for the ones corresponding to this configuration_type, fill the + * constraints vector with the constraint values: */ +@@ -35,8 +35,7 @@ + } + + /*Assemble: */ +- VecAssemblyBegin(ys); +- VecAssemblyEnd(ys); ++ ys->Assemble(); + + /*Assign output pointers: */ + *pys=ys; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h (revision 11679) +@@ -8,6 +8,6 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void CreateNodalConstraintsx( Vec* pys, Nodes* nodes,int configuration_type); ++void CreateNodalConstraintsx( Vector** pys, Nodes* nodes,int configuration_type); + + #endif /* _CREATENODALCONSTRAINTSX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp (revision 11679) +@@ -9,7 +9,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vec yg){ ++void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vector* yg){ + + int configuration_type; + double* yg_serial=NULL; +@@ -18,7 +18,7 @@ + parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + + /*serialize yg, so nodes can index into it: */ +- VecToMPISerial(&yg_serial,yg); ++ yg_serial=yg->ToMPISerial(); + + for(int i=0;iSize();i++){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h (revision 11679) +@@ -8,6 +8,6 @@ + #include "../../Container/Container.h" + #include "../../objects/objects.h" + +-void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vec yg); ++void UpdateDynamicConstraintsx(Constraints* constraints,Nodes* nodes,Parameters* parameters,Vector* yg); + + #endif /* _UPDATESPCSX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11679) +@@ -343,6 +343,7 @@ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h\ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ + ./modules/Solverx/Solverx.cpp\ ++ ./modules/Solverx/SolverxPetsc.cpp\ + ./modules/Solverx/Solverx.h\ + ./modules/Solverx/DofTypesToIndexSet.cpp\ + ./modules/VecMergex/VecMergex.cpp\ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp (revision 11679) +@@ -244,8 +244,8 @@ + /*}}}*/ + + /*ElementMatrix specific routines: */ +-/*FUNCTION ElementMatrix::AddToGlobal(Mat Kff, Mat Kfs){{{1*/ +-void ElementMatrix::AddToGlobal(Mat Kff, Mat Kfs){ ++/*FUNCTION ElementMatrix::AddToGlobal(Matrix* Kff, Matrix* Kfs){{{1*/ ++void ElementMatrix::AddToGlobal(Matrix* Kff, Matrix* Kfs){ + + int i,j; + double* localvalues=NULL; +@@ -259,48 +259,52 @@ + /*In debugging mode, check consistency (no NaN, and values not too big)*/ + this->CheckConsistency(); + +- if(this->dofsymmetrical){ +- /*only use row dofs to add values into global matrices: */ +- +- if(this->row_fsize){ +- /*first, retrieve values that are in the f-set from the g-set values matrix: */ +- localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); +- for(i=0;irow_fsize;i++){ +- for(j=0;jrow_fsize;j++){ +- *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); ++ #ifdef _HAVE_PETSC_ ++ if(this->dofsymmetrical){ ++ /*only use row dofs to add values into global matrices: */ ++ ++ if(this->row_fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values matrix: */ ++ localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); ++ for(i=0;irow_fsize;i++){ ++ for(j=0;jrow_fsize;j++){ ++ *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); ++ } + } ++ /*add local values into global matrix, using the fglobaldoflist: */ ++ MatSetValues(Kff->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); ++ ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- /*add local values into global matrix, using the fglobaldoflist: */ +- MatSetValues(Kff,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); + +- /*Free ressources:*/ +- xfree((void**)&localvalues); +- } + ++ if((this->row_ssize!=0) && (this->row_fsize!=0)){ ++ /*first, retrieve values that are in the f and s-set from the g-set values matrix: */ ++ localvalues=(double*)xmalloc(this->row_fsize*this->row_ssize*sizeof(double)); ++ for(i=0;irow_fsize;i++){ ++ for(j=0;jrow_ssize;j++){ ++ *(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]); ++ } ++ } ++ /*add local values into global matrix, using the fglobaldoflist: */ ++ MatSetValues(Kfs->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,(const double*)localvalues,ADD_VALUES); + +- if((this->row_ssize!=0) && (this->row_fsize!=0)){ +- /*first, retrieve values that are in the f and s-set from the g-set values matrix: */ +- localvalues=(double*)xmalloc(this->row_fsize*this->row_ssize*sizeof(double)); +- for(i=0;irow_fsize;i++){ +- for(j=0;jrow_ssize;j++){ +- *(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]); +- } ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- /*add local values into global matrix, using the fglobaldoflist: */ +- MatSetValues(Kfs,this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,(const double*)localvalues,ADD_VALUES); +- +- /*Free ressources:*/ +- xfree((void**)&localvalues); + } +- } +- else{ +- _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); +- } ++ else{ ++ _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); ++ } ++ #else ++ _error_("not supported yet!"); ++ #endif + + } + /*}}}*/ +-/*FUNCTION ElementMatrix::AddToGlobal(Mat Jff){{{1*/ +-void ElementMatrix::AddToGlobal(Mat Jff){ ++/*FUNCTION ElementMatrix::AddToGlobal(Matrix* Jff){{{1*/ ++void ElementMatrix::AddToGlobal(Matrix* Jff){ + + int i,j; + double* localvalues=NULL; +@@ -311,29 +315,33 @@ + /*In debugging mode, check consistency (no NaN, and values not too big)*/ + this->CheckConsistency(); + +- if(this->dofsymmetrical){ +- /*only use row dofs to add values into global matrices: */ ++ #ifdef _HAVE_PETSC_ ++ if(this->dofsymmetrical){ ++ /*only use row dofs to add values into global matrices: */ + +- if(this->row_fsize){ +- /*first, retrieve values that are in the f-set from the g-set values matrix: */ +- localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); +- for(i=0;irow_fsize;i++){ +- for(j=0;jrow_fsize;j++){ +- *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); ++ if(this->row_fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values matrix: */ ++ localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); ++ for(i=0;irow_fsize;i++){ ++ for(j=0;jrow_fsize;j++){ ++ *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); ++ } + } ++ /*add local values into global matrix, using the fglobaldoflist: */ ++ MatSetValues(Jff->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); ++ ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- /*add local values into global matrix, using the fglobaldoflist: */ +- MatSetValues(Jff,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); + +- /*Free ressources:*/ +- xfree((void**)&localvalues); + } ++ else{ ++ _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); ++ } ++ #else ++ _error_("not supported yet!"); ++ #endif + +- } +- else{ +- _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); +- } +- + } + /*}}}*/ + /*FUNCTION ElementMatrix::CheckConsistency{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.h (revision 11679) +@@ -39,8 +39,8 @@ + ~ElementVector(); + /*}}}*/ + /*ElementVector specific routines {{{1*/ +- void AddToGlobal(Vec pf); +- void InsertIntoGlobal(Vec pf); ++ void AddToGlobal(Vector* pf); ++ void InsertIntoGlobal(Vector* pf); + void Echo(void); + void Init(ElementVector* pe); + void SetValue(double scalar); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11679) +@@ -23,11 +23,11 @@ + /*FUNCTION Vector::Vector(){{{1*/ + Vector::Vector(){ + ++ this->M=0; + #ifdef _HAVE_PETSC_ + this->vector=NULL; + #else + this->vector=NULL; +- this->M=0; + #endif + #ifdef _HAVE_ADOLC_ + this->avector=NULL; +@@ -97,7 +97,152 @@ + #else + _error_("not implemented yet!"); + #endif ++ return dataref; + + } + /*}}}*/ + #endif ++/*FUNCTION Vector::Assemble{{{1*/ ++void Vector::Assemble(void){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecAssemblyBegin(this->vector); ++ VecAssemblyEnd(this->vector); ++ #else ++ /*do nothing*/ ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::SetValues{{{1*/ ++void Vector::SetValues(int ssize, int* list, double* values, int mode){ ++ ++ ++ #ifdef _HAVE_PETSC_ ++ VecSetValues(this->vector,ssize,list,values,(InsertMode)mode); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::GetSize{{{1*/ ++void Vector::GetSize(int* pM){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecGetSize(this->vector,pM); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::GetLocalSize{{{1*/ ++void Vector::GetLocalSize(int* pM){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecGetLocalSize(this->vector,pM); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::Duplicate{{{1*/ ++Vector* Vector::Duplicate(void){ ++ ++ Vector* output=NULL; ++ output=new Vector(); ++ #ifdef _HAVE_PETSC_ ++ Vec vec_output=NULL; ++ VecDuplicate(this->vector,&vec_output); ++ output->vector=vec_output; ++ VecGetSize(output->vector,&output->M); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ return output; ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::Set{{{1*/ ++void Vector::Set(double value){ ++ ++ #ifdef _HAVE_PETSC_ ++ this->Set(value); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::AXPY{{{1*/ ++void Vector::AXPY(Vector* X, double a){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecAXPY(this->vector,a,X->vector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::AYPX{{{1*/ ++void Vector::AYPX(Vector* X, double a){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecAYPX(this->vector,a,X->vector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::ToMPISerial{{{1*/ ++double* Vector::ToMPISerial(void){ ++ ++ double* vec_serial=NULL; ++ ++ #ifdef _HAVE_PETSC_ ++ VecToMPISerial(&vec_serial, this->vector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++ return vec_serial; ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::Copy{{{1*/ ++void Vector::Copy(Vector* to){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecCopy(this->vector,to->vector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::Norm{{{1*/ ++double Vector::Norm(int norm_type){ ++ ++ double norm=0; ++ #ifdef _HAVE_PETSC_ ++ VecNorm(this->vector,(NormType)norm_type,&norm); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ return norm; ++} ++/*}}}*/ ++/*FUNCTION Vector::Scale{{{1*/ ++void Vector::Scale(double scale_factor){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecScale(this->vector,scale_factor); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.h (revision 11679) +@@ -57,8 +57,8 @@ + ~ElementMatrix(); + /*}}}*/ + /*ElementMatrix specific routines {{{1*/ +- void AddToGlobal(Mat Kff, Mat Kfs); +- void AddToGlobal(Mat Jff); ++ void AddToGlobal(Matrix* Kff, Matrix* Kfs); ++ void AddToGlobal(Matrix* Jff); + void Echo(void); + void CheckConsistency(void); + void Transpose(void); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11679) +@@ -139,7 +139,64 @@ + #else + _error_("not implemented yet!"); + #endif ++ return dataref; + + } + /*}}}*/ + #endif ++/*FUNCTION Matrix::Assemble{{{1*/ ++void Matrix::Assemble(void){ ++ #ifdef _HAVE_PETSC_ ++ MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); ++ MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); ++ #if _PETSC_MAJOR_ == 2 ++ MatCompress(this->matrix); ++ #endif ++ #else ++ /*do nothing:*/ ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Matrix::Norm{{{1*/ ++double Matrix::Norm(int norm_type){ ++ ++ double norm=0; ++ #ifdef _HAVE_PETSC_ ++ MatNorm(this->matrix,(NormType)norm_type,&norm); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ return norm; ++} ++/*}}}*/ ++/*FUNCTION Matrix::GetSize{{{1*/ ++void Matrix::GetSize(int* pM,int* pN){ ++ ++ #ifdef _HAVE_PETSC_ ++ MatGetSize(this->matrix,pM,pN); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::GetLocalSize{{{1*/ ++void Matrix::GetLocalSize(int* pM,int* pN){ ++ ++ #ifdef _HAVE_PETSC_ ++ MatGetLocalSize(this->matrix,pM,pN); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::MatMult{{{1*/ ++void Matrix::MatMult(Vector* X,Vector* AX){ ++ ++ #ifdef _HAVE_PETSC_ ++ MatMultPatch(this->matrix,X->vector,AX->vector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11679) +@@ -53,6 +53,18 @@ + #ifdef _SERIAL_ + mxArray* ToMatlabVector(void); + #endif ++ void Assemble(void); ++ void SetValues(int ssize, int* list, double* values, int mode); ++ void GetSize(int* pM); ++ void GetLocalSize(int* pM); ++ Vector* Duplicate(void); ++ void Set(double value); ++ void AXPY(Vector* X, double a); ++ void AYPX(Vector* X, double a); ++ double* ToMPISerial(void); ++ void Copy(Vector* to); ++ double Norm(int norm_type); ++ void Scale(double scale_factor); + /*}}}*/ + }; + #endif //#ifndef _VECTOR_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11679) +@@ -24,6 +24,7 @@ + #ifdef _SERIAL_ + #include "mex.h" + #endif ++class Vector; + + /*}}}*/ + +@@ -54,6 +55,11 @@ + #ifdef _SERIAL_ + mxArray* ToMatlabMatrix(void); + #endif ++ void Assemble(void); ++ double Norm(int norm_type); ++ void GetSize(int* pM,int* pN); ++ void GetLocalSize(int* pM,int* pN); ++ void MatMult(Vector* X,Vector* AX); + /*}}}*/ + + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp (revision 11679) +@@ -159,44 +159,54 @@ + /*}}}*/ + + /*ElementVector specific routines: */ +-/*FUNCTION ElementVector::AddToGlobal(Vec pf){{{1*/ +-void ElementVector::AddToGlobal(Vec pf){ ++/*FUNCTION ElementVector::AddToGlobal(Vector* pf){{{1*/ ++void ElementVector::AddToGlobal(Vector* pf){ + + int i; + double* localvalues=NULL; + +- if(this->fsize){ +- /*first, retrieve values that are in the f-set from the g-set values vector: */ +- localvalues=(double*)xmalloc(this->fsize*sizeof(double)); +- for(i=0;ifsize;i++){ +- localvalues[i]=this->values[this->flocaldoflist[i]]; ++ #ifdef _HAVE_PETSC_ ++ if(this->fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values vector: */ ++ localvalues=(double*)xmalloc(this->fsize*sizeof(double)); ++ for(i=0;ifsize;i++){ ++ localvalues[i]=this->values[this->flocaldoflist[i]]; ++ } ++ /*add local values into global vector, using the fglobaldoflist: */ ++ VecSetValues(pf->vector,this->fsize,this->fglobaldoflist,(const double*)localvalues,ADD_VALUES); ++ ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- /*add local values into global vector, using the fglobaldoflist: */ +- VecSetValues(pf,this->fsize,this->fglobaldoflist,(const double*)localvalues,ADD_VALUES); +- +- /*Free ressources:*/ +- xfree((void**)&localvalues); +- } ++ #else ++ _error_("not supported yet!"); ++ #endif ++ + } + /*}}}*/ +-/*FUNCTION ElementVector::InsertIntoGlobal(Vec pf){{{1*/ +-void ElementVector::InsertIntoGlobal(Vec pf){ ++/*FUNCTION ElementVector::InsertIntoGlobal(Vector* pf){{{1*/ ++void ElementVector::InsertIntoGlobal(Vector* pf){ + + int i; + double* localvalues=NULL; + +- if(this->fsize){ +- /*first, retrieve values that are in the f-set from the g-set values vector: */ +- localvalues=(double*)xmalloc(this->fsize*sizeof(double)); +- for(i=0;ifsize;i++){ +- localvalues[i]=this->values[this->flocaldoflist[i]]; ++ #ifdef _HAVE_PETSC_ ++ if(this->fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values vector: */ ++ localvalues=(double*)xmalloc(this->fsize*sizeof(double)); ++ for(i=0;ifsize;i++){ ++ localvalues[i]=this->values[this->flocaldoflist[i]]; ++ } ++ /*add local values into global vector, using the fglobaldoflist: */ ++ VecSetValues(pf->vector,this->fsize,this->fglobaldoflist,(const double*)localvalues,INSERT_VALUES); ++ ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- /*add local values into global vector, using the fglobaldoflist: */ +- VecSetValues(pf,this->fsize,this->fglobaldoflist,(const double*)localvalues,INSERT_VALUES); ++ #else ++ _error_("not supported yet!"); ++ #endif + +- /*Free ressources:*/ +- xfree((void**)&localvalues); +- } + } + /*}}}*/ + /*FUNCTION ElementVector::Echo{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.h (revision 11679) +@@ -73,12 +73,12 @@ + /*Load virtual functions definitions: {{{1*/ + void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff); +- void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); +- void PenaltyCreatePVector(Vec pf, double kmax); +- void PenaltyCreateJacobianMatrix(Mat Jff,double kmax); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff); ++ void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); ++ void PenaltyCreatePVector(Vector* pf, double kmax); ++ void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax); + bool InAnalysis(int analysis_type); + /*}}}*/ + /*Load management: {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp (revision 11679) +@@ -333,7 +333,7 @@ + } + /*}}}*/ + /*FUNCTION Numericalflux::CreateKMatrix {{{1*/ +-void Numericalflux::CreateKMatrix(Mat Kff, Mat Kfs){ ++void Numericalflux::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ + + /*recover some parameters*/ + ElementMatrix* Ke=NULL; +@@ -364,7 +364,7 @@ + } + /*}}}*/ + /*FUNCTION Numericalflux::CreatePVector {{{1*/ +-void Numericalflux::CreatePVector(Vec pf){ ++void Numericalflux::CreatePVector(Vector* pf){ + + /*recover some parameters*/ + ElementVector* pe=NULL; +@@ -394,7 +394,7 @@ + } + /*}}}*/ + /*FUNCTION Numericalflux::PenaltyCreateKMatrix {{{1*/ +-void Numericalflux::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ ++void Numericalflux::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ + + /*No stiffness loads applied, do nothing: */ + return; +@@ -402,7 +402,7 @@ + } + /*}}}*/ + /*FUNCTION Numericalflux::PenaltyCreatePVector{{{1*/ +-void Numericalflux::PenaltyCreatePVector(Vec pf,double kmax){ ++void Numericalflux::PenaltyCreatePVector(Vector* pf,double kmax){ + + /*No penalty loads applied, do nothing: */ + return; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.cpp (revision 11679) +@@ -198,7 +198,7 @@ + } + /*}}}1*/ + /*FUNCTION Penpair::CreateKMatrix {{{1*/ +-void Penpair::CreateKMatrix(Mat Kff, Mat Kfs){ ++void Penpair::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ + /*If you code this piece, don't forget that a penalty will be inactive if it is dealing with clone nodes*/ + /*No loads applied, do nothing: */ + return; +@@ -206,7 +206,7 @@ + } + /*}}}1*/ + /*FUNCTION Penpair::CreatePVector {{{1*/ +-void Penpair::CreatePVector(Vec pf){ ++void Penpair::CreatePVector(Vector* pf){ + + /*No loads applied, do nothing: */ + return; +@@ -214,12 +214,12 @@ + } + /*}}}1*/ + /*FUNCTION Penpair::CreateJacobianMatrix{{{1*/ +-void Penpair::CreateJacobianMatrix(Mat Jff){ ++void Penpair::CreateJacobianMatrix(Matrix* Jff){ + this->CreateKMatrix(Jff,NULL); + } + /*}}}1*/ + /*FUNCTION Penpair::PenaltyCreateKMatrix {{{1*/ +-void Penpair::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ ++void Penpair::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ + + /*Retrieve parameters: */ + ElementMatrix* Ke=NULL; +@@ -245,13 +245,13 @@ + } + /*}}}1*/ + /*FUNCTION Penpair::PenaltyCreatePVector {{{1*/ +-void Penpair::PenaltyCreatePVector(Vec pf,double kmax){ ++void Penpair::PenaltyCreatePVector(Vector* pf,double kmax){ + /*No loads applied, do nothing: */ + return; + } + /*}}}1*/ + /*FUNCTION Penpair::PenaltyCreateJacobianMatrix{{{1*/ +-void Penpair::PenaltyCreateJacobianMatrix(Mat Jff,double kmax){ ++void Penpair::PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){ + this->PenaltyCreateKMatrix(Jff,NULL,kmax); + } + /*}}}1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.h (revision 11679) +@@ -81,12 +81,12 @@ + /*Load virtual functions definitions: {{{1*/ + void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff){_error_("Not implemented yet");}; +- void PenaltyCreateJacobianMatrix(Mat Jff,double kmax){_error_("Not implemented yet");}; +- void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); +- void PenaltyCreatePVector(Vec pf, double kmax); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");}; ++ void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){_error_("Not implemented yet");}; ++ void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); ++ void PenaltyCreatePVector(Vector* pf, double kmax); + bool InAnalysis(int analysis_type); + /*}}}*/ + /*Riftfront specific routines: {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Numericalflux.h (revision 11679) +@@ -69,12 +69,12 @@ + /*Load virtual functions definitions: {{{1*/ + void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff){_error_("Not implemented yet");}; +- void PenaltyCreateJacobianMatrix(Mat Jff,double kmax){_error_("Not implemented yet");}; +- void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); +- void PenaltyCreatePVector(Vec pf, double kmax); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");}; ++ void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){_error_("Not implemented yet");}; ++ void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); ++ void PenaltyCreatePVector(Vector* pf, double kmax); + bool InAnalysis(int analysis_type); + /*}}}*/ + /*Numericalflux management:{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Penpair.h (revision 11679) +@@ -61,12 +61,12 @@ + /*Load virtual functions definitions: {{{1*/ + void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff); +- void PenaltyCreateKMatrix(Mat Kff,Mat Kfs,double kmax); +- void PenaltyCreatePVector(Vec pf, double kmax); +- void PenaltyCreateJacobianMatrix(Mat Jff,double kmax); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff); ++ void PenaltyCreateKMatrix(Matrix* Kff,Matrix* Kfs,double kmax); ++ void PenaltyCreatePVector(Vector* pf, double kmax); ++ void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax); + bool InAnalysis(int analysis_type); + /*}}}*/ + /*Penpair management: {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Load.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Load.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Load.h (revision 11679) +@@ -11,6 +11,8 @@ + /*Headers:*/ + /*{{{1*/ + class Object; ++class Matrix; ++class Vector; + + #include "../Object.h" + #include "../../toolkits/toolkits.h" +@@ -26,12 +28,12 @@ + /*Virtual functions: {{{1*/ + virtual void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; + virtual void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; +- virtual void CreateKMatrix(Mat Kff, Mat Kfs)=0; +- virtual void CreatePVector(Vec pf)=0; +- virtual void CreateJacobianMatrix(Mat Jff)=0; +- virtual void PenaltyCreateJacobianMatrix(Mat Jff,double kmax)=0; +- virtual void PenaltyCreateKMatrix(Mat Kff, Mat Kfs, double kmax)=0; +- virtual void PenaltyCreatePVector(Vec pf, double kmax)=0; ++ virtual void CreateKMatrix(Matrix* Kff, Matrix* Kfs)=0; ++ virtual void CreatePVector(Vector* pf)=0; ++ virtual void CreateJacobianMatrix(Matrix* Jff)=0; ++ virtual void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax)=0; ++ virtual void PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, double kmax)=0; ++ virtual void PenaltyCreatePVector(Vector* pf, double kmax)=0; + virtual bool InAnalysis(int analysis_type)=0; + /*}}}*/ + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.cpp (revision 11679) +@@ -294,7 +294,7 @@ + } + /*}}}1*/ + /*FUNCTION Pengrid::CreateKMatrix {{{1*/ +-void Pengrid::CreateKMatrix(Mat Kff, Mat Kfs){ ++void Pengrid::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ + + /*No loads applied, do nothing: */ + return; +@@ -302,7 +302,7 @@ + } + /*}}}1*/ + /*FUNCTION Pengrid::CreatePVector {{{1*/ +-void Pengrid::CreatePVector(Vec pf){ ++void Pengrid::CreatePVector(Vector* pf){ + + /*No loads applied, do nothing: */ + return; +@@ -310,7 +310,7 @@ + } + /*}}}1*/ + /*FUNCTION Pengrid::PenaltyCreateMatrix {{{1*/ +-void Pengrid::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ ++void Pengrid::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ + + /*Retrieve parameters: */ + ElementMatrix* Ke=NULL; +@@ -343,7 +343,7 @@ + } + /*}}}1*/ + /*FUNCTION Pengrid::PenaltyCreatePVector {{{1*/ +-void Pengrid::PenaltyCreatePVector(Vec pf,double kmax){ ++void Pengrid::PenaltyCreatePVector(Vector* pf,double kmax){ + + /*Retrieve parameters: */ + ElementVector* pe=NULL; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Icefront.cpp (revision 11679) +@@ -315,7 +315,7 @@ + } + /*}}}*/ + /*FUNCTION Icefront::CreateKMatrix {{{1*/ +-void Icefront::CreateKMatrix(Mat Kff, Mat Kfs){ ++void Icefront::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ + + /*No stiffness loads applied, do nothing: */ + return; +@@ -323,7 +323,7 @@ + } + /*}}}*/ + /*FUNCTION Icefront::CreatePVector {{{1*/ +-void Icefront::CreatePVector(Vec pf){ ++void Icefront::CreatePVector(Vector* pf){ + + /*Checks in debugging mode*/ + /*{{{2*/ +@@ -361,24 +361,24 @@ + } + /*}}}*/ + /*FUNCTION Icefront::CreateJacobianMatrix{{{1*/ +-void Icefront::CreateJacobianMatrix(Mat Jff){ ++void Icefront::CreateJacobianMatrix(Matrix* Jff){ + this->CreateKMatrix(Jff,NULL); + } + /*}}}1*/ + /*FUNCTION Icefront::PenaltyCreateKMatrix {{{1*/ +-void Icefront::PenaltyCreateKMatrix(Mat Kff, Mat Kfs, double kmax){ ++void Icefront::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, double kmax){ + /*do nothing: */ + return; + } + /*}}}*/ + /*FUNCTION Icefront::PenaltyCreatePVector{{{1*/ +-void Icefront::PenaltyCreatePVector(Vec pf,double kmax){ ++void Icefront::PenaltyCreatePVector(Vector* pf,double kmax){ + /*do nothing: */ + return; + } + /*}}}*/ + /*FUNCTION Icefront::PenaltyCreateJacobianMatrix{{{1*/ +-void Icefront::PenaltyCreateJacobianMatrix(Mat Jff,double kmax){ ++void Icefront::PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){ + this->PenaltyCreateKMatrix(Jff,NULL,kmax); + } + /*}}}1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Pengrid.h (revision 11679) +@@ -74,12 +74,12 @@ + /*Load virtual functions definitions: {{{1*/ + void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff){_error_("Not implemented yet");}; +- void PenaltyCreateJacobianMatrix(Mat Jff,double kmax){_error_("Not implemented yet");}; +- void PenaltyCreateKMatrix(Mat Kff, Mat kfs, double kmax); +- void PenaltyCreatePVector(Vec pf, double kmax); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff){_error_("Not implemented yet");}; ++ void PenaltyCreateJacobianMatrix(Matrix* Jff,double kmax){_error_("Not implemented yet");}; ++ void PenaltyCreateKMatrix(Matrix* Kff, Matrix* kfs, double kmax); ++ void PenaltyCreatePVector(Vector* pf, double kmax); + bool InAnalysis(int analysis_type); + /*}}}*/ + /*Pengrid management {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Loads/Riftfront.cpp (revision 11679) +@@ -427,7 +427,7 @@ + } + /*}}}*/ + /*FUNCTION Riftfront::PenaltyCreateKMatrix {{{1*/ +-void Riftfront::PenaltyCreateKMatrix(Mat Kff, Mat Kfs,double kmax){ ++void Riftfront::PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs,double kmax){ + + /*Retrieve parameters: */ + ElementMatrix* Ke=NULL; +@@ -453,7 +453,7 @@ + } + /*}}}1*/ + /*FUNCTION Riftfront::PenaltyCreatePVector {{{1*/ +-void Riftfront::PenaltyCreatePVector(Vec pf,double kmax){ ++void Riftfront::PenaltyCreatePVector(Vector* pf,double kmax){ + + /*Retrieve parameters: */ + ElementVector* pe=NULL; +@@ -479,13 +479,13 @@ + } + /*}}}1*/ + /*FUNCTION Riftfront::CreateKMatrix {{{1*/ +-void Riftfront::CreateKMatrix(Mat Kff, Mat Kfs){ ++void Riftfront::CreateKMatrix(Matrix* Kff, Matrix* Kfs){ + /*do nothing: */ + return; + } + /*}}}1*/ + /*FUNCTION Riftfront::CreatePVector {{{1*/ +-void Riftfront::CreatePVector(Vec pf){ ++void Riftfront::CreatePVector(Vector* pf){ + /*do nothing: */ + return; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h (revision 11679) +@@ -15,6 +15,8 @@ + class IoModel; + class DataSet; + class Vertices; ++class Vector; ++class Matrix; + #include "./Update.h" + /*}}}*/ + +@@ -66,7 +68,7 @@ + /*}}}*/ + /*Node numerical routines {{{1*/ + void Configure(DataSet* nodes,Vertices* vertices); +- void CreateNodalConstraints(Vec ys); ++ void CreateNodalConstraints(Vector* ys); + void SetCurrentConfiguration(DataSet* nodes,Vertices* vertices); + int Sid(void); + int GetVertexDof(void); +@@ -100,8 +102,8 @@ + int IsFloating(); + int IsGrounded(); + void UpdateSpcs(double* ys); +- void VecMerge(Vec ug, double* vector_serial,int setnum); +- void VecReduce(Vec vector, double* ug_serial,int setnum); ++ void VecMerge(Vector* ug, double* vector_serial,int setenum); ++ void VecReduce(Vector* vector, double* ug_serial,int setnum); + + /*}}}*/ + /*Dof Object routines {{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11679) +@@ -15,6 +15,8 @@ + class DataSet; + class Parameters; + class Patch; ++class Matrix; ++class Vector; + + #include "../../toolkits/toolkits.h" + /*}}}*/ +@@ -27,10 +29,10 @@ + + virtual void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0; + virtual void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0; +- virtual void CreateKMatrix(Mat Kff, Mat Kfs,Vec df)=0; +- virtual void CreatePVector(Vec pf)=0; +- virtual void CreateJacobianMatrix(Mat Jff)=0; +- virtual void GetSolutionFromInputs(Vec solution)=0; ++ virtual void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df)=0; ++ virtual void CreatePVector(Vector* pf)=0; ++ virtual void CreateJacobianMatrix(Matrix* Jff)=0; ++ virtual void GetSolutionFromInputs(Vector* solution)=0; + virtual int GetNodeIndex(Node* node)=0; + virtual int Sid()=0; + virtual bool IsFloating()=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11679) +@@ -318,7 +318,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::CreateKMatrix {{{1*/ +-void Tria::CreateKMatrix(Mat Kff, Mat Kfs,Vec df){ ++void Tria::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){ + + /*retreive parameters: */ + ElementMatrix* Ke=NULL; +@@ -671,7 +671,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::CreatePVector {{{1*/ +-void Tria::CreatePVector(Vec pf){ ++void Tria::CreatePVector(Vector* pf){ + + /*retrive parameters: */ + ElementVector* pe=NULL; +@@ -891,7 +891,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::CreateJacobianMatrix{{{1*/ +-void Tria::CreateJacobianMatrix(Mat Jff){ ++void Tria::CreateJacobianMatrix(Matrix* Jff){ + + /*retrieve parameters: */ + ElementMatrix* Ke=NULL; +@@ -1273,7 +1273,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetSolutionFromInputs{{{1*/ +-void Tria::GetSolutionFromInputs(Vec solution){ ++void Tria::GetSolutionFromInputs(Vector* solution){ + + /*retrive parameters: */ + int analysis_type; +@@ -3138,7 +3138,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetSolutionFromInputsDiagnosticHoriz{{{1*/ +-void Tria::GetSolutionFromInputsDiagnosticHoriz(Vec solution){ ++void Tria::GetSolutionFromInputsDiagnosticHoriz(Vector* solution){ + + const int numdof=NDOF2*NUMVERTICES; + +@@ -3169,7 +3169,7 @@ + values[i*NDOF2+1]=vy; + } + +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -3177,7 +3177,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetSolutionFromInputsDiagnosticHutter{{{1*/ +-void Tria::GetSolutionFromInputsDiagnosticHutter(Vec solution){ ++void Tria::GetSolutionFromInputsDiagnosticHutter(Vector* solution){ + + const int numdof=NDOF2*NUMVERTICES; + +@@ -3208,7 +3208,7 @@ + values[i*NDOF2+1]=vy; + } + +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -4880,6 +4880,7 @@ + xfree((void**)&doflist); + } + /*}}}*/ ++ + /*FUNCTION Tria::InputUpdateFromSolutionAdjointBalancethickness {{{1*/ + void Tria::InputUpdateFromSolutionAdjointBalancethickness(double* solution){ + +@@ -5184,7 +5185,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetSolutionFromInputsHydrology{{{1*/ +-void Tria::GetSolutionFromInputsHydrology(Vec solution){ ++void Tria::GetSolutionFromInputsHydrology(Vector* solution){ + + const int numdof=NDOF1*NUMVERTICES; + +@@ -5212,7 +5213,7 @@ + values[i]=watercolumn; + } + +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11679) +@@ -81,9 +81,9 @@ + void ComputeStressTensor(); + void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs,Vec df); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff); + int GetNodeIndex(Node* node); + int Sid(); + bool IsOnBed(); +@@ -91,7 +91,7 @@ + bool IsNodeOnShelf(); + bool IsNodeOnShelfFromFlags(double* flags); + bool IsOnWater(); +- void GetSolutionFromInputs(Vec solution); ++ void GetSolutionFromInputs(Vector* solution); + void GetVectorFromInputs(Vec vector, int name_enum); + void GetVectorFromResults(Vec vector,int offset,int interp); + void InputArtificialNoise(int enum_type,double min, double max); +@@ -209,8 +209,8 @@ + ElementVector* CreatePVectorDiagnosticMacAyeal(void); + ElementVector* CreatePVectorDiagnosticHutter(void); + ElementMatrix* CreateJacobianDiagnosticMacayeal(void); +- void GetSolutionFromInputsDiagnosticHoriz(Vec solution); +- void GetSolutionFromInputsDiagnosticHutter(Vec solution); ++ void GetSolutionFromInputsDiagnosticHoriz(Vector* solution); ++ void GetSolutionFromInputsDiagnosticHutter(Vector* solution); + void InputUpdateFromSolutionDiagnosticHoriz( double* solution); + void InputUpdateFromSolutionDiagnosticHutter( double* solution); + #endif +@@ -229,7 +229,7 @@ + ElementMatrix* CreateKMatrixHydrology(void); + ElementVector* CreatePVectorHydrology(void); + void CreateHydrologyWaterVelocityInput(void); +- void GetSolutionFromInputsHydrology(Vec solution); ++ void GetSolutionFromInputsHydrology(Vector* solution); + void InputUpdateFromSolutionHydrology(double* solution); + #endif + #ifdef _HAVE_BALANCED_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11679) +@@ -566,7 +566,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::CreateKMatrix {{{1*/ +-void Penta::CreateKMatrix(Mat Kff, Mat Kfs,Vec df){ ++void Penta::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){ + + /*retrieve parameters: */ + ElementMatrix* Ke=NULL; +@@ -670,7 +670,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::CreatePVector {{{1*/ +-void Penta::CreatePVector(Vec pf){ ++void Penta::CreatePVector(Vector* pf){ + + /*retrive parameters: */ + ElementVector* pe=NULL; +@@ -772,7 +772,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::CreateJacobianMatrix{{{1*/ +-void Penta::CreateJacobianMatrix(Mat Jff){ ++void Penta::CreateJacobianMatrix(Matrix* Jff){ + + /*retrieve parameters: */ + ElementMatrix* Ke=NULL; +@@ -1090,7 +1090,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputs{{{1*/ +-void Penta::GetSolutionFromInputs(Vec solution){ ++void Penta::GetSolutionFromInputs(Vector* solution){ + + int analysis_type; + +@@ -4179,7 +4179,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputsThermal{{{1*/ +-void Penta::GetSolutionFromInputsThermal(Vec solution){ ++void Penta::GetSolutionFromInputsThermal(Vector* solution){ + + const int numdof=NDOF1*NUMVERTICES; + +@@ -4202,7 +4202,7 @@ + } + + /*Add value to global vector*/ +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -4210,7 +4210,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputsEnthalpy{{{1*/ +-void Penta::GetSolutionFromInputsEnthalpy(Vec solution){ ++void Penta::GetSolutionFromInputsEnthalpy(Vector* solution){ + + const int numdof=NDOF1*NUMVERTICES; + +@@ -4233,7 +4233,7 @@ + } + + /*Add value to global vector*/ +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -7839,7 +7839,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputsDiagnosticHoriz{{{1*/ +-void Penta::GetSolutionFromInputsDiagnosticHoriz(Vec solution){ ++void Penta::GetSolutionFromInputsDiagnosticHoriz(Vector* solution){ + + const int numdof=NDOF2*NUMVERTICES; + +@@ -7873,7 +7873,7 @@ + } + + /*Add value to global vector*/ +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -7881,7 +7881,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputsDiagnosticHutter{{{1*/ +-void Penta::GetSolutionFromInputsDiagnosticHutter(Vec solution){ ++void Penta::GetSolutionFromInputsDiagnosticHutter(Vector* solution){ + + const int numdof=NDOF2*NUMVERTICES; + +@@ -7909,7 +7909,7 @@ + } + + /*Add value to global vector*/ +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -7917,7 +7917,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputsDiagnosticVert{{{1*/ +-void Penta::GetSolutionFromInputsDiagnosticVert(Vec solution){ ++void Penta::GetSolutionFromInputsDiagnosticVert(Vector* solution){ + + const int numdof=NDOF1*NUMVERTICES; + +@@ -7942,7 +7942,7 @@ + } + + /*Add value to global vector*/ +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +@@ -7950,7 +7950,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputsDiagnosticStokes{{{1*/ +-void Penta::GetSolutionFromInputsDiagnosticStokes(Vec solution){ ++void Penta::GetSolutionFromInputsDiagnosticStokes(Vector* solution){ + + const int numdof=NDOF4*NUMVERTICES; + +@@ -7987,7 +7987,7 @@ + } + + /*Add value to global vector*/ +- VecSetValues(solution,numdof,doflist,(const double*)values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INSERT_VALUES); + + /*Free ressources:*/ + delete gauss; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11679) +@@ -85,12 +85,12 @@ + void ComputeStressTensor(); + void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); +- void CreateKMatrix(Mat Kff, Mat Kfs,Vec df); +- void CreatePVector(Vec pf); +- void CreateJacobianMatrix(Mat Jff); ++ void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df); ++ void CreatePVector(Vector* pf); ++ void CreateJacobianMatrix(Matrix* Jff); + void DeleteResults(void); + int GetNodeIndex(Node* node); +- void GetSolutionFromInputs(Vec solution); ++ void GetSolutionFromInputs(Vector* solution); + double GetZcoord(GaussPenta* gauss); + void GetVectorFromInputs(Vec vector,int name_enum); + void GetVectorFromResults(Vec vector,int offset,int interp); +@@ -182,7 +182,7 @@ + void GetInputListOnVertices(double* pvalue,int enumtype,double defaultvalue); + void GetInputValue(double* pvalue,Node* node,int enumtype); + void GetPhi(double* phi, double* epsilon, double viscosity); +- void GetSolutionFromInputsEnthalpy(Vec solutiong); ++ void GetSolutionFromInputsEnthalpy(Vector* solutiong); + double GetStabilizationParameter(double u, double v, double w, double diameter, double kappa); + void GetStrainRate3dPattyn(double* epsilon,double* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input); + void GetStrainRate3d(double* epsilon,double* xyz_list, GaussPenta* gauss, Input* vx_input, Input* vy_input, Input* vz_input); +@@ -249,10 +249,10 @@ + void InputUpdateFromSolutionDiagnosticHutter( double* solutiong); + void InputUpdateFromSolutionDiagnosticVert( double* solutiong); + void InputUpdateFromSolutionDiagnosticStokes( double* solutiong); +- void GetSolutionFromInputsDiagnosticHoriz(Vec solutiong); +- void GetSolutionFromInputsDiagnosticHutter(Vec solutiong); +- void GetSolutionFromInputsDiagnosticStokes(Vec solutiong); +- void GetSolutionFromInputsDiagnosticVert(Vec solutiong); ++ void GetSolutionFromInputsDiagnosticHoriz(Vector* solutiong); ++ void GetSolutionFromInputsDiagnosticHutter(Vector* solutiong); ++ void GetSolutionFromInputsDiagnosticStokes(Vector* solutiong); ++ void GetSolutionFromInputsDiagnosticVert(Vector* solutiong); + ElementVector* CreatePVectorCouplingMacAyealStokes(void); + ElementVector* CreatePVectorCouplingMacAyealStokesViscous(void); + ElementVector* CreatePVectorCouplingMacAyealStokesFriction(void); +@@ -306,7 +306,7 @@ + ElementVector* CreatePVectorThermalVolume(void); + ElementVector* CreatePVectorThermalShelf(void); + ElementVector* CreatePVectorThermalSheet(void); +- void GetSolutionFromInputsThermal(Vec solutiong); ++ void GetSolutionFromInputsThermal(Vector* solutiong); + void InputUpdateFromSolutionThermal( double* solutiong); + void InputUpdateFromSolutionEnthalpy( double* solutiong); + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp (revision 11679) +@@ -593,7 +593,7 @@ + } + /*}}}*/ + /*FUNCTION Node::CreateNodalConstraints{{{1*/ +-void Node::CreateNodalConstraints(Vec ys){ ++void Node::CreateNodalConstraints(Vector* ys){ + + int i; + double* values=NULL; +@@ -612,7 +612,7 @@ + } + + /*Add values into constraint vector: */ +- VecSetValues(ys,this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); ++ ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); + } + + /*Free ressources:*/ +@@ -874,7 +874,7 @@ + } + /*}}}*/ + /*FUNCTION Node::VecMerge {{{1*/ +-void Node::VecMerge(Vec ug, double* vector_serial,int setenum){ ++void Node::VecMerge(Vector* ug, double* vector_serial,int setenum){ + + double* values=NULL; + int* indices=NULL; +@@ -896,7 +896,7 @@ + } + + /*Add values into ug: */ +- VecSetValues(ug,this->indexing.fsize,indices,(const double*)values,INSERT_VALUES); ++ ug->SetValues(this->indexing.fsize,indices,values,INSERT_VALUES); + } + } + else if(setenum==SsetEnum){ +@@ -914,7 +914,7 @@ + } + + /*Add values into ug: */ +- VecSetValues(ug,this->indexing.ssize,indices,(const double*)values,INSERT_VALUES); ++ ug->SetValues(this->indexing.ssize,indices,values,INSERT_VALUES); + } + } + else _error_("VecMerge can only merge from the s or f-set onto the g-set!"); +@@ -925,7 +925,7 @@ + } + /*}}}*/ + /*FUNCTION Node::VecReduce {{{1*/ +-void Node::VecReduce(Vec vector, double* ug_serial,int setenum){ ++void Node::VecReduce(Vector* vector, double* ug_serial,int setenum){ + + double* values=NULL; + int count=0; +@@ -944,7 +944,7 @@ + } + + /*Add values into ug: */ +- VecSetValues(vector,this->indexing.fsize,this->indexing.fdoflist,(const double*)values,INSERT_VALUES); ++ vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INSERT_VALUES); + } + } + else if(setenum==SsetEnum){ +@@ -960,7 +960,7 @@ + } + + /*Add values into ug: */ +- VecSetValues(vector,this->indexing.ssize,this->indexing.sdoflist,(const double*)values,INSERT_VALUES); ++ vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); + } + } + else _error_("VecReduce can only merge from the s or f-set onto the g-set!"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_nonlinear.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_nonlinear.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_nonlinear.cpp (revision 11679) +@@ -13,12 +13,15 @@ + void solver_nonlinear(FemModel* femmodel,bool conserve_loads){ + + /*intermediary: */ +- Mat Kff = NULL, Kfs = NULL; +- Vec ug = NULL, old_ug = NULL; +- Vec uf = NULL, old_uf = NULL; +- Vec pf = NULL; +- Vec df = NULL; +- Vec ys = NULL; ++ Matrix* Kff = NULL; ++ Matrix* Kfs = NULL; ++ Vector* ug = NULL; ++ Vector* old_ug = NULL; ++ Vector* uf = NULL; ++ Vector* old_uf = NULL; ++ Vector* pf = NULL; ++ Vector* df = NULL; ++ Vector* ys = NULL; + + Loads* loads=NULL; + bool converged; +@@ -55,16 +58,16 @@ + for(;;){ + + //save pointer to old velocity +- VecFree(&old_ug);old_ug=ug; +- VecFree(&old_uf);old_uf=uf; ++ xdelete(&old_ug);old_ug=ug; ++ xdelete(&old_uf);old_uf=uf; + + SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf, Kfs, ys); MatFree(&Kfs); ++ Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); + Solverx(&uf, Kff, pf, old_uf, df, femmodel->parameters); +- Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&ys); ++ Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); + +- convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); MatFree(&Kff);VecFree(&pf); VecFree(&df); ++ convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); xdelete(&Kff); xdelete(&pf); xdelete(&df); + InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); + InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); + +@@ -95,8 +98,8 @@ + + /*clean-up*/ + if(conserve_loads) delete loads; +- VecFree(&uf); +- VecFree(&ug); +- VecFree(&old_ug); +- VecFree(&old_uf); ++ xdelete(&uf); ++ xdelete(&ug); ++ xdelete(&old_ug); ++ xdelete(&old_uf); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_linear.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_linear.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_linear.cpp (revision 11679) +@@ -10,12 +10,13 @@ + void solver_linear(FemModel* femmodel){ + + /*intermediary: */ +- Mat Kff = NULL, Kfs = NULL; +- Vec ug = NULL; +- Vec uf = NULL; +- Vec pf = NULL; +- Vec df = NULL; +- Vec ys = NULL; ++ Matrix* Kff = NULL; ++ Matrix* Kfs = NULL; ++ Vector* ug = NULL; ++ Vector* uf = NULL; ++ Vector* pf = NULL; ++ Vector* df = NULL; ++ Vector* ys = NULL; + int configuration_type; + + /*Recover parameters: */ +@@ -24,9 +25,10 @@ + + SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf, Kfs, ys); MatFree(&Kfs); +- Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); MatFree(&Kff); VecFree(&pf); VecFree(&df); +- Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&uf);VecFree(&ys); ++ Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); ++ Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); ++ xdelete(&Kff); xdelete(&pf); xdelete(&df); ++ Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&uf); xdelete(&ys); + InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); +- VecFree(&ug); VecFree(&uf); ++ xdelete(&ug); xdelete(&uf); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_newton.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_newton.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_newton.cpp (revision 11679) +@@ -17,12 +17,18 @@ + int num_unstable_constraints; + int count; + double kmax; +- Mat Kff = NULL, Kfs = NULL, Jff = NULL; +- Vec ug = NULL, old_ug = NULL; +- Vec uf = NULL, old_uf = NULL, duf = NULL; +- Vec pf = NULL, pJf = NULL; +- Vec df = NULL; +- Vec ys = NULL; ++ Matrix* Kff = NULL; ++ Matrix* Kfs = NULL; ++ Matrix* Jff = NULL; ++ Vector* ug = NULL; ++ Vector* old_ug = NULL; ++ Vector* uf = NULL; ++ Vector* old_uf = NULL; ++ Vector* duf = NULL; ++ Vector* pf = NULL; ++ Vector* pJf = NULL; ++ Vector* df = NULL; ++ Vector* ys = NULL; + + /*parameters:*/ + int max_nonlinear_iterations; +@@ -46,20 +52,20 @@ + + for(;;){ + +- VecFree(&old_ug);old_ug=ug; +- VecFree(&old_uf);old_uf=uf; ++ xdelete(&old_ug);old_ug=ug; ++ xdelete(&old_uf);old_uf=uf; + + /*Solver forward model*/ + SystemMatricesx(&Kff,&Kfs,&pf,&df,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf,Kfs,ys);MatFree(&Kfs); +- Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);VecFree(&df); +- Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&ys); +- InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug);VecFree(&ug); ++ Reduceloadx(pf,Kfs,ys);xdelete(&Kfs); ++ Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);xdelete(&df); ++ Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); ++ InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug);xdelete(&ug); + + /*Check convergence*/ + convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); +- MatFree(&Kff);VecFree(&pf); ++ xdelete(&Kff); xdelete(&pf); + if(converged==true) break; + if(count>=max_nonlinear_iterations){ + _printf_(true," maximum number of iterations (%i) exceeded\n",max_nonlinear_iterations); +@@ -69,17 +75,15 @@ + /*Prepare next iteration using Newton's method*/ + SystemMatricesx(&Kff,&Kfs,&pf,NULL,&kmax,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf,Kfs,ys); MatFree(&Kfs); ++ Reduceloadx(pf,Kfs,ys); xdelete(&Kfs); + +- VecDuplicate(pf,&pJf); +- MatMultPatch(Kff,uf,pJf); MatFree(&Kff); +- VecScale(pJf,-1.); +- VecAXPY(pJf,+1.,pf); VecFree(&pf); ++ pJf=pf->Duplicate(); Kff->MatMult(uf,pJf); xdelete(&Kff); ++ pJf->Scale(-1.0); pJf->AXPY(pf,+1.0); xdelete(&pf); + + CreateJacobianMatrixx(&Jff,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,kmax); +- Solverx(&duf,Jff,pJf,NULL,NULL,femmodel->parameters); MatFree(&Jff);VecFree(&pJf); +- VecAXPY(uf,1.,duf); VecFree(&duf); +- Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);VecFree(&ys); ++ Solverx(&duf,Jff,pJf,NULL,NULL,femmodel->parameters); xdelete(&Jff); xdelete(&pJf); ++ uf->AXPY(duf, 1.0); xdelete(&duf); ++ Mergesolutionfromftogx(&ug,uf,ys,femmodel->nodes,femmodel->parameters);xdelete(&ys); + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ug); + + count++; +@@ -88,8 +92,8 @@ + _printf_(VerboseConvergence(),"\n total number of iterations: %i\n",count-1); + + /*clean-up*/ +- VecFree(&uf); +- VecFree(&ug); +- VecFree(&old_ug); +- VecFree(&old_uf); ++ xdelete(&uf); ++ xdelete(&ug); ++ xdelete(&old_ug); ++ xdelete(&old_uf); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_stokescoupling_nonlinear.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_stokescoupling_nonlinear.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_stokescoupling_nonlinear.cpp (revision 11679) +@@ -13,15 +13,20 @@ + void solver_stokescoupling_nonlinear(FemModel* femmodel,bool conserve_loads){ + + /*intermediary: */ +- Mat Kff_horiz = NULL, Kfs_horiz = NULL; +- Vec ug_horiz = NULL, uf_horiz = NULL, old_uf_horiz = NULL; +- Vec pf_horiz = NULL; +- Vec df_horiz = NULL; +- Mat Kff_vert = NULL, Kfs_vert = NULL; +- Vec ug_vert = NULL, uf_vert = NULL; +- Vec pf_vert = NULL; +- Vec df_vert = NULL; +- Vec ys = NULL; ++ Matrix* Kff_horiz = NULL; ++ Matrix* Kfs_horiz = NULL; ++ Vector* ug_horiz = NULL; ++ Vector* uf_horiz = NULL; ++ Vector* old_uf_horiz = NULL; ++ Vector* pf_horiz = NULL; ++ Vector* df_horiz = NULL; ++ Matrix* Kff_vert = NULL; ++ Matrix* Kfs_vert = NULL; ++ Vector* ug_vert = NULL; ++ Vector* uf_vert = NULL; ++ Vector* pf_vert = NULL; ++ Vector* df_vert = NULL; ++ Vector* ys = NULL; + bool converged; + int constraints_converged; + int num_unstable_constraints; +@@ -53,20 +58,20 @@ + + //Update once again the solution to make sure that vx and vxold are similar (for next step in transient or steadystate) + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug_horiz); +- VecFree(&ug_horiz); ++ xdelete(&ug_horiz); + + //save pointer to old velocity +- VecFree(&old_uf_horiz);old_uf_horiz=uf_horiz; ++ xdelete(&old_uf_horiz); old_uf_horiz=uf_horiz; + + /*solve: */ + SystemMatricesx(&Kff_horiz, &Kfs_horiz, &pf_horiz, &df_horiz, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf_horiz, Kfs_horiz, ys); MatFree(&Kfs_horiz); ++ Reduceloadx(pf_horiz, Kfs_horiz, ys); xdelete(&Kfs_horiz); + Solverx(&uf_horiz, Kff_horiz, pf_horiz, old_uf_horiz, df_horiz,femmodel->parameters); +- Mergesolutionfromftogx(&ug_horiz, uf_horiz,ys,femmodel->nodes,femmodel->parameters); VecFree(&ys); ++ Mergesolutionfromftogx(&ug_horiz, uf_horiz,ys,femmodel->nodes,femmodel->parameters); xdelete(&ys); + InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug_horiz); + +- convergence(&converged,Kff_horiz,pf_horiz,uf_horiz,old_uf_horiz,femmodel->parameters); MatFree(&Kff_horiz);VecFree(&pf_horiz); VecFree(&df_horiz); ++ convergence(&converged,Kff_horiz,pf_horiz,uf_horiz,old_uf_horiz,femmodel->parameters); xdelete(&Kff_horiz); xdelete(&pf_horiz); xdelete(&df_horiz); + + /*Second compute vertical velocity: */ + femmodel->SetCurrentConfiguration(DiagnosticVertAnalysisEnum); +@@ -75,11 +80,11 @@ + /*solve: */ + SystemMatricesx(&Kff_vert, &Kfs_vert, &pf_vert, &df_vert,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf_vert, Kfs_vert, ys); MatFree(&Kfs_vert); +- Solverx(&uf_vert, Kff_vert, pf_vert, NULL, df_vert,femmodel->parameters); MatFree(&Kff_vert); VecFree(&pf_vert); VecFree(&df_vert); +- Mergesolutionfromftogx(&ug_vert, uf_vert,ys,femmodel->nodes,femmodel->parameters);VecFree(&uf_vert); VecFree(&ys); ++ Reduceloadx(pf_vert, Kfs_vert, ys); xdelete(&Kfs_vert); ++ Solverx(&uf_vert, Kff_vert, pf_vert, NULL, df_vert,femmodel->parameters); xdelete(&Kff_vert); xdelete(&pf_vert); xdelete(&df_vert); ++ Mergesolutionfromftogx(&ug_vert, uf_vert,ys,femmodel->nodes,femmodel->parameters);xdelete(&uf_vert); xdelete(&ys); + InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug_vert); +- VecFree(&ug_vert); VecFree(&uf_vert); ++ xdelete(&ug_vert); xdelete(&uf_vert); + + /*Increase count: */ + count++; +@@ -91,8 +96,8 @@ + } + + /*clean-up*/ +- VecFree(&old_uf_horiz); +- VecFree(&uf_horiz); +- VecFree(&ug_horiz); +- VecFree(&ys); ++ xdelete(&old_uf_horiz); ++ xdelete(&uf_horiz); ++ xdelete(&ug_horiz); ++ xdelete(&ys); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_thermal_nonlinear.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_thermal_nonlinear.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_thermal_nonlinear.cpp (revision 11679) +@@ -11,17 +11,17 @@ + void solver_thermal_nonlinear(FemModel* femmodel){ + + /*solution : */ +- Vec tg=NULL; +- Vec tf=NULL; +- Vec tf_old=NULL; +- Vec ys=NULL; ++ Vector* tg=NULL; ++ Vector* tf=NULL; ++ Vector* tf_old=NULL; ++ Vector* ys=NULL; + double melting_offset; + + /*intermediary: */ +- Mat Kff=NULL; +- Mat Kfs=NULL; +- Vec pf=NULL; +- Vec df=NULL; ++ Matrix* Kff=NULL; ++ Matrix* Kfs=NULL; ++ Vector* pf=NULL; ++ Vector* df=NULL; + + bool converged; + int constraints_converged; +@@ -55,11 +55,11 @@ + + SystemMatricesx(&Kff, &Kfs, &pf,&df, &melting_offset,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf, Kfs, ys); MatFree(&Kfs); VecFree(&tf); ++ Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); xdelete(&tf); + Solverx(&tf, Kff, pf,tf_old, df, femmodel->parameters); +- VecFree(&tf_old); VecDuplicatePatch(&tf_old,tf); +- MatFree(&Kff);VecFree(&pf);VecFree(&tg); VecFree(&df); +- Mergesolutionfromftogx(&tg, tf,ys,femmodel->nodes,femmodel->parameters); VecFree(&ys); ++ xdelete(&tf_old); tf_old=tf->Duplicate(); ++ xdelete(&Kff);xdelete(&pf);xdelete(&tg); xdelete(&df); ++ Mergesolutionfromftogx(&tg, tf,ys,femmodel->nodes,femmodel->parameters); xdelete(&ys); + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,tg); + + ConstraintsStatex(&constraints_converged, &num_unstable_constraints, femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); +@@ -83,8 +83,8 @@ + InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,melting_offset,MeltingOffsetEnum); + + /*Free ressources: */ +- VecFree(&tg); +- VecFree(&tf); +- VecFree(&tf_old); +- VecFree(&ys); ++ xdelete(&tg); ++ xdelete(&tf); ++ xdelete(&tf_old); ++ xdelete(&ys); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_adjoint_linear.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_adjoint_linear.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solvers/solver_adjoint_linear.cpp (revision 11679) +@@ -12,11 +12,13 @@ + * use the flag "true" so that all spc are taken as 0*/ + + /*intermediary: */ +- Mat Kff = NULL, Kfs = NULL; +- Vec ug = NULL, uf = NULL; +- Vec pf = NULL; +- Vec df = NULL; +- Vec ys = NULL; ++ Matrix* Kff = NULL; ++ Matrix* Kfs = NULL; ++ Vector* ug = NULL; ++ Vector* uf = NULL; ++ Vector* pf = NULL; ++ Vector* df = NULL; ++ Vector* ys = NULL; + int configuration_type; + + /*Recover parameters: */ +@@ -25,9 +27,9 @@ + + SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); +- Reduceloadx(pf, Kfs, ys,true); MatFree(&Kfs); //true means spc = 0 +- Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); MatFree(&Kff); VecFree(&pf); VecFree(&df); +- Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters,true); VecFree(&uf);VecFree(&ys); //true means spc0 ++ Reduceloadx(pf, Kfs, ys,true); xdelete(&Kfs); //true means spc = 0 ++ Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); xdelete(&Kff); xdelete(&pf); xdelete(&df); ++ Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters,true); xdelete(&uf);xdelete(&ys); //true means spc0 + InputUpdateFromSolutionx(femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); +- VecFree(&ug); VecFree(&uf); ++ xdelete(&ug); xdelete(&uf); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11679) +@@ -10,7 +10,7 @@ + Constraints *constraints = NULL; + Nodes *nodes = NULL; + Parameters *parameters = NULL; +- Vec yg = NULL; ++ Vector* yg = NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -31,7 +31,7 @@ + WriteMatlabData(CONSTRAINTSOUT,constraints); + + /*Free ressources: */ +- VecFree(&yg); ++ delete yg; + delete constraints; + delete nodes; + delete parameters; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp (revision 11679) +@@ -13,7 +13,7 @@ + Loads* loads=NULL; + Materials* materials=NULL; + Parameters* parameters=NULL; +- Vec ug=NULL; ++ Vector* ug=NULL; + + /* output datasets: elements and loads*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reduceload/Reduceload.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reduceload/Reduceload.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reduceload/Reduceload.cpp (revision 11679) +@@ -7,9 +7,9 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Vec pf = NULL; +- Mat Kfs = NULL; +- Vec ys = NULL; ++ Vector* pf = NULL; ++ Matrix* Kfs = NULL; ++ Vector* ys = NULL; + bool flag_ys0=false; + + /*Boot module: */ +@@ -39,9 +39,9 @@ + WriteMatlabData(PFOUT,pf); + + /*Free ressources: */ +- VecFree(&pf); +- MatFree(&Kfs); +- VecFree(&ys); ++ delete pf; ++ delete Kfs; ++ delete ys; + + MODULEEND(); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11679) +@@ -11,7 +11,7 @@ + int analysis_type; + + /* output datasets: */ +- Vec ys=NULL; ++ Vector* ys=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -31,7 +31,7 @@ + + /*Free ressources: */ + delete nodes; +- VecFree(&ys); ++ delete ys; + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11679) +@@ -7,12 +7,12 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Vec ug=NULL; ++ Vector* ug=NULL; + Nodes* nodes=NULL; + Parameters* parameters=NULL; + + /* output datasets: */ +- Vec uf=NULL; ++ Vector* uf=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -34,8 +34,8 @@ + /*Free ressources: */ + delete nodes; + delete parameters; +- VecFree(&ug); +- VecFree(&uf); ++ delete ug; ++ delete uf; + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11679) +@@ -16,10 +16,10 @@ + bool kflag,pflag,penalty_kflag,penalty_pflag; + + /* output datasets: */ +- Mat Kff = NULL; +- Mat Kfs = NULL; +- Vec pf = NULL; +- Vec df = NULL; ++ Matrix* Kff = NULL; ++ Matrix* Kfs = NULL; ++ Vector* pf = NULL; ++ Vector* df = NULL; + + double kmax; + +@@ -71,10 +71,10 @@ + delete loads; + delete materials; + delete parameters; +- MatFree(&Kff); +- MatFree(&Kfs); +- VecFree(&pf); +- VecFree(&df); ++ delete Kff; ++ delete Kfs; ++ delete pf; ++ delete df; + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11679) +@@ -13,7 +13,7 @@ + Loads* loads=NULL; + Materials* materials=NULL; + Parameters* parameters=NULL; +- Vec solution=NULL; ++ Vector* solution=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -49,7 +49,7 @@ + delete loads; + delete materials; + delete parameters; +- VecFree(&solution); ++ delete solution; + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11679) +@@ -7,12 +7,12 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Vec yg=NULL; ++ Vector* yg=NULL; + Nodes* nodes=NULL; + Parameters* parameters=NULL; + + /* output datasets: */ +- Vec ys=NULL; ++ Vector* ys=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -34,8 +34,8 @@ + /*Free ressources: */ + delete nodes; + delete parameters; +- VecFree(&yg); +- VecFree(&ys); ++ delete yg; ++ delete ys; + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11679) +@@ -8,13 +8,13 @@ + + /*input datasets: */ + bool flag_ys0; +- Vec uf = NULL; +- Vec ys = NULL; ++ Vector* uf = NULL; ++ Vector* ys = NULL; + Nodes* nodes = NULL; + Parameters* parameters = NULL; + + /* output datasets: */ +- Vec ug=NULL; ++ Vector* ug=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -44,9 +44,9 @@ + WriteMatlabData(UG,ug); + + /*Free ressources: */ +- VecFree(&uf); +- VecFree(&ug); +- VecFree(&ys); ++ delete uf; ++ delete ug; ++ delete ys; + delete nodes; + delete parameters; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp (revision 11679) +@@ -16,7 +16,7 @@ + double kmax; + + /* output datasets: */ +- Mat Jff = NULL; ++ Matrix* Jff = NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -52,7 +52,7 @@ + delete loads; + delete materials; + delete parameters; +- MatFree(&Jff); ++ delete Jff; + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp (revision 11678) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp (revision 11679) +@@ -7,11 +7,11 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Mat Kff = NULL; +- Vec pf = NULL; +- Vec uf0 = NULL; +- Vec uf = NULL; +- Vec df = NULL; ++ Matrix* Kff = NULL; ++ Vector* pf = NULL; ++ Vector* uf0 = NULL; ++ Vector* uf = NULL; ++ Vector* df = NULL; + Parameters *parameters = NULL; + int analysis_type; + char option[100]; +@@ -65,11 +65,11 @@ + } + + /*Free ressources: */ +- MatFree(&Kff); +- VecFree(&pf); +- VecFree(&uf0); +- VecFree(&uf); +- VecFree(&df); ++ delete Kff; ++ delete pf; ++ delete uf0; ++ delete uf; ++ delete df; + delete parameters; + + MODULEEND(); Index: /issm/oecreview/Archive/11666-11680/ISSM-11679-11680.diff =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-11679-11680.diff (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-11679-11680.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11679) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11680) +@@ -257,10 +257,10 @@ + DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + ;; + *darwin*) +- DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver " ++ DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" ++ dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack" + ;; + esac +- dnl DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lgslcblas -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" + AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src]) + AC_SUBST([DAKOTAINCL]) + AC_SUBST([DAKOTALIB]) Index: /issm/oecreview/Archive/11666-11680/ISSM-DocReview-11666-11680.tex =================================================================== --- /issm/oecreview/Archive/11666-11680/ISSM-DocReview-11666-11680.tex (revision 11991) +++ /issm/oecreview/Archive/11666-11680/ISSM-DocReview-11666-11680.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11666-11680/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11666-11680/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11666-11680/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11666-11680 Index: /issm/oecreview/Archive/11666-11680/Makefile =================================================================== --- /issm/oecreview/Archive/11666-11680/Makefile (revision 11991) +++ /issm/oecreview/Archive/11666-11680/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11666-11680 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11666-11680/log.tex =================================================================== --- /issm/oecreview/Archive/11666-11680/log.tex (revision 11991) +++ /issm/oecreview/Archive/11666-11680/log.tex (revision 11991) @@ -0,0 +1,28 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11666-11667.diff: \\ Function name: \\M /issm/trunk-jpl/configure.ac \\ Export determination: 6. \\Rationale: Took out ad/Makefile.am in configure.ac +A /issm/trunk-jpl/cron/configs/linux64\_borstad\_daily A /issm/trunk-jpl/cron/configs/linux64\_borstad\_nightly A /issm/trunk-jpl/cron/configs/linux64\_borstad\_ucitrunk A /issm/trunk-jpl/cron/configs/linux64\_borstad\_validation A /issm/trunk-jpl/cron/configs/macosx64\_borstad A /issm/trunk-jpl/cron/configs/macosx64\_borstad\_daily borstad config files for nightly runs \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11667-11668.diff: \\ Function name: \\A /issm/trunk-jpl/cron/configs/linux64\_borstad\_daily A /issm/trunk-jpl/cron/configs/linux64\_borstad\_nightly A /issm/trunk-jpl/cron/configs/linux64\_borstad\_ucitrunk A /issm/trunk-jpl/cron/configs/linux64\_borstad\_validation A /issm/trunk-jpl/cron/configs/macosx64\_borstad A /issm/trunk-jpl/cron/configs/macosx64\_borstad\_daily \\ Export determination: 6. \\Rationale: borstad config files for nightly runs +M /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt fix some typos \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11668-11669.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/windows/InstallInstructions.txt \\ Export determination: 6. \\Rationale: fix some typos +M /issm/trunk-jpl/m4/issm\_options.m4 Added adolc package \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11669-11670.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: Added adolc package +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/matlabio.h A /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp A /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h A /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp A /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/objects/objects.h A /issm/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp A /issm/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp M /issm/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h Starting abstraction of Matrix and Vector objects, to step away from Petsc libraries. \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11670-11671.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/matlabio.h A /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp A /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h A /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp A /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/objects/objects.h A /issm/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp A /issm/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp M /issm/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h \\ Export determination: 6. \\Rationale: Starting abstraction of Matrix and Vector objects, to step away from Petsc libraries. +D /issm/trunk-jpl/externalpackages/android Not needed anymore \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11671-11672.diff: \\ Function name: \\D /issm/trunk-jpl/externalpackages/android \\ Export determination: 6. \\Rationale: Not needed anymore +A /issm/trunk-jpl/src/android New android directory for development. Not connected \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11672-11673.diff: \\ Function name: \\A /issm/trunk-jpl/src/android \\ Export determination: 6. \\Rationale: New android directory for development. Not connected +M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh A /issm/trunk-jpl/externalpackages/android-emulators A /issm/trunk-jpl/externalpackages/android-ndk A /issm/trunk-jpl/externalpackages/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 A /issm/trunk-jpl/externalpackages/android-ndk/install.sh A /issm/trunk-jpl/externalpackages/android-sdk A /issm/trunk-jpl/externalpackages/android-sdk/android-sdk-r16-macosx.zip A /issm/trunk-jpl/externalpackages/android-sdk/apache-ant-1.8.2-bin.zip A /issm/trunk-jpl/externalpackages/android-sdk/install.sh Setting up the externalpackages for the android build. \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11673-11674.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh A /issm/trunk-jpl/externalpackages/android-emulators A /issm/trunk-jpl/externalpackages/android-ndk A /issm/trunk-jpl/externalpackages/android-ndk/android-ndk-r7b-darwin-x86.tar.bz2 A /issm/trunk-jpl/externalpackages/android-ndk/install.sh A /issm/trunk-jpl/externalpackages/android-sdk A /issm/trunk-jpl/externalpackages/android-sdk/android-sdk-r16-macosx.zip A /issm/trunk-jpl/externalpackages/android-sdk/apache-ant-1.8.2-bin.zip A /issm/trunk-jpl/externalpackages/android-sdk/install.sh \\ Export determination: 6. \\Rationale: Setting up the externalpackages for the android build. +M /issm/trunk-jpl/src/m/classes/friction.m minor display of friction \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11674-11675.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/classes/friction.m \\ Export determination: 6. \\Rationale: minor display of friction +M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp Added support for 'single' matlab format \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11675-11676.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp \\ Export determination: 6. \\Rationale: Added support for 'single' matlab format +A /issm/trunk-jpl/examples/Jakobshavn A /issm/trunk-jpl/examples/Jakobshavn/Domain.exp A /issm/trunk-jpl/examples/Jakobshavn/Front.exp A /issm/trunk-jpl/examples/Jakobshavn/Jks.par A /issm/trunk-jpl/examples/Jakobshavn/WeakB.exp A /issm/trunk-jpl/examples/Jakobshavn/runme.m M /issm/trunk-jpl/examples/SquareIceShelf/runme.m Added Jks tutorial \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11676-11677.diff: \\ Function name: \\A /issm/trunk-jpl/examples/Jakobshavn A /issm/trunk-jpl/examples/Jakobshavn/Domain.exp A /issm/trunk-jpl/examples/Jakobshavn/Front.exp A /issm/trunk-jpl/examples/Jakobshavn/Jks.par A /issm/trunk-jpl/examples/Jakobshavn/WeakB.exp A /issm/trunk-jpl/examples/Jakobshavn/runme.m M /issm/trunk-jpl/examples/SquareIceShelf/runme.m \\ Export determination: 6. \\Rationale: Added Jks tutorial +M /issm/trunk-jpl/examples/SquareIceShelf/runme.m reverted back to normal \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11677-11678.diff: \\ Function name: \\M /issm/trunk-jpl/examples/SquareIceShelf/runme.m \\ Export determination: 6. \\Rationale: reverted back to normal +M /issm/trunk-jpl/examples/Jakobshavn/Jks.par simplified \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11678-11679.diff: \\ Function name: \\M /issm/trunk-jpl/examples/Jakobshavn/Jks.par \\ Export determination: 6. \\Rationale: simplified +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp M /issm/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h M /issm/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp M /issm/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h M /issm/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h M /issm/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp M /issm/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h M /issm/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp M /issm/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.h M /issm/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp M /issm/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h M /issm/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp M /issm/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.h A /issm/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h M /issm/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp M /issm/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h M /issm/trunk-jpl/src/c/modules/VecMergex/VecMergex.cpp M /issm/trunk-jpl/src/c/modules/VecMergex/VecMergex.h M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/c/objects/Loads/Icefront.cpp M /issm/trunk-jpl/src/c/objects/Loads/Icefront.h M /issm/trunk-jpl/src/c/objects/Loads/Load.h M /issm/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp M /issm/trunk-jpl/src/c/objects/Loads/Numericalflux.h M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.cpp M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.h M /issm/trunk-jpl/src/c/objects/Loads/Penpair.cpp M /issm/trunk-jpl/src/c/objects/Loads/Penpair.h M /issm/trunk-jpl/src/c/objects/Loads/Riftfront.cpp M /issm/trunk-jpl/src/c/objects/Loads/Riftfront.h M /issm/trunk-jpl/src/c/objects/Node.cpp M /issm/trunk-jpl/src/c/objects/Node.h M /issm/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementMatrix.h M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.h M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp M /issm/trunk-jpl/src/c/shared/Alloc/alloc.h M /issm/trunk-jpl/src/c/solutions/ResetBoundaryConditions.cpp M /issm/trunk-jpl/src/c/solutions/convergence.cpp M /issm/trunk-jpl/src/c/solutions/solutions.h M /issm/trunk-jpl/src/c/solvers/solver\_adjoint\_linear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_linear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_newton.cpp M /issm/trunk-jpl/src/c/solvers/solver\_nonlinear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_stokescoupling\_nonlinear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_thermal\_nonlinear.cpp M /issm/trunk-jpl/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp M /issm/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp M /issm/trunk-jpl/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp M /issm/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp M /issm/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp M /issm/trunk-jpl/src/mex/Reduceload/Reduceload.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp M /issm/trunk-jpl/src/mex/Solver/Solver.cpp M /issm/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp M /issm/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp Large commit, to strip out Petsc from the code. Created new Matrix and Vector wrapper objects to the Petsc Mat and Vec objects. These wrappers make it possible to hook up a different package to handle matrix and vector operations. \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11679-11680.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp M /issm/trunk-jpl/src/c/modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h M /issm/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.cpp M /issm/trunk-jpl/src/c/modules/CreateNodalConstraintsx/CreateNodalConstraintsx.h M /issm/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetSolutionFromInputsx/GetSolutionFromInputsx.h M /issm/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.cpp M /issm/trunk-jpl/src/c/modules/InputUpdateFromSolutionx/InputUpdateFromSolutionx.h M /issm/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp M /issm/trunk-jpl/src/c/modules/Mergesolutionfromftogx/Mergesolutionfromftogx.h M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.h M /issm/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.cpp M /issm/trunk-jpl/src/c/modules/Reducevectorgtofx/Reducevectorgtofx.h M /issm/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.cpp M /issm/trunk-jpl/src/c/modules/Reducevectorgtosx/Reducevectorgtosx.h M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.h A /issm/trunk-jpl/src/c/modules/Solverx/SolverxPetsc.cpp M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h M /issm/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.cpp M /issm/trunk-jpl/src/c/modules/UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h M /issm/trunk-jpl/src/c/modules/VecMergex/VecMergex.cpp M /issm/trunk-jpl/src/c/modules/VecMergex/VecMergex.h M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/c/objects/Loads/Icefront.cpp M /issm/trunk-jpl/src/c/objects/Loads/Icefront.h M /issm/trunk-jpl/src/c/objects/Loads/Load.h M /issm/trunk-jpl/src/c/objects/Loads/Numericalflux.cpp M /issm/trunk-jpl/src/c/objects/Loads/Numericalflux.h M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.cpp M /issm/trunk-jpl/src/c/objects/Loads/Pengrid.h M /issm/trunk-jpl/src/c/objects/Loads/Penpair.cpp M /issm/trunk-jpl/src/c/objects/Loads/Penpair.h M /issm/trunk-jpl/src/c/objects/Loads/Riftfront.cpp M /issm/trunk-jpl/src/c/objects/Loads/Riftfront.h M /issm/trunk-jpl/src/c/objects/Node.cpp M /issm/trunk-jpl/src/c/objects/Node.h M /issm/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementMatrix.h M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.h M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp M /issm/trunk-jpl/src/c/shared/Alloc/alloc.h M /issm/trunk-jpl/src/c/solutions/ResetBoundaryConditions.cpp M /issm/trunk-jpl/src/c/solutions/convergence.cpp M /issm/trunk-jpl/src/c/solutions/solutions.h M /issm/trunk-jpl/src/c/solvers/solver\_adjoint\_linear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_linear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_newton.cpp M /issm/trunk-jpl/src/c/solvers/solver\_nonlinear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_stokescoupling\_nonlinear.cpp M /issm/trunk-jpl/src/c/solvers/solver\_thermal\_nonlinear.cpp M /issm/trunk-jpl/src/mex/CreateJacobianMatrix/CreateJacobianMatrix.cpp M /issm/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp M /issm/trunk-jpl/src/mex/GetSolutionFromInputs/GetSolutionFromInputs.cpp M /issm/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp M /issm/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp M /issm/trunk-jpl/src/mex/Reduceload/Reduceload.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp M /issm/trunk-jpl/src/mex/Solver/Solver.cpp M /issm/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp M /issm/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp \\ Export determination: 6. \\Rationale: Large commit, to strip out Petsc from the code. Created new Matrix and Vector wrapper objects to the Petsc Mat and Vec objects. These wrappers make it possible to hook up a different package to handle matrix and vector operations. +M /issm/trunk-jpl/m4/issm\_options.m4 Simplifying dakota glitch \\\\ Index: /issm/oecreview/Archive/11666-11680/r1.tex =================================================================== --- /issm/oecreview/Archive/11666-11680/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11666-11680/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11666 Index: /issm/oecreview/Archive/11666-11680/r2.tex =================================================================== --- /issm/oecreview/Archive/11666-11680/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11666-11680/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11680 Index: /issm/oecreview/Archive/11681-11700/Date.tex =================================================================== --- /issm/oecreview/Archive/11681-11700/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11681-11700/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11681-11700/ISSM-11684-11685.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11684-11685.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11684-11685.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11684) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11685) +@@ -50,7 +50,7 @@ + + + /*Free ressources and return*/ +- delete y_s0; +- delete Kfsy_s; ++ xdelete(&y_s0); ++ xdelete(&Kfsy_s); + + } Index: /issm/oecreview/Archive/11681-11700/ISSM-11685-11686.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11685-11686.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11685-11686.diff (revision 11991) @@ -0,0 +1,164 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp (revision 11686) +@@ -31,7 +31,7 @@ + WriteMatlabData(CONSTRAINTSOUT,constraints); + + /*Free ressources: */ +- delete yg; ++ xdelete(&yg); + delete constraints; + delete nodes; + delete parameters; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reduceload/Reduceload.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reduceload/Reduceload.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reduceload/Reduceload.cpp (revision 11686) +@@ -39,9 +39,9 @@ + WriteMatlabData(PFOUT,pf); + + /*Free ressources: */ +- delete pf; +- delete Kfs; +- delete ys; ++ xdelete(&pf); ++ xdelete(&Kfs); ++ xdelete(&ys); + + MODULEEND(); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp (revision 11686) +@@ -31,7 +31,7 @@ + + /*Free ressources: */ + delete nodes; +- delete ys; ++ xdelete(&ys); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11686) +@@ -34,8 +34,8 @@ + /*Free ressources: */ + delete nodes; + delete parameters; +- delete ug; +- delete uf; ++ xdelete(&ug); ++ xdelete(&uf); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp (revision 11686) +@@ -71,10 +71,10 @@ + delete loads; + delete materials; + delete parameters; +- delete Kff; +- delete Kfs; +- delete pf; +- delete df; ++ xdelete(&Kff); ++ xdelete(&Kfs); ++ xdelete(&pf); ++ xdelete(&df); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp (revision 11686) +@@ -7,13 +7,13 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Elements* elements=NULL; +- Nodes* nodes=NULL; +- Vertices* vertices=NULL; +- Loads* loads=NULL; +- Materials* materials=NULL; +- Parameters* parameters=NULL; +- Vector* solution=NULL; ++ Elements *elements = NULL; ++ Nodes *nodes = NULL; ++ Vertices *vertices = NULL; ++ Loads *loads = NULL; ++ Materials *materials = NULL; ++ Parameters *parameters = NULL; ++ Vector *solution = NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -49,7 +49,7 @@ + delete loads; + delete materials; + delete parameters; +- delete solution; ++ xdelete(&solution); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp (revision 11686) +@@ -34,8 +34,8 @@ + /*Free ressources: */ + delete nodes; + delete parameters; +- delete yg; +- delete ys; ++ xdelete(&yg); ++ xdelete(&ys); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp (revision 11686) +@@ -44,9 +44,9 @@ + WriteMatlabData(UG,ug); + + /*Free ressources: */ +- delete uf; +- delete ug; +- delete ys; ++ xdelete(&uf); ++ xdelete(&ug); ++ xdelete(&ys); + delete nodes; + delete parameters; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp (revision 11685) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp (revision 11686) +@@ -65,11 +65,11 @@ + } + + /*Free ressources: */ +- delete Kff; +- delete pf; +- delete uf0; +- delete uf; +- delete df; ++ xdelete(&Kff); ++ xdelete(&pf); ++ xdelete(&uf0); ++ xdelete(&uf); ++ xdelete(&df); + delete parameters; + + MODULEEND(); Index: /issm/oecreview/Archive/11681-11700/ISSM-11686-11687.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11686-11687.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11686-11687.diff (revision 11991) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11686) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11687) +@@ -20,10 +20,12 @@ + uf=new Vector(); + + #ifdef _HAVE_PETSC_ +- Vec uf0_vector=NULL; +- if (uf0)uf0_vector=uf0->vector; ++ Vec uf0_vector = NULL; ++ Vec df_vector = NULL; ++ if(uf0) uf0_vector=uf0->vector; ++ if(df) df_vector = df->vector; + +- SolverxPetsc(&uf->vector, Kff->matrix, pf->vector, uf0_vector, df->vector, parameters); ++ SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); + VecGetSize(uf->vector,&uf->M); + #else + _error_("not supported yet!"); Index: /issm/oecreview/Archive/11681-11700/ISSM-11687-11688.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11687-11688.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11687-11688.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11687) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11688) +@@ -169,7 +169,7 @@ + void Vector::Set(double value){ + + #ifdef _HAVE_PETSC_ +- this->Set(value); ++ this->vector->Set(value); + #else + _error_("not implemented yet!"); + #endif Index: /issm/oecreview/Archive/11681-11700/ISSM-11688-11689.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11688-11689.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11688-11689.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11688) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11689) +@@ -169,7 +169,7 @@ + void Vector::Set(double value){ + + #ifdef _HAVE_PETSC_ +- this->vector->Set(value); ++ this->vector->VecSet(value); + #else + _error_("not implemented yet!"); + #endif Index: /issm/oecreview/Archive/11681-11700/ISSM-11689-11690.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11689-11690.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11689-11690.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11689) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11690) +@@ -169,7 +169,7 @@ + void Vector::Set(double value){ + + #ifdef _HAVE_PETSC_ +- this->vector->VecSet(value); ++ VecSet(this->vector,value); + #else + _error_("not implemented yet!"); + #endif Index: /issm/oecreview/Archive/11681-11700/ISSM-11690-11691.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11690-11691.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11690-11691.diff (revision 11991) @@ -0,0 +1,43 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11690) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11691) +@@ -68,8 +68,6 @@ + Kff->Assemble(); + Kfs->Assemble(); + df->Assemble(); +- +- + } + + if(pflag){ +@@ -87,7 +85,6 @@ + load=(Load*)loads->GetObjectByOffset(i); + if (load->InAnalysis(configuration_type)) load->CreatePVector(pf); + } +- + pf->Assemble(); + } + +@@ -118,17 +115,16 @@ + } + + pf->Assemble(); +- pf->Assemble(); + } + + /*Assign output pointers: */ + if(pKff) *pKff=Kff; +- else delete Kff; ++ else xdelete(&Kff); + if(pKfs) *pKfs=Kfs; +- else delete Kfs; ++ else xdelete(&Kfs); + if(ppf) *ppf=pf; +- else delete pf; ++ else xdelete(&pf); + if(pdf) *pdf=df; +- else delete df; ++ else xdelete(&df); + if(pkmax) *pkmax=kmax; + } Index: /issm/oecreview/Archive/11681-11700/ISSM-11691-11692.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11691-11692.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11691-11692.diff (revision 11991) @@ -0,0 +1,56 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11691) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11692) +@@ -66,40 +66,36 @@ + return memptr; + } + +-void xfree( void* *pv){ ++void xfree(void* *pv){ + +- if (pv && *pv) { +- ++ if (pv && *pv){ + #ifdef _SERIAL_ +- mxFree(*pv); ++ mxFree(*pv); + #else +- free(*pv); ++ free(*pv); + #endif + + *pv=NULL; + } + } + +-void xdelete( Matrix** pv){ +- +- if (pv && *pv) { +- ++void xdelete(Matrix** pv){ ++ if (pv && *pv){ + delete *pv; + *pv=NULL; + } + } + +-void xdelete( Vector** pv){ +- +- if (pv && *pv) { +- +- delete *pv; ++void xdelete(Vector** pv){ ++ if (pv && *pv){ ++ //delete *pv; ++ VecFree(&(*pv)->vector); + *pv=NULL; + } + } + + +-void* xrealloc ( void* pv, int size){ ++void* xrealloc( void* pv, int size){ + + register void* value=NULL; + Index: /issm/oecreview/Archive/11681-11700/ISSM-11692-11693.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11692-11693.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11692-11693.diff (revision 11991) @@ -0,0 +1,34 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11692) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11693) +@@ -80,16 +80,27 @@ + } + + void xdelete(Matrix** pv){ ++ + if (pv && *pv){ ++ #ifdef _HAVE_PARALLEL_ ++ /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we ++ * don't actually free memory in Matlab, we let the memory manager do that. We only ++ * free in parallel: */ + delete *pv; ++ #endif + *pv=NULL; + } + } + + void xdelete(Vector** pv){ ++ + if (pv && *pv){ +- //delete *pv; +- VecFree(&(*pv)->vector); ++ #ifdef _HAVE_PARALLEL_ ++ /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we ++ * don't actually free memory in Matlab, we let the memory manager do that. We only ++ * free in parallel: */ ++ delete *pv; ++ #endif + *pv=NULL; + } + } Index: /issm/oecreview/Archive/11681-11700/ISSM-11693-11694.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11693-11694.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11693-11694.diff (revision 11991) @@ -0,0 +1,26 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11693) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11694) +@@ -87,6 +87,10 @@ + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ + delete *pv; ++ #else ++ /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ ++ * correctly: */ ++ MatFree(&(*pv)->matrix); + #endif + *pv=NULL; + } +@@ -100,6 +104,10 @@ + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ + delete *pv; ++ #else ++ /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ ++ * correctly: */ ++ VecFree(&(*pv)->vector); + #endif + *pv=NULL; + } Index: /issm/oecreview/Archive/11681-11700/ISSM-11694-11695.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11694-11695.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11694-11695.diff (revision 11991) @@ -0,0 +1,6972 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11695) +@@ -51,8 +51,8 @@ + KUF=KU->Duplicate(); KU->Copy(KUF); KUF->AYPX(pf,-1.0); + + //compute norm(KUF), norm(F) and residue +- nKUF=KUF->Norm(NORM_2); +- nF=pf->Norm(NORM_2); ++ nKUF=KUF->Norm(NORM_TWO); ++ nF=pf->Norm(NORM_TWO); + solver_residue=nKUF/nF; + _printf_(true,"\n%s%g\n"," solver residue: norm(KU-F)/norm(F)=",solver_residue); + +@@ -66,8 +66,8 @@ + //compute K[n]U[n-1]F = K[n]U[n-1] - F + KUold=uf->Duplicate(); Kff->MatMult(old_uf,KUold); + KUoldF=KUold->Duplicate();KUold->Copy(KUoldF); KUoldF->AYPX(pf,-1.0); +- nKUoldF=KUoldF->Norm(NORM_2); +- nF=pf->Norm(NORM_2); ++ nKUoldF=KUoldF->Norm(NORM_TWO); ++ nF=pf->Norm(NORM_TWO); + res=nKUoldF/nF; + if (isnan(res)){ + _printf_(true,"norm nf = %lf and norm kuold = %lf\n",nF,nKUoldF); +@@ -93,7 +93,7 @@ + + //compute norm(du)/norm(u) + duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); +- ndu=duf->Norm(NORM_2); nu=old_uf->Norm(NORM_2); ++ ndu=duf->Norm(NORM_TWO); nu=old_uf->Norm(NORM_TWO); + + if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); + +@@ -119,7 +119,7 @@ + + //compute max(du) + duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); +- ndu=duf->Norm(NORM_2); nduinf=duf->Norm(NORM_INFINITY); ++ ndu=duf->Norm(NORM_TWO); nduinf=duf->Norm(NORM_INF); + if (isnan(ndu) || isnan(nu)) _error_("convergence criterion is NaN!"); + + //clean up +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/gradient_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/gradient_core.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/gradient_core.cpp (revision 11695) +@@ -17,9 +17,9 @@ + /*Intermediaries*/ + double norm_inf; + double *norm_list = NULL; +- Vec new_gradient = NULL; +- Vec gradient = NULL; +- Vec old_gradient = NULL; ++ Vector* new_gradient = NULL; ++ Vector* gradient = NULL; ++ Vector* old_gradient = NULL; + + /*Compute gradient*/ + _printf_(VerboseControl()," compute cost function gradient\n"); +@@ -28,20 +28,20 @@ + if (orthogonalize){ + _printf_(VerboseControl()," orthogonalization\n"); + ControlInputGetGradientx(&old_gradient,femmodel->elements,femmodel->nodes, femmodel->vertices,femmodel->loads, femmodel->materials,femmodel->parameters); +- Orthx(&new_gradient,gradient,old_gradient); VecFree(&old_gradient); VecFree(&gradient); ++ Orthx(&new_gradient,gradient,old_gradient); xdelete(&old_gradient); xdelete(&gradient); + } + else{ + new_gradient=gradient; + } + + /*Check that gradient is clean*/ +- VecNorm(new_gradient,NORM_INFINITY,&norm_inf); ++ norm_inf=new_gradient->Norm(NORM_INF); + if(norm_inf<=0) _error_("||∂J/∂α||∞ = 0 gradient norm is zero"); + if(isnan(norm_inf))_error_("||∂J/∂α||∞ = NaN gradient norm is NaN"); + + /*plug back into inputs: */ + ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,new_gradient); +- VecFree(&new_gradient); ++ xdelete(&new_gradient); + + /*Scale Gradients*/ + ControlInputScaleGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,norm_list,step); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 11695) +@@ -36,6 +36,7 @@ + double start, finish; + double start_core, finish_core; + double start_init, finish_init; ++ int ierr; + + MODULEBOOT(); + +@@ -43,9 +44,14 @@ + _error_(" parallel executable was compiled without support of parallel libraries!"); + #endif + +- /*Initialize Petsc and get start time*/ +- int ierr=PetscInitialize(&argc,&argv,(char*)0,""); ++ /*Initialize environments: Petsc, MPI, etc...: */ ++ #ifdef _HAVE_PETSC_ ++ ierr=PetscInitialize(&argc,&argv,(char*)0,""); + if(ierr) _error_("Could not initialize Petsc"); ++ #else ++ MPI_Init(&argc,&argv); ++ #endif ++ + MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); + + /*Size and rank: */ +@@ -129,8 +135,14 @@ + _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",finish_init-start_init); + _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",finish_core-start_core); + _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600),int(int(finish-start)%3600/60),int(finish-start)%60); ++ ++ + _printf_(true,"closing MPI and Petsc\n"); ++ #ifdef _HAVE_PETSC_ + PetscFinalize(); ++ #else ++ MPI_Finalize(); ++ #endif + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 11695) +@@ -263,8 +263,8 @@ + PenpairEnum, + PentaEnum, + PentaP1InputEnum, +- PetscMatParamEnum, +- PetscVecParamEnum, ++ MatrixParamEnum, ++ VectorParamEnum, + RiftfrontEnum, + SegmentEnum, + SegmentRiftfrontEnum, +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Parameters.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Parameters.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Parameters.cpp (revision 11695) +@@ -226,8 +226,8 @@ + _error_("could not find parameter %s",EnumToStringx(enum_type)); + } + /*}}}*/ +-/*FUNCTION Parameters::FindParam(Vec* pvec,int enum_type){{{1*/ +-void Parameters::FindParam(Vec* pvec,int enum_type){ _assert_(this); ++/*FUNCTION Parameters::FindParam(Vector** pvec,int enum_type){{{1*/ ++void Parameters::FindParam(Vector** pvec,int enum_type){ _assert_(this); + + vector::iterator object; + Param* param=NULL; +@@ -244,8 +244,8 @@ + + } + /*}}}*/ +-/*FUNCTION Parameters::FindParam(Mat* pmat,int enum_type){{{1*/ +-void Parameters::FindParam(Mat* pmat,int enum_type){ _assert_(this); ++/*FUNCTION Parameters::FindParam(Matrix** pmat,int enum_type){{{1*/ ++void Parameters::FindParam(Matrix** pmat,int enum_type){ _assert_(this); + + vector::iterator object; + Param* param=NULL; +@@ -388,8 +388,8 @@ + else this->AddObject(new IntMatParam(enum_type,intarray,M,N)); //just add the new parameter. + } + /*}}}*/ +-/*FUNCTION Parameters::SetParam(Vec vector,int enum_type);{{{1*/ +-void Parameters::SetParam(Vec vector,int enum_type){ ++/*FUNCTION Parameters::SetParam(Vector* vector,int enum_type);{{{1*/ ++void Parameters::SetParam(Vector* vector,int enum_type){ + + Param* param=NULL; + +@@ -397,11 +397,11 @@ + param=(Param*)this->FindParamObject(enum_type); + + if(param) param->SetValue(vector); //already exists, just set it. +- else this->AddObject(new PetscVecParam(enum_type,vector)); //just add the new parameter. ++ else this->AddObject(new VectorParam(enum_type,vector)); //just add the new parameter. + } + /*}}}*/ +-/*FUNCTION Parameters::SetParam(Mat matrix,int enum_type);{{{1*/ +-void Parameters::SetParam(Mat matrix,int enum_type){ ++/*FUNCTION Parameters::SetParam(Matrix* matrix,int enum_type);{{{1*/ ++void Parameters::SetParam(Matrix* matrix,int enum_type){ + + Param* param=NULL; + +@@ -409,7 +409,7 @@ + param=(Param*)this->FindParamObject(enum_type); + + if(param) param->SetValue(matrix); //already exists, just set it. +- else this->AddObject(new PetscMatParam(enum_type,matrix)); //just add the new parameter. ++ else this->AddObject(new MatrixParam(enum_type,matrix)); //just add the new parameter. + } + /*}}}*/ + /*FUNCTION Parameters::SetParam(FILE* fid,int enum_type);{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Parameters.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Parameters.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Parameters.h (revision 11695) +@@ -6,6 +6,8 @@ + #define _CONTAINER_PARAMETERS_H_ + + /*forward declarations */ ++class Matrix; ++class Vector; + class Materials; + class Parameters; + class Elements; +@@ -36,8 +38,8 @@ + void FindParam(double** pdoublearray,int* pM,int enum_type); + void FindParam(double** pdoublearray,int* pM,int* pN,int enum_type); + void FindParam(double*** parray,int* pM, int** pmdims_array,int** pndims_array,int enum_type); +- void FindParam(Vec* pvec,int enum_type); +- void FindParam(Mat* pmat,int enum_type); ++ void FindParam(Vector** pvec,int enum_type); ++ void FindParam(Matrix** pmat,int enum_type); + void FindParam(FILE** pfid,int enum_type); + + void SetParam(bool boolean,int enum_type); +@@ -49,8 +51,8 @@ + void SetParam(double* doublearray,int M,int N,int enum_type); + void SetParam(int* intarray,int M,int enum_type); + void SetParam(int* intarray,int M,int N,int enum_type); +- void SetParam(Vec vec,int enum_type); +- void SetParam(Mat mat,int enum_type); ++ void SetParam(Vector* vec,int enum_type); ++ void SetParam(Matrix* mat,int enum_type); + void SetParam(FILE* fid,int enum_type); + void UnitConversion(int direction_enum); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Elements.cpp (revision 11695) +@@ -174,7 +174,7 @@ + int *resultssteps = NULL; + double *resultstimes = NULL; + double *vector_serial= NULL; +- Vec vector = NULL; ++ Vector* vector = NULL; + bool io_gather; + bool results_as_patches; + int numberofvertices,numberofelements; +@@ -224,24 +224,23 @@ + if(resultssizes[i]==P1Enum) vectorsize=numberofvertices; + else if(resultssizes[i]==P0Enum) vectorsize=numberofelements; + else _error_("Unkown result size: %s",EnumToStringx(resultssizes[i])); +- vector=NewVec(vectorsize); ++ vector=new Vector(vectorsize); + + for(int j=0;jSize();j++){ + Element* element=(Element*)this->GetObjectByOffset(j); + element->GetVectorFromResults(vector,i,resultssizes[i]); + } +- VecAssemblyBegin(vector); +- VecAssemblyEnd(vector); ++ vector->Assemble(); + + /*Serialize and add to results*/ +- VecToMPISerial(&vector_serial,vector); ++ vector_serial=vector->ToMPISerial(); + if(my_rank==0){ + /*No need to add this vector for all cpus*/ + results->AddObject(new DoubleVecExternalResult(results->Size()+1,resultsenums[i],vector_serial,vectorsize,resultssteps[i],resultstimes[i])); + } + + /*clean up*/ +- VecFree(&vector); ++ xdelete(&vector); + xfree((void**)&vector_serial); + } + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp (revision 11695) +@@ -5,6 +5,13 @@ + + #include "../../toolkits/toolkits.h" + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ + int my_rank; + int num_procs; + +@@ -15,34 +22,36 @@ + num_procs=1; + + /*Some test for MPI_Init crash with mpich2 1.4 on larsen, just ignore*/ +- #if _PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 1 +- if(0){ +- int mp_init = 0; +- PetscErrorCode ierr; +- extern PetscBool PetscBeganMPI; +- MPI_Initialized(&mp_init); +- if(mp_init!=1){ +- MPI_Init(NULL,NULL); +- PetscBeganMPI = PETSC_TRUE; +- ierr=PetscInitializeNoArguments();CHKERRQ(ierr); +- } +- } +- else if (0){ +- PetscErrorCode ierr; +- PetscBool flg; +- ierr=PetscInitialized(&flg);CHKERRQ(ierr); +- if(flg){ ++ #ifdef _HAVE_PETSC_ ++ #if _PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 1 ++ if(0){ ++ int mp_init = 0; ++ PetscErrorCode ierr; + extern PetscBool PetscBeganMPI; +- PetscBeganMPI = PETSC_FALSE; +- ierr=PetscFinalize();CHKERRQ(ierr); ++ MPI_Initialized(&mp_init); ++ if(mp_init!=1){ ++ MPI_Init(NULL,NULL); ++ PetscBeganMPI = PETSC_TRUE; ++ ierr=PetscInitializeNoArguments();CHKERRQ(ierr); ++ } + } +- ierr=PetscInitializeNoArguments();CHKERRQ(ierr); +- ierr=PetscPopSignalHandler();CHKERRQ(ierr); +- } ++ else if (0){ ++ PetscErrorCode ierr; ++ PetscBool flg; ++ ierr=PetscInitialized(&flg);CHKERRQ(ierr); ++ if(flg){ ++ extern PetscBool PetscBeganMPI; ++ PetscBeganMPI = PETSC_FALSE; ++ ierr=PetscFinalize();CHKERRQ(ierr); ++ } ++ ierr=PetscInitializeNoArguments();CHKERRQ(ierr); ++ ierr=PetscPopSignalHandler();CHKERRQ(ierr); ++ } ++ #endif ++ ++ /*Initialize Petsc: */ ++ PetscInitializeNoArguments(); + #endif + +- /*Initialize Petsc: */ +- PetscInitializeNoArguments(); +- + return 1; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/PetscOptionsFromAnalysis.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/PetscOptionsFromAnalysis.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/PetscOptionsFromAnalysis.cpp (revision 11695) +@@ -14,54 +14,12 @@ + + void PetscOptionsFromAnalysis(Parameters* parameters,int analysis_type){ + +- int dummy; +- double* analyses=NULL; +- char** strings=NULL; +- int numanalyses; +- char* string=NULL; +- int found=-1; +- int i; ++ /*intermediary: */ ++ char* options=NULL; + +- numanalyses=0; +- parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum); ++ /*Recover first the options string for this analysis: */ ++ options=OptionsFromAnalysis(parameters,analysis_type); + +- #ifdef _SERIAL_ //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis +- if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); +- } +- else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); +- #else +- parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); +- #endif +- +- if(numanalyses==0)return; //we did not find petsc options, don't bother. +- +- /*ok, go through analyses and figure out if it corresponds to our analysis_type: */ +- found=-1; +- for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../../objects/objects.h" ++#include "../../Container/Parameters.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++ ++char* OptionsFromAnalysis(Parameters* parameters,int analysis_type){ ++ ++ /*output: */ ++ char* outstring=NULL; ++ ++ /*intermediary: */ ++ int dummy; ++ double* analyses=NULL; ++ char** strings=NULL; ++ char* string=NULL; ++ int numanalyses; ++ int found=-1; ++ int i; ++ ++ numanalyses=0; ++ parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum); ++ ++ #ifdef _SERIAL_ //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis ++ if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); ++ } ++ else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); ++ #else ++ parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); ++ #endif ++ ++ if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. ++ ++ /*ok, go through analyses and figure out if it corresponds to our analysis_type: */ ++ found=-1; ++ for(i=0;i do not change it if != 0 +- VecGetValues(in,1,&i,&value); ++ in->GetValue(&value,i); + if (value){ + /*this vertex already is inside one of the contours, continue*/ + continue; +@@ -50,12 +50,12 @@ + else{ + value=pnpoly(numvertices,xc,yc,x0,y0,edgevalue); + } +- VecSetValues(in,1,&i,&value,INSERT_VALUES); ++ in->SetValue(i,value,INS_VAL); + } + return 1; + }/*}}}*/ + /*IsOutsidePoly {{{1*/ +-int IsOutsidePoly(Vec in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ ++int IsOutsidePoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue){ + + int i,j; + double x0,y0; +@@ -77,7 +77,7 @@ + for (i=i0;i do not change it if != 0 +- VecGetValues(in,1,&i,&value); ++ in->GetValue(&value,i); + if (value){ + /*this vertex already is inside one of the contours, continue*/ + continue; +@@ -91,7 +91,7 @@ + else{ + value=1-pnpoly(numvertices,xc,yc,x0,y0,edgevalue); + } +- VecSetValues(in,1,&i,&value,INSERT_VALUES); ++ in->SetValue(i,value,INS_VAL); + } + return 1; + }/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11695) +@@ -275,33 +275,6 @@ + + } + /*}}}*/ +-/*FUNCTION FetchMatlabData(Mat* pmatrix,const mxArray* dataref){{{1*/ +-void FetchMatlabData(Mat* pmatrix,const mxArray* dataref){ +- +- Mat outmatrix=NULL; +- int dummy=0; +- +- if (mxIsClass(dataref,"double") ){ +- +- /*Check dataref is not pointing to NaN: */ +- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ +- outmatrix=NULL; +- } +- else{ +- +- /*Convert matlab matrix to petsc matrix: */ +- MatlabMatrixToPetscMatrix(&outmatrix,&dummy,&dummy,dataref); +- } +- } +- else{ +- /*This is an error: we don't have the correct input!: */ +- _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); +- } +- +- /*Assign output pointers:*/ +- *pmatrix=outmatrix; +-} +-/*}}}*/ + /*FUNCTION FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){{{1*/ + void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref){ + +@@ -452,30 +425,6 @@ + if (pM)*pM=outvector_rows; + } + /*}}}*/ +-/*FUNCTION FetchMatlabData(Vec* pvector,const mxArray* dataref){{{1*/ +-void FetchMatlabData(Vec* pvector,const mxArray* dataref){ +- +- Vec vector=NULL; +- int dummy; +- +- if(mxIsEmpty(dataref)){ +- /*Nothing to pick up. Just initialize matrix pointer to NULL: */ +- vector=NULL; +- } +- else if (mxIsClass(dataref,"double") ){ +- +- /*Convert matlab vector to petsc vector: */ +- MatlabVectorToPetscVector(&vector,&dummy,dataref); +- } +- else{ +- /*This is an error: we don't have the correct input!: */ +- _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); +- } +- +- /*Assign output pointers:*/ +- *pvector=vector; +-} +-/*}}}*/ + /*FUNCTION FetchMatlabData(Vector** pvector,const mxArray* dataref){{{1*/ + void FetchMatlabData(Vector** pvector,const mxArray* dataref){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp (revision 11695) +@@ -40,23 +40,6 @@ + + } + /*}}}*/ +-/*FUNCTION WriteMatlabData(mxArray** pdataref,Mat matrix){{{1*/ +-void WriteMatlabData(mxArray** pdataref,Mat matrix){ +- +- mxArray* dataref=NULL; +- +- if(matrix){ +- +- /*call toolkit routine: */ +- PetscMatrixToMatlabMatrix(&dataref,matrix); +- } +- else{ +- dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- } +- +- *pdataref=dataref; +-} +-/*}}}*/ + /*FUNCTION WriteMatlabData(mxArray** pdataref,Matrix* matrix){{{1*/ + void WriteMatlabData(mxArray** pdataref,Matrix* matrix){ + +@@ -124,23 +107,6 @@ + *pdataref=dataref; + } + /*}}}*/ +-/*FUNCTION WriteMatlabData(mxArray** pdataref,Vec vector){{{1*/ +-void WriteMatlabData(mxArray** pdataref,Vec vector){ +- +- mxArray* dataref=NULL; +- +- if(vector){ +- +- /*call toolkit routine: */ +- PetscVectorToMatlabVector(&dataref,vector); +- } +- else{ +- dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- } +- *pdataref=dataref; +- +-} +-/*}}}*/ + /*FUNCTION WriteMatlabData(mxArray** pdataref,Vector* vector){{{1*/ + void WriteMatlabData(mxArray** pdataref,Vector* vector){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/matlabio.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/matlabio.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/matlabio.h (revision 11695) +@@ -15,11 +15,9 @@ + #ifdef _SERIAL_ + #include + void WriteMatlabData(mxArray** pdataref,DataSet* dataset); +-void WriteMatlabData(mxArray** pdataref,Mat matrix); + void WriteMatlabData(mxArray** pdataref,Matrix* matrix); + void WriteMatlabData(mxArray** pdataref,double* matrix, int M,int N); + void WriteMatlabData(mxArray** pdataref,int* matrix, int M,int N); +-void WriteMatlabData(mxArray** pdataref,Vec vector); + void WriteMatlabData(mxArray** pdataref,Vector* vector); + void WriteMatlabData(mxArray** pdataref,double* vector, int M); + void WriteMatlabData(mxArray** pdataref,int integer); +@@ -34,13 +32,11 @@ + void FetchMatlabData(int** pmatrix,int* pM,int *pN,const mxArray* dataref); + void FetchMatlabData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref); + void FetchMatlabData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +-void FetchMatlabData(Mat* pmatrix,const mxArray* dataref); + void FetchMatlabData(Matrix** pmatrix,const mxArray* dataref); + void FetchMatlabData(int** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(float** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(double** pvector,int* pM,const mxArray* dataref); + void FetchMatlabData(bool** pvector,int* pM,const mxArray* dataref); +-void FetchMatlabData(Vec* pvector,const mxArray* dataref); + void FetchMatlabData(Vector** pvector,const mxArray* dataref); + void FetchMatlabData(char** pstring,const mxArray* dataref); + void FetchMatlabData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp (revision 11695) +@@ -12,7 +12,7 @@ + int UpdateVertexPositionsx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters){ + + int i; +- Vec vz = NULL; ++ Vector* vz = NULL; + Vertex *vertex = NULL; + double *thickness = NULL; + double *bed = NULL; +@@ -22,7 +22,7 @@ + GetVectorFromInputsx(&bed ,elements,nodes, vertices, loads, materials, parameters, BedEnum, VertexEnum); + + /*Allocate vector*/ +- vz=NewVec(vertices->NumberOfVertices()); ++ vz=new Vector(vertices->NumberOfVertices()); + + /*Update verices new geometry: */ + for (i=0;iSize();i++){ +@@ -31,8 +31,7 @@ + } + + /*Assemble mesh velocity*/ +- VecAssemblyBegin(vz); +- VecAssemblyEnd(vz); ++ vz->Assemble(); + + /*Update element inputs*/ + InputUpdateFromVectorx(elements,nodes,vertices,loads,materials,parameters,vz,VzMeshEnum,VertexEnum); +@@ -40,6 +39,6 @@ + /*Free ressources:*/ + xfree((void**)&thickness); + xfree((void**)&bed); +- VecFree(&vz); ++ delete vz; + return 1; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp (revision 11695) +@@ -9,12 +9,12 @@ + #include "../../objects/objects.h" + #include "../modules.h" + +-int InterpFromMesh2dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, ++int InterpFromMesh2dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, + double* default_values,int num_default_values,Contour** contours,int numcontours){ + + + /*Output*/ +- Vec data_prime=NULL; ++ Vector* data_prime=NULL; + + /*Intermediary*/ + int i,j; +@@ -27,7 +27,7 @@ + double ymin,ymax; + + /*contours: */ +- Vec vec_incontour=NULL; ++ Vector* vec_incontour=NULL; + double* incontour=NULL; + + /*threading: */ +@@ -71,16 +71,16 @@ + } + + /*Initialize output*/ +- data_prime=NewVec(nods_prime); ++ data_prime=new Vector(nods_prime); + if(num_default_values){ +- if(num_default_values==1)for (i=0;iSetValue(i,default_values[0],INS_VAL); ++ else for (i=0;iSetValue(i,default_values[i],INS_VAL); + } + + /*Build indices of contour: */ + if(numcontours){ + ContourToNodesx( &vec_incontour,x_prime,y_prime,nods_prime,contours,numcontours,1); +- VecToMPISerial(&incontour,vec_incontour); ++ incontour=vec_incontour->ToMPISerial(); + } + else{ + incontour=(double*)xmalloc(nods_prime*sizeof(double)); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp (revision 11695) +@@ -23,7 +23,7 @@ + double xmin,xmax; + double ymin,ymax; + int nods_prime; +- Vec data_prime=NULL; ++ Vector* data_prime=NULL; + double* x_prime=NULL; + double* y_prime=NULL; + double* default_values=NULL; +@@ -119,7 +119,7 @@ + } + + /*insert value and go to the next point*/ +- VecSetValue(data_prime,j,data_value,INSERT_VALUES); ++ data_prime->SetValue(j,data_value,INS_VAL); + } + } + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h (revision 11695) +@@ -22,7 +22,7 @@ + double xmin,xmax; + double ymin,ymax; + int nods_prime; +- Vec data_prime; ++ Vector* data_prime; + double* x_prime; + double* y_prime; + double* default_values; +@@ -32,7 +32,7 @@ + + } InterpFromMesh2dxThreadStruct; + +-int InterpFromMesh2dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, ++int InterpFromMesh2dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, int nods_prime, + double* default_values,int num_default_values,Contour** contours,int numcontours); + + void* InterpFromMesh2dxt(void* vInterpFromMesh2dxThreadStruct); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp (revision 11695) +@@ -29,11 +29,11 @@ + xfree((void**)&control_type); + + } +-void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec gradient){ ++void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* gradient){ + + /*Serialize gradient*/ + double* serial_gradient=NULL; +- VecToMPISerial(&serial_gradient,gradient); ++ serial_gradient=gradient->ToMPISerial(); + + ControlInputSetGradientx(elements,nodes,vertices, loads, materials, parameters,serial_gradient); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h (revision 11695) +@@ -8,6 +8,6 @@ + #include "../../Container/Container.h" + + void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* gradient); +-void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec gradient); ++void ControlInputSetGradientx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* gradient); + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 11695) +@@ -266,8 +266,8 @@ + else if (strcmp(name,"Penpair")==0) return PenpairEnum; + else if (strcmp(name,"Penta")==0) return PentaEnum; + else if (strcmp(name,"PentaP1Input")==0) return PentaP1InputEnum; +- else if (strcmp(name,"PetscMatParam")==0) return PetscMatParamEnum; +- else if (strcmp(name,"PetscVecParam")==0) return PetscVecParamEnum; ++ else if (strcmp(name,"MatrixParam")==0) return MatrixParamEnum; ++ else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; + else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; + else if (strcmp(name,"Segment")==0) return SegmentEnum; + else if (strcmp(name,"SegmentRiftfront")==0) return SegmentRiftfrontEnum; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 11695) +@@ -259,8 +259,8 @@ + case PenpairEnum : return "Penpair"; + case PentaEnum : return "Penta"; + case PentaP1InputEnum : return "PentaP1Input"; +- case PetscMatParamEnum : return "PetscMatParam"; +- case PetscVecParamEnum : return "PetscVecParam"; ++ case MatrixParamEnum : return "MatrixParam"; ++ case VectorParamEnum : return "VectorParam"; + case RiftfrontEnum : return "Riftfront"; + case SegmentEnum : return "Segment"; + case SegmentRiftfrontEnum : return "SegmentRiftfront"; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp (revision 11695) +@@ -28,9 +28,9 @@ + int numberofvertices; + + /*output: */ +- Vec partition_contributions=NULL; +- Vec partition_areas=NULL; +- Vec vec_average=NULL; ++ Vector* partition_contributions=NULL; ++ Vector* partition_areas=NULL; ++ Vector* vec_average=NULL; + double* average=NULL; + + /*First, recover qmu partition of vertices: */ +@@ -43,9 +43,9 @@ + /*average onto the separate areas. The result will be a npart sized vector. */ + + /*allocate: */ +- partition_contributions=NewVec(npart); +- partition_areas=NewVec(npart); +- vec_average=NewVec(npart); ++ partition_contributions=new Vector(npart); ++ partition_areas=new Vector(npart); ++ vec_average=new Vector(npart); + + /*loop on each element, and add contribution of the element to the partition (surface weighted average): */ + for(i=0;iSize();i++){ +@@ -54,23 +54,20 @@ + } + + /*Assemble: */ +- VecAssemblyBegin(partition_contributions); +- VecAssemblyEnd(partition_contributions); ++ partition_contributions->Assemble(); ++ partition_areas->Assemble(); + +- VecAssemblyBegin(partition_areas); +- VecAssemblyEnd(partition_areas); +- + /*We have the partition_areas and the partition_contributions for each partition -> compute the surfae weighted average: */ +- VecPointwiseDivide(vec_average,partition_contributions,partition_areas); ++ vec_average->PointwiseDivide(partition_contributions,partition_areas); + + /*serialize:*/ +- VecToMPISerial(&average,vec_average); ++ average=vec_average->ToMPISerial(); + + /*Free ressources:*/ + xfree((void**)&qmu_part); +- VecFree(&partition_contributions); +- VecFree(&partition_areas); +- VecFree(&vec_average); ++ xdelete(&partition_contributions); ++ xdelete(&partition_areas); ++ xdelete(&vec_average); + + /*Assign output pointers:*/ + *paverage=average; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 11695) +@@ -31,7 +31,7 @@ + int verbose=0; + + /*default values: */ +- Vec vec_incontour=NULL; ++ Vector* vec_incontour=NULL; + double* incontour=NULL; + bool skip_bamg=false; + +@@ -50,7 +50,7 @@ + /*If default values supplied, figure out which nodes are inside the contour, including the border of the contour: */ + if(num_default_values){ + ContourToNodesx( &vec_incontour,x_interp,y_interp,nods_interp,contours,numcontours,1); +- VecToMPISerial(&incontour,vec_incontour); ++ incontour=vec_incontour->ToMPISerial(); + } + + /*Initialize output*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp (revision 11695) +@@ -8,11 +8,11 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name, int type){ ++void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name, int type){ + + double* serial_vector=NULL; + +- VecToMPISerial(&serial_vector,vector); ++ serial_vector=vector->ToMPISerial(); + + InputUpdateFromVectorx( elements,nodes, vertices, loads, materials, parameters,serial_vector,name, type); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h (revision 11695) +@@ -9,7 +9,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name,int type); ++void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name,int type); + void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* vector, int name,int type); + void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int* vector, int name,int type); + void InputUpdateFromVectorx( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,bool* vector, int name,int type); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 11695) +@@ -16,7 +16,7 @@ + double* vertices_potentially_ungrounding = NULL; + double* vertices_ungrounding = NULL; + double* old_floatingice = NULL; +- Vec vec_old_floatingice = NULL; ++ Vector* vec_old_floatingice = NULL; + Element* element = NULL; + + _printf_(VerboseModule()," Migrating grounding line\n"); +@@ -38,7 +38,7 @@ + + /*Create vector with vertices initially floating and serialize*/ + vec_old_floatingice=CreateNodesOnFloatingIce(nodes,analysis_type); +- VecToMPISerial(&old_floatingice,vec_old_floatingice); ++ old_floatingice=vec_old_floatingice->ToMPISerial(); + + /*Migrate grounding line : */ + for(i=0;iSize();i++){ +@@ -47,36 +47,35 @@ + } + + /*free ressouces: */ +- VecFree(&vec_old_floatingice); ++ xdelete(&vec_old_floatingice); + xfree((void**)&vertices_potentially_ungrounding); + xfree((void**)&vertices_ungrounding); + xfree((void**)&old_floatingice); + } + + /*FUNCTION CreateNodesOnFloatingIce {{{1*/ +-Vec CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type){ ++Vector* CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type){ + + int i,numnods; +- Vec vec_nodes_on_floatingice = NULL; ++ Vector* vec_nodes_on_floatingice = NULL; + Node *node = NULL; + + /*First, initialize nodes_on_floatingice, which will track which nodes have changed status: */ + numnods=nodes->NumberOfNodes(configuration_type); +- vec_nodes_on_floatingice=NewVec(numnods); ++ vec_nodes_on_floatingice=new Vector(numnods); + + /*Loop through nodes, and fill vec_nodes_on_floatingice: */ + for(i=0;iSize();i++){ + node=(Node*)nodes->GetObjectByOffset(i); + if(node->InAnalysis(configuration_type)){ + if(node->IsFloating()){ +- VecSetValue(vec_nodes_on_floatingice,node->Sid(),1.0,INSERT_VALUES); ++ vec_nodes_on_floatingice->SetValue(node->Sid(),1.0,INS_VAL); + } + } + } + + /*Assemble vector: */ +- VecAssemblyBegin(vec_nodes_on_floatingice); +- VecAssemblyEnd(vec_nodes_on_floatingice); ++ vec_nodes_on_floatingice->Assemble(); + + return vec_nodes_on_floatingice; + } +@@ -86,12 +85,12 @@ + + int i,numberofvertices; + double* vertices_potentially_ungrounding = NULL; +- Vec vec_vertices_potentially_ungrounding = NULL; ++ Vector* vec_vertices_potentially_ungrounding = NULL; + Element* element = NULL; + + /*Initialize vector with number of vertices*/ + numberofvertices=vertices->NumberOfVertices(); +- vec_vertices_potentially_ungrounding=NewVec(numberofvertices); //grounded vertex that could start floating ++ vec_vertices_potentially_ungrounding=new Vector(numberofvertices); //grounded vertex that could start floating + + /*Fill vector vertices_potentially_floating: */ + for(i=0;iSize();i++){ +@@ -100,12 +99,11 @@ + } + + /*Assemble vector and serialize */ +- VecAssemblyBegin(vec_vertices_potentially_ungrounding); +- VecAssemblyEnd(vec_vertices_potentially_ungrounding); +- VecToMPISerial(&vertices_potentially_ungrounding,vec_vertices_potentially_ungrounding); ++ vec_vertices_potentially_ungrounding->Assemble(); ++ vertices_potentially_ungrounding=vec_vertices_potentially_ungrounding->ToMPISerial(); + + /*free ressouces and return: */ +- VecFree(&vec_vertices_potentially_ungrounding); ++ xdelete(&vec_vertices_potentially_ungrounding); + return vertices_potentially_ungrounding; + } + /*}}}*/ +@@ -117,8 +115,8 @@ + int nflipped,local_nflipped; + double* nodes_on_floatingice = NULL; + double* elements_neighboring_floatingce = NULL; +- Vec vec_elements_neighboring_floatingice = NULL; +- Vec vec_nodes_on_floatingice = NULL; ++ Vector* vec_elements_neighboring_floatingice = NULL; ++ Vector* vec_nodes_on_floatingice = NULL; + Node* node = NULL; + Element* element = NULL; + +@@ -129,24 +127,23 @@ + + /*recover vec_nodes_on_floatingice*/ + vec_nodes_on_floatingice=CreateNodesOnFloatingIce(nodes,analysis_type); +- VecToMPISerial(&nodes_on_floatingice,vec_nodes_on_floatingice); ++ nodes_on_floatingice=vec_nodes_on_floatingice->ToMPISerial(); + + nflipped=1; //bootstrap + while(nflipped){ + + /*Vector of size number of elements*/ +- vec_elements_neighboring_floatingice=NewVec(elements->NumberOfElements(),true); ++ vec_elements_neighboring_floatingice=new Vector(elements->NumberOfElements(),true); + + /*Figure out if any of the nodes of the element will be floating -> elements neighbouting the floating ice*/ + for(i=0;iSize();i++){ + element=(Element*)elements->GetObjectByOffset(i); +- VecSetValue(vec_elements_neighboring_floatingice,element->Sid(),element->IsNodeOnShelfFromFlags(nodes_on_floatingice)?1.0:0.0,INSERT_VALUES); ++ vec_elements_neighboring_floatingice->SetValue(element->Sid(),element->IsNodeOnShelfFromFlags(nodes_on_floatingice)?1.0:0.0,INS_VAL); + } + + /*Assemble vector and serialize: */ +- VecAssemblyBegin(vec_elements_neighboring_floatingice); +- VecAssemblyEnd(vec_elements_neighboring_floatingice); +- VecToMPISerial(&elements_neighboring_floatingce,vec_elements_neighboring_floatingice); ++ vec_elements_neighboring_floatingice->Assemble(); ++ elements_neighboring_floatingce=vec_elements_neighboring_floatingice->ToMPISerial(); + + /*Go through elements_neighboring_floatingce, and update vector of the nodes that will start floating*/ + local_nflipped=0; +@@ -156,8 +153,7 @@ + local_nflipped+=element->UpdatePotentialSheetUngrounding(vertices_potentially_ungrounding,vec_nodes_on_floatingice,nodes_on_floatingice); + } + } +- VecAssemblyBegin(vec_nodes_on_floatingice); +- VecAssemblyEnd(vec_nodes_on_floatingice); ++ vec_nodes_on_floatingice->Assemble(); + + MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + _printf_(VerboseConvergence()," Additional number of vertices allowed to unground: %i\n",nflipped); +@@ -167,12 +163,12 @@ + xfree((void**)&nodes_on_floatingice); + + /*Assemble and serialize:*/ +- VecFree(&vec_elements_neighboring_floatingice); +- VecToMPISerial(&nodes_on_floatingice,vec_nodes_on_floatingice); ++ xdelete(&vec_elements_neighboring_floatingice); ++ nodes_on_floatingice=vec_nodes_on_floatingice->ToMPISerial(); + } + + /*Free ressources:*/ +- VecFree(&vec_nodes_on_floatingice); ++ xdelete(&vec_nodes_on_floatingice); + xfree((void**)&elements_neighboring_floatingce); + + return nodes_on_floatingice; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h (revision 11695) +@@ -13,7 +13,7 @@ + /* local prototypes: */ + void GroundinglineMigrationx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters); + +-Vec CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type); ++Vector* CreateNodesOnFloatingIce(Nodes* nodes,int configuration_type); + double* PotentialSheetUngrounding(Elements* elements,Vertices* vertices,Parameters* parameters); + double* PropagateFloatingiceToGroundedNeighbors(Elements* elements,Nodes* nodes,Vertices* vertices,Parameters* parameters,double* vertices_potentially_ungrounding); + #endif /* _GROUNDINGLINEMIGRATIONX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 11695) +@@ -8,18 +8,18 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void GetVectorFromControlInputsx(Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){ ++void GetVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){ + + int num_controls; + int *control_type = NULL; +- Vec vector=NULL; ++ Vector* vector=NULL; + + /*Retrieve some parameters*/ + parameters->FindParam(&num_controls,InversionNumControlParametersEnum); + parameters->FindParam(&control_type,NULL,InversionControlParametersEnum); + + /*Allocate and populate gradient*/ +- vector=NewVec(num_controls*vertices->NumberOfVertices()); ++ vector=new Vector(num_controls*vertices->NumberOfVertices()); + + for(int i=0;iSize();j++){ +@@ -28,8 +28,7 @@ + } + } + +- VecAssemblyBegin(vector); +- VecAssemblyEnd(vector); ++ vector->Assemble(); + + /*Assign output pointers:*/ + xfree((void**)&control_type); +@@ -42,13 +41,13 @@ + double* vector=NULL; + + /*intermediary: */ +- Vec vec_vector=NULL; ++ Vector* vec_vector=NULL; + + GetVectorFromControlInputsx( &vec_vector, elements,nodes, vertices, loads, materials, parameters,data); +- VecToMPISerial(&vector,vec_vector); ++ vector=vec_vector->ToMPISerial(); + + /*Free ressources:*/ +- VecFree(&vec_vector); ++ xdelete(&vec_vector); + + /*Assign output pointers:*/ + *pvector=vector; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h (revision 11695) +@@ -8,7 +8,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void GetVectorFromControlInputsx( Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); ++void GetVectorFromControlInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); + void GetVectorFromControlInputsx( double** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); + + #endif /* _GETVECTORFROMCONTROLINPUTSXX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp (revision 11695) +@@ -9,7 +9,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void ComputeStrainRatex( Vec* peps,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ ++void ComputeStrainRatex( Vector** peps,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ + + /*Intermediary*/ + int i; +@@ -18,13 +18,13 @@ + Element* element=NULL; + + /*output: */ +- Vec eps=NULL; ++ Vector* eps=NULL; + + /*Recover numberofelements: */ + parameters->FindParam(&numberofelements,MeshNumberofelementsEnum); + + /*Allocate eps on numberofelements (only 1 dof): */ +- eps=NewVec(numberofelements); ++ eps=new Vector(numberofelements); + + /*Compute basal stress for each element: */ + for (i=0;iSize();i++){ +@@ -33,8 +33,7 @@ + } + + /*Assemble vector: */ +- VecAssemblyBegin(eps); +- VecAssemblyEnd(eps); ++ eps->Assemble(); + + /*Assign output pointers: */ + *peps=eps; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h (revision 11695) +@@ -9,7 +9,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void ComputeStrainRatex(Vec* eps_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); ++void ComputeStrainRatex(Vector** eps_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); + + #endif /* _COMPUTESTRAINRATEX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h (revision 11695) +@@ -9,7 +9,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void ComputeBasalStressx( Vec* pp_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); ++void ComputeBasalStressx( Vector** pp_g,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); + + #endif /* _COMPUTEBASALSTRESSX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp (revision 11695) +@@ -9,7 +9,7 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void ComputeBasalStressx( Vec* psigma,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ ++void ComputeBasalStressx( Vector** psigma,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials,Parameters* parameters){ + + /*Intermediary*/ + int i; +@@ -18,13 +18,13 @@ + Element* element=NULL; + + /*output: */ +- Vec sigma=NULL; ++ Vector* sigma=NULL; + + /*Recover numberofelements: */ + parameters->FindParam(&numberofelements,MeshNumberofelementsEnum); + + /*Allocate sigma on numberofelements: */ +- sigma=NewVec((int)numberofelements); ++ sigma=new Vector((int)numberofelements); + + /*Compute basal stress for each element: */ + for (i=0;iSize();i++){ +@@ -33,8 +33,7 @@ + } + + /*Assemble vector: */ +- VecAssemblyBegin(sigma); +- VecAssemblyEnd(sigma); ++ sigma->Assemble(); + + /*Assign output pointers: */ + *psigma=sigma; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 11695) +@@ -10,7 +10,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-int ContourToNodesx( Vec* pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue); ++int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue); + + #endif /* _CONTOURTONODESX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 11695) +@@ -3,7 +3,7 @@ + + #include "./ContourToNodesx.h" + +-int ContourToNodesx( Vec* pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue){ ++int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue){ + + int i; + int m,n; +@@ -16,9 +16,9 @@ + double value; + + /*output: */ +- Vec flags=NULL; ++ Vector* flags=NULL; + +- flags=NewVec(nods); ++ flags=new Vector(nods); + + /*Loop through all contours: */ + for (i=0;iAssemble(); + + /*Assign output pointers: */ + *pflags=flags; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp (revision 11695) +@@ -8,15 +8,15 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void GetVectorFromInputsx( Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, int name, int type){ ++void GetVectorFromInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, int name, int type){ + + int i; +- Vec vector=NULL; ++ Vector* vector=NULL; + + if(type==VertexEnum){ + + /*Allocate vector*/ +- vector=NewVec(vertices->NumberOfVertices()); ++ vector=new Vector(vertices->NumberOfVertices()); + + /*Look up in elements*/ + for(i=0;iSize();i++){ +@@ -34,8 +34,7 @@ + _error_("%s%s%s"," vector type: ",EnumToStringx(type)," not supported yet!"); + } + +- VecAssemblyBegin(vector); +- VecAssemblyEnd(vector); ++ vector->Assemble(); + + /*Assign output pointers:*/ + *pvector=vector; +@@ -47,13 +46,13 @@ + double* vector=NULL; + + /*intermediary: */ +- Vec vec_vector=NULL; ++ Vector* vec_vector=NULL; + + GetVectorFromInputsx( &vec_vector, elements,nodes, vertices, loads, materials, parameters, name, type); +- VecToMPISerial(&vector,vec_vector); ++ vector=vec_vector->ToMPISerial(); + + /*Free ressources:*/ +- VecFree(&vec_vector); ++ xdelete(&vec_vector); + + /*Assign output pointers:*/ + *pvector=vector; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h (revision 11695) +@@ -8,7 +8,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void GetVectorFromInputsx( Vec* pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int name,int type); ++void GetVectorFromInputsx( Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int name,int type); + void GetVectorFromInputsx( double** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int name,int type); + + #endif /* _GETVECTORFROMINPUTSXX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp (revision 11695) +@@ -8,11 +8,11 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name, int type){ ++void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name, int type){ + + double* serial_vector=NULL; + +- VecToMPISerial(&serial_vector,vector); ++ serial_vector=vector->ToMPISerial(); + + InputUpdateFromVectorDakotax( elements,nodes, vertices, loads, materials, parameters,serial_vector,name, type); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h (revision 11695) +@@ -9,7 +9,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec vector, int name,int type); ++void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* vector, int name,int type); + void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* vector, int name,int type); + void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,int* vector, int name,int type); + void InputUpdateFromVectorDakotax( Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,bool* vector, int name,int type); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 11695) +@@ -27,11 +27,11 @@ + xfree((void**)&control_type); + } + +-void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vec vector){ ++void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Vector* vector){ + + double* serial_vector=NULL; + +- VecToMPISerial(&serial_vector,vector); ++ serial_vector=vector->ToMPISerial(); + + SetControlInputsFromVectorx(elements,nodes, vertices, loads, materials, parameters,serial_vector); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h (revision 11695) +@@ -8,7 +8,7 @@ + #include "../../Container/Container.h" + + /* local prototypes: */ +-void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vec vector); ++void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,Vector* vector); + void SetControlInputsFromVectorx(Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,double* vector); + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp (revision 11695) +@@ -6,10 +6,10 @@ + #include "../../shared/shared.h" + #include "../../include/include.h" + +-int InterpFromMeshToMesh3dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value) { ++int InterpFromMeshToMesh3dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value) { + + /*Output*/ +- Vec data_prime=NULL; ++ Vector* data_prime=NULL; + + /*Intermediary*/ + int i,j; +@@ -53,8 +53,8 @@ + } + + /*Initialize output*/ +- data_prime=NewVec(nods_prime); +- for (i=0;iSetValue(i,default_value,INS_VAL); + + /*Loop over the elements*/ + if (debug) printf(" interpolation progress: %5.2lf %%",0.0); +@@ -126,7 +126,7 @@ + if (isnan(data_value)) data_value=default_value; + + /*insert value and go to the next point*/ +- VecSetValue(data_prime,j,data_value,INSERT_VALUES); ++ data_prime->SetValue(j,data_value,INS_VAL); + } + } + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h (revision 11695) +@@ -7,7 +7,7 @@ + + #include "../../toolkits/toolkits.h" + +-int InterpFromMeshToMesh3dx( Vec* pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value); ++int InterpFromMeshToMesh3dx( Vector** pdata_prime,double* index_data, double* x_data, double* y_data, double* z_data, int nods_data,int nels_data, double* data, int data_length, double* x_prime, double* y_prime, double* z_prime, int nods_prime,double default_value); + + #endif /* _INTERPFROMMESHTOMESH3DX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11695) +@@ -19,13 +19,22 @@ + Vector* uf=NULL; + uf=new Vector(); + ++ /*Intermediary: */ ++ int analysis_type; ++ + #ifdef _HAVE_PETSC_ + Vec uf0_vector = NULL; + Vec df_vector = NULL; + if(uf0) uf0_vector=uf0->vector; + if(df) df_vector = df->vector; + +- SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); ++ /*In serial mode, the Petsc Options database has not been initialized properly: */ ++ #ifdef _SERIAL_ ++ parameters->FindParam(&analysis_type,AnalysisTypeEnum); ++ PetscOptionsFromAnalysis(parameters,analysis_type); ++ #endif ++ ++ SolverxPetsc(&uf->vector, Kff->matrix, pf->vector, uf0_vector, df->vector, parameters); + VecGetSize(uf->vector,&uf->M); + #else + _error_("not supported yet!"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h (revision 11695) +@@ -5,11 +5,21 @@ + #ifndef _SOLVERX_H + #define _SOLVERX_H + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ + #include "../../objects/objects.h" + + /* local prototypes: */ + void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters); ++ ++#ifdef _HAVE_PETSC_ + void SolverxPetsc(Vec* puf, Mat Kff, Vec pf, Vec uf0,Vec df, Parameters* parameters); + void DofTypesToIndexSet(IS* pisv, IS* pisp, Vec df,int typeenum); ++#endif ++ + #endif /* _SOLVERX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp (revision 11695) +@@ -15,10 +15,10 @@ + /*}}}*/ + + /*InterpFromGridToMeshx{{{*/ +-int InterpFromGridToMeshx( Vec* pdata_mesh,double* x_in, int x_rows, double* y_in, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods,double default_value, int interpenum){ ++int InterpFromGridToMeshx( Vector** pdata_mesh,double* x_in, int x_rows, double* y_in, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods,double default_value, int interpenum){ + + /*output: */ +- Vec data_mesh=NULL; ++ Vector* data_mesh=NULL; + + /*Intermediary*/ + double* x=NULL; +@@ -45,7 +45,7 @@ + } + + /*Allocate output vector: */ +- data_mesh=NewVec(nods); ++ data_mesh=new Vector(nods); + + /*Find out what kind of coordinates (x_in,y_in) have been given is input*/ + if(N==(x_rows-1) && M==(y_rows-1)){ +@@ -123,7 +123,7 @@ + double *x = gate->x; + double *y = gate->y; + int nods = gate->nods; +- Vec data_mesh = gate->data_mesh; ++ Vector* data_mesh = gate->data_mesh; + double *data = gate->data; + double default_value = gate->default_value; + int interpenum = gate->interp; +@@ -178,7 +178,7 @@ + data_value=default_value; + } + +- VecSetValue(data_mesh,i,data_value,INSERT_VALUES); ++ data_mesh->SetValue(i,data_value,INS_VAL); + } + }/*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h (revision 11695) +@@ -22,10 +22,10 @@ + int nods; + double* x_mesh; + double* y_mesh; +- Vec data_mesh; ++ Vector* data_mesh; + } InterpFromGridToMeshxThreadStruct; + +-int InterpFromGridToMeshx( Vec* pdata_mesh,double* x, int x_rows, double* y, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods, double default_value, int interpenum=BilinearInterpEnum); ++int InterpFromGridToMeshx( Vector** pdata_mesh,double* x, int x_rows, double* y, int y_rows, double* data, int M, int N, double* x_mesh, double* y_mesh, int nods, double default_value, int interpenum=BilinearInterpEnum); + void* InterpFromGridToMeshxt(void* vInterpFromGridToMeshxThreadStruct); + bool findindices(int* pn,int* pm,double* x,int x_rows, double* y,int y_rows, double xgrid,double ygrid); + double triangleinterp(double x1,double x2,double y1,double y2,double Q11,double Q12,double Q21,double Q22,double x,double y); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Orthx/Orthx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Orthx/Orthx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Orthx/Orthx.cpp (revision 11695) +@@ -4,26 +4,26 @@ + + #include "./Orthx.h" + +-void Orthx( Vec* pnewgradj, Vec gradj, Vec oldgradj){ ++void Orthx( Vector** pnewgradj, Vector* gradj, Vector* oldgradj){ + + /*output: */ +- Vec newgradj=NULL; ++ Vector* newgradj=NULL; + + /*intermediary:*/ + double norm_new,norm_old,dot_product;; + + /*Initialize output*/ +- VecDuplicate(gradj,&newgradj); +- VecCopy(gradj,newgradj); ++ newgradj=gradj->Duplicate(); ++ gradj->Copy(newgradj); + + /*rough orthagonalization + gradient=gradient-(gradient'*oldgradient)*oldgradient /norm(oldgradient)^2; */ + if(oldgradj){ +- VecNorm(oldgradj,NORM_2,&norm_old); ++ norm_old=oldgradj->Norm(NORM_TWO); + _assert_(norm_old!=0); +- VecDot(newgradj,oldgradj,&dot_product); ++ dot_product=newgradj->Dot(oldgradj); + _assert_(dot_product!=NAN); +- VecAXPY(newgradj, -dot_product/pow(norm_old,2), oldgradj); ++ newgradj->AXPY(oldgradj,-dot_product/pow(norm_old,2)); + } + + /*Assign correct pointer*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Orthx/Orthx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Orthx/Orthx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Orthx/Orthx.h (revision 11695) +@@ -10,7 +10,7 @@ + #include "../../shared/shared.h" + + /* local prototypes: */ +-void Orthx( Vec* pnewgradj, Vec gradj, Vec oldgradj); ++void Orthx( Vector** pnewgradj, Vector* gradj, Vector* oldgradj); + + #endif /* _ORTHX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 11695) +@@ -89,7 +89,7 @@ + } + + /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ +- kmax=Kff->Norm(NORM_INFINITY); ++ kmax=Kff->Norm(NORM_INF); + + /*Now, deal with penalties*/ + if(penalty_kflag){ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Gradjx/Gradjx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Gradjx/Gradjx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Gradjx/Gradjx.cpp (revision 11695) +@@ -9,15 +9,15 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void Gradjx(Vec* pgradient,double** pnorm_list, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ ++void Gradjx(Vector** pgradient,double** pnorm_list, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ + + int i,j,numberofvertices; + int num_controls; + double norm_inf; + double *norm_list = NULL; + int *control_type = NULL; +- Vec gradient = NULL; +- Vec *gradient_list = NULL; ++ Vector* gradient = NULL; ++ Vector* *gradient_list = NULL; + + /*retrieve some parameters: */ + parameters->FindParam(&num_controls,InversionNumControlParametersEnum); _assert_(num_controls); +@@ -25,12 +25,12 @@ + numberofvertices=vertices->NumberOfVertices(); + + /*Allocate gradient_list */ +- gradient_list = (Vec*)xmalloc(num_controls*sizeof(Vec)); ++ gradient_list = (Vector**)xmalloc(num_controls*sizeof(Vector*)); + norm_list = (double*)xmalloc(num_controls*sizeof(double)); + for(i=0;iGradj(gradient_list[i],control_type[i],i); + } + +- VecAssemblyBegin(gradient_list[i]); +- VecAssemblyEnd(gradient_list[i]); ++ gradient_list[i]->Assemble(); + +- VecNorm(gradient_list[i],NORM_INFINITY,&norm_list[i]); ++ norm_list[i]=gradient_list[i]->Norm(NORM_INF); + } + + /*Add all gradient_list together*/ + for(i=0;iAXPY(gradient_list[i],1.0); ++ xdelete(&gradient_list[i]); + } + + /*Check that gradient is clean*/ +- VecNorm(gradient,NORM_INFINITY,&norm_inf); ++ norm_inf=gradient->Norm(NORM_INF); + if(norm_inf<=0) _error_("||∂J/∂α||∞ = 0 gradient norm is zero"); + if(isnan(norm_inf))_error_("||∂J/∂α||∞ = NaN gradient norm is NaN"); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Gradjx/Gradjx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Gradjx/Gradjx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Gradjx/Gradjx.h (revision 11695) +@@ -9,6 +9,6 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-void Gradjx(Vec* pgrad_g,double** pgrad_norm,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters); ++void Gradjx(Vector** pgrad_g,double** pgrad_norm,Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters); + + #endif /* _GRADJX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 11695) +@@ -10,7 +10,7 @@ + + #include "./ContourToMeshx.h" + +-int ContourToMeshx( Vec* pin_nod,Vec* pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { ++int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { + + int noerr=1; + int i; +@@ -29,11 +29,11 @@ + + + /*output: */ +- Vec in_nod=NULL; +- Vec in_elem=NULL; ++ Vector* in_nod=NULL; ++ Vector* in_elem=NULL; + +- in_nod=NewVec(nods); +- in_elem=NewVec(nel); ++ in_nod=new Vector(nods); ++ in_elem=new Vector(nel); + + /*initialize thread parameters: */ + gate.numcontours=numcontours; +@@ -48,24 +48,22 @@ + LaunchThread(ContourToMeshxt,(void*)&gate,num); + + /*Assemble in_nod: */ +- VecAssemblyBegin(in_nod); +- VecAssemblyEnd(in_nod); ++ in_nod->Assemble(); + + /*Get in_nod serialised for next operation: */ +- VecToMPISerial(&in_nod_serial,in_nod); ++ in_nod_serial=in_nod->ToMPISerial(); + + /*Take care of the case where an element interpolation has been requested: */ + if ((strcmp(interptype,"element")==0) || (strcmp(interptype,"element and node")==0)){ + for (n=0;nSetValue(n,value,INS_VAL); + } + } + } + + /*Assemble vectors: */ +- VecAssemblyBegin(in_elem); +- VecAssemblyEnd(in_elem); ++ in_elem->Assemble(); + + /*Assign output pointers: */ + *pin_nod=in_nod; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 11695) +@@ -38,7 +38,7 @@ + int edgevalue; + double* x=NULL; + double* y=NULL; +- Vec in_nod=NULL; ++ Vector* in_nod=NULL; + + + /*recover handle and gate: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 11695) +@@ -16,7 +16,7 @@ + Contour** contours; + int nods; + int edgevalue; +- Vec in_nod; ++ Vector* in_nod; + double* x; + double* y; + +@@ -24,7 +24,7 @@ + + + /* local prototypes: */ +-int ContourToMeshx( Vec* pin_nods,Vec* pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); ++int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); + + void* ContourToMeshxt(void* vContourToMeshxThreadStruct); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp (revision 11695) +@@ -8,19 +8,19 @@ + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +-void ControlInputGetGradientx( Vec* pgradient, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ ++void ControlInputGetGradientx( Vector** pgradient, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters){ + + /*Intermediaries*/ + int num_controls; + int *control_type = NULL; +- Vec gradient=NULL; ++ Vector* gradient=NULL; + + /*Retrieve some parameters*/ + parameters->FindParam(&num_controls,InversionNumControlParametersEnum); + parameters->FindParam(&control_type,NULL,InversionControlParametersEnum); + + /*Allocate and populate gradient*/ +- gradient=NewVec(num_controls*vertices->NumberOfVertices()); ++ gradient=new Vector(num_controls*vertices->NumberOfVertices()); + + for(int i=0;iSize();j++){ +@@ -29,8 +29,7 @@ + } + } + +- VecAssemblyBegin(gradient); +- VecAssemblyEnd(gradient); ++ gradient->Assemble(); + + /*Clean up and return*/ + xfree((void**)&control_type); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h (revision 11695) +@@ -7,6 +7,6 @@ + #include "../../objects/objects.h" + #include "../../Container/Container.h" + +-void ControlInputGetGradientx( Vec* pgradient, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); ++void ControlInputGetGradientx( Vector** pgradient, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters); + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp (revision 11695) +@@ -16,7 +16,7 @@ + double* y; + int nods; + double mindistance; +- Vec flags; ++ Vector* flags; + + /*recover handle and gate: */ + handle=(pthread_handle*)vpthread_handle; +@@ -61,8 +61,8 @@ + if(distance<=mindistance){ + + /*insert value and go to the next point*/ +- if(!already[i]) VecSetValue(flags,i,1,INSERT_VALUES); +- if(!already[j]) VecSetValue(flags,j,2,INSERT_VALUES); ++ if(!already[i]) flags->SetValue(i,1,INS_VAL); ++ if(!already[j]) flags->SetValue(j,2,INS_VAL); + already[i]=true; + already[j]=true; + break; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h (revision 11695) +@@ -10,7 +10,7 @@ + #include "../../objects/objects.h" + + /* local prototypes: */ +-int PointCloudFindNeighborsx( Vec* pflags,double* x, double* y, int nods, double mindistance,double multithread); ++int PointCloudFindNeighborsx( Vector** pflags,double* x, double* y, int nods, double mindistance,double multithread); + + /*threading: */ + typedef struct{ +@@ -19,7 +19,7 @@ + double* y; + int nods; + double mindistance; +- Vec flags; ++ Vector* flags; + + + } PointCloudFindNeighborsThreadStruct; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp (revision 11695) +@@ -3,11 +3,11 @@ + + #include "./PointCloudFindNeighborsx.h" + +-int PointCloudFindNeighborsx( Vec* pflags,double* x, double* y, int nods, double mindistance,double multithread){ ++int PointCloudFindNeighborsx( Vector** pflags,double* x, double* y, int nods, double mindistance,double multithread){ + + /*output: */ +- Vec flags=NULL; +- flags=NewVec(nods); ++ Vector* flags=NULL; ++ flags=new Vector(nods); + + /*threading: */ + PointCloudFindNeighborsThreadStruct gate; +@@ -30,8 +30,7 @@ + LaunchThread(PointCloudFindNeighborsxt,(void*)&gate,num); + + /*Assemble vector: */ +- VecAssemblyBegin(flags); +- VecAssemblyEnd(flags); ++ flags->Assemble(); + + /*Assign output pointers: */ + *pflags=flags; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/mpi/patches/MPI_Boundariesfromrange.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/mpi/patches/MPI_Boundariesfromrange.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/mpi/patches/MPI_Boundariesfromrange.cpp (revision 11695) +@@ -3,7 +3,6 @@ + * bounds for the current cpu. + */ + +-#include "../../petsc/patches/petscpatches.h" + #include "./mpipatches.h" + #include "../../../shared/shared.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp (revision 11695) +@@ -0,0 +1,50 @@ ++/* \file DetermineLocalSize.cpp ++ * \brief: routine to determine local size of a global petsc matrix or vector. ++ */ ++ ++#include ++#include ++ ++ ++#include "../../../shared/shared.h" ++ ++int DetermineLocalSize(int global_size){ ++ ++ /*output: */ ++ int local_size; ++ ++ /*intermediary: */ ++ int i; ++ int row_rest; ++ int* num_local_rows=NULL; ++ ++ /*from MPI: */ ++ extern int num_procs; ++ extern int my_rank; ++ ++ /*We are not bound by any library, just use what seems most logical*/ ++ num_local_rows=(int*)xmalloc(num_procs*sizeof(int)); ++ ++ for (i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++typedef enum {INS_VAL, ADD_VAL} InsMode; ++typedef enum {NORM_INF,NORM_TWO} NormMode; ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/double.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/double.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/double.h (revision 11695) +@@ -0,0 +1,14 @@ ++/*\file double.h ++ * \brief: our own double matrix ++ */ ++ ++#ifndef _DOUBLE_H_ ++#define _DOUBLE_H_ ++ ++#ifdef _SERIAL_ ++#include "mex.h" ++int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix); ++int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector); ++#endif ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp (revision 11695) +@@ -0,0 +1,92 @@ ++/* \file MatlabVectorToDoubleVector.cpp ++ * \brief: convert a sparse or dense matlab vector to a serial vector: ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#ifdef _SERIAL_ ++ ++#include ++ ++/*Matlab includes: */ ++#include "mex.h" ++ ++#include "../../shared/shared.h" ++ ++int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ ++ ++ int rows,cols; ++ double* mxvector_ptr=NULL; ++ int ierr; ++ int i,j; ++ ++ /*output: */ ++ double* vector=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ double* pr=NULL; ++ int count; ++ int nnz; ++ int nz; ++ ++ /*Ok, first check if we are dealing with a sparse or full vector: */ ++ if (mxIsSparse(mxvector)){ ++ ++ /*Dealing with sparse vector: recover size first: */ ++ mxvector_ptr=(double*)mxGetPr(mxvector); ++ rows=mxGetM(mxvector); ++ cols=mxGetN(mxvector); ++ nnz=mxGetNzmax(mxvector); ++ ++ /*Check that input is actualy a vector*/ ++ if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); ++ ++ nz=(int)((double)nnz/(double)rows); ++ ++ vector=(double*)xcalloc(rows,sizeof(double)); ++ ++ /*Now, get ir,jc and pr: */ ++ pr=mxGetPr(mxvector); ++ ir=mxGetIr(mxvector); ++ jc=mxGetJc(mxvector); ++ ++ /*Now, start inserting data into sparse vector: */ ++ count=0; ++ for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#ifdef _SERIAL_ ++ ++/*Matlab includes: */ ++#include "mex.h" ++ ++#include "../../shared/shared.h" ++ ++int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ ++ ++ int i,j,count,rows,cols; ++ double *pmxdoublematrix = NULL; ++ float *pmxsinglematrix = NULL; ++ ++ /*output: */ ++ double* matrix=NULL; ++ ++ /*matlab indices: */ ++ mwIndex* ir=NULL; ++ mwIndex* jc=NULL; ++ ++ /*Ok, first check if we are dealing with a sparse or full matrix: */ ++ if (mxIsSparse(mxmatrix)){ ++ ++ /*Dealing with sparse matrix: recover size first: */ ++ pmxdoublematrix=(double*)mxGetPr(mxmatrix); ++ rows=mxGetM(mxmatrix); ++ cols=mxGetN(mxmatrix); ++ matrix=(double*)xcalloc(rows*cols,sizeof(double)); ++ ++ /*Now, get ir,jc and pr: */ ++ ir=mxGetIr(mxmatrix); ++ jc=mxGetJc(mxmatrix); ++ ++ /*Now, start inserting data into double* matrix: */ ++ count=0; ++ for(i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ + #include "PLA.h" + + /* missing Plapack prototypes: */ + int PLA_General_invert( int method, PLA_Obj A ); + + /*our own patches: */ ++#ifdef _HAVE_PETSC_ + #include "patches/petscpatches.h" ++#endif + + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp (revision 11695) +@@ -1,98 +0,0 @@ +-/* \file MatlabVectorToDoubleVector.cpp +- * \brief: convert a sparse or dense matlab vector to a serial vector: +- */ +- +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-#ifdef _SERIAL_ +- +-#include +- +-/*Petsc includes: */ +-#include "petscmat.h" +-#include "petscvec.h" +-#include "petscksp.h" +- +- +-/*Matlab includes: */ +-#include "mex.h" +- +-#include "../../../shared/shared.h" +- +-int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ +- +- int rows,cols; +- double* mxvector_ptr=NULL; +- int ierr; +- int i,j; +- +- /*output: */ +- double* vector=NULL; +- +- /*matlab indices: */ +- mwIndex* ir=NULL; +- mwIndex* jc=NULL; +- double* pr=NULL; +- int count; +- int nnz; +- int nz; +- +- /*Ok, first check if we are dealing with a sparse or full vector: */ +- if (mxIsSparse(mxvector)){ +- +- /*Dealing with sparse vector: recover size first: */ +- mxvector_ptr=(double*)mxGetPr(mxvector); +- rows=mxGetM(mxvector); +- cols=mxGetN(mxvector); +- nnz=mxGetNzmax(mxvector); +- +- /*Check that input is actualy a vector*/ +- if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); +- +- nz=(int)((double)nnz/(double)rows); +- +- vector=(double*)xcalloc(rows,sizeof(double)); +- +- /*Now, get ir,jc and pr: */ +- pr=mxGetPr(mxvector); +- ir=mxGetIr(mxvector); +- jc=mxGetJc(mxvector); +- +- /*Now, start inserting data into sparse vector: */ +- count=0; +- for(i=0;i +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-#ifdef _SERIAL_ +- +-/*Petsc includes: */ +-#include "petscmat.h" +-#include "petscvec.h" +-#include "petscksp.h" +- +-/*Matlab includes: */ +-#include "mex.h" +- +-#include "../../../shared/shared.h" +- +-int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ +- +- int i,j,count,rows,cols; +- double *pmxdoublematrix = NULL; +- float *pmxsinglematrix = NULL; +- +- /*output: */ +- double* matrix=NULL; +- +- /*matlab indices: */ +- mwIndex* ir=NULL; +- mwIndex* jc=NULL; +- +- /*Ok, first check if we are dealing with a sparse or full matrix: */ +- if (mxIsSparse(mxmatrix)){ +- +- /*Dealing with sparse matrix: recover size first: */ +- pmxdoublematrix=(double*)mxGetPr(mxmatrix); +- rows=mxGetM(mxmatrix); +- cols=mxGetN(mxmatrix); +- matrix=(double*)xcalloc(rows*cols,sizeof(double)); +- +- /*Now, get ir,jc and pr: */ +- ir=mxGetIr(mxmatrix); +- jc=mxGetJc(mxmatrix); +- +- /*Now, start inserting data into double* matrix: */ +- count=0; +- for(i=0;i +-#include +- +- +-#include "../../../shared/shared.h" +- +-int PetscDetermineLocalSize(int global_size){ +- +- /*output: */ +- int local_size; +- +- /*intermediary: */ +- int i; +- int row_rest; +- int* num_local_rows=NULL; +- +- /*from MPI: */ +- extern int num_procs; +- extern int my_rank; +- +- /*We are not bound by any library, just use what seems most logical*/ +- num_local_rows=(int*)xmalloc(num_procs*sizeof(int)); +- +- for (i=0;i ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++/*Petsc includes: */ ++#include "petscmat.h" ++#include "petscvec.h" ++#include "petscksp.h" ++ ++/*ISSM includes: */ ++#include "../../toolkitsenums.h" ++#include "../../../shared/shared.h" ++ ++ ++InsertMode ISSMToPetscInsertMode(InsMode mode){ ++ ++ switch(mode){ ++ case ADD_VAL: ++ return ADD_VALUES; ++ break; ++ case INS_VAL: ++ return INSERT_VALUES; ++ break; ++ default: ++ _error_("unknown insert mode!"); ++ break; ++ } ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 11695) +@@ -14,6 +14,7 @@ + #include "petscksp.h" + + #include "../../../shared/shared.h" ++#include "../../mpi/patches/mpipatches.h" + + int MatPartition(Mat* poutmatrix,Mat matrixA,double* row_partition_vector,int row_partition_vector_size , + double* col_partition_vector,int col_partition_vector_size){ +@@ -96,7 +97,7 @@ + #endif + + /*Call MatGetSubMatrix*/ +- csize=PetscDetermineLocalSize(col_partition_vector_size); ++ csize=DetermineLocalSize(col_partition_vector_size); + if(col_partition_vector_size==row_partition_vector_size){ + #if _PETSC_MAJOR_ >= 3 + MatGetSubMatrix(matrixA,row_index,col_index,MAT_INITIAL_MATRIX,&outmatrix); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp (revision 11695) +@@ -0,0 +1,35 @@ ++/* \file ISSMToPetscNormMode.cpp ++ * \brief: convert NormMode from ISSM to Petsc ++ */ ++ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++/*Petsc includes: */ ++#include "petscmat.h" ++#include "petscvec.h" ++#include "petscksp.h" ++ ++/*ISSM includes: */ ++#include "../../toolkitsenums.h" ++#include "../../../shared/shared.h" ++ ++ ++NormType ISSMToPetscNormMode(NormMode mode){ ++ ++ switch(mode){ ++ case NORM_INF: ++ return NORM_INFINITY; ++ break; ++ case NORM_TWO: ++ return NORM_2; ++ break; ++ default: ++ _error_("unknown norm !"); ++ break; ++ } ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatToSerial.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatToSerial.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatToSerial.cpp (revision 11695) +@@ -2,6 +2,13 @@ + * \brief gather a Petsc Mat matrix onto cpu 0 + */ + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ + #include "../petscincludes.h" + #include "../../../shared/shared.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/VecToMPISerial.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/VecToMPISerial.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/VecToMPISerial.cpp (revision 11695) +@@ -2,6 +2,13 @@ + * \brief gather a Petsc Vector spread across the cluster, onto node 0, and then broadcast to all nodes. + */ + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ + #include "../petscincludes.h" + #include "../../../shared/shared.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewVec.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewVec.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewVec.cpp (revision 11695) +@@ -14,6 +14,7 @@ + #include "petscksp.h" + + #include "./petscpatches.h" ++#include "../../mpi/patches/mpipatches.h" + + Vec NewVec(int size,bool fromlocalsize){ + +@@ -28,7 +29,7 @@ + local_size=size; + } + else{ +- local_size=PetscDetermineLocalSize(size); ++ local_size=DetermineLocalSize(size); + } + + VecCreate(PETSC_COMM_WORLD,&vector); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp (revision 11695) +@@ -17,6 +17,7 @@ + + #include "../../../shared/shared.h" + #include "../../../include/include.h" ++#include "../../mpi/patches/mpipatches.h" + + /*NewMat(int M,int N){{{1*/ + Mat NewMat(int M,int N){ +@@ -30,8 +31,8 @@ + int d_nz,o_nz,nnz; + + /*Determine local sizes: */ +- m=PetscDetermineLocalSize(M); +- n=PetscDetermineLocalSize(N); ++ m=DetermineLocalSize(M); ++ n=DetermineLocalSize(N); + + nnz=(int)((double)M*(double)N*sparsity); //number of non zeros. + d_nz=(int)((double)nnz/(double)M/2.0); //number of non zeros per row/2 +@@ -54,8 +55,8 @@ + int nnz; + + /*Determine local sizes: */ +- m=PetscDetermineLocalSize(M); +- n=PetscDetermineLocalSize(N); ++ m=DetermineLocalSize(M); ++ n=DetermineLocalSize(N); + + nnz=(int)((double)M*(double)N*sparsity); //number of non zeros. + d_nz=(int)((double)nnz/(double)M/2.0); //number of non zeros per row/2 +@@ -84,8 +85,8 @@ + #endif + + /*Determine local sizes: */ +- m=PetscDetermineLocalSize(M); +- n=PetscDetermineLocalSize(N); ++ m=DetermineLocalSize(M); ++ n=DetermineLocalSize(N); + + /*Figure out number of non zeros per row: */ + d_nz=(int)connectivity*numberofdofspernode/2; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/petscpatches.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/petscpatches.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/petscpatches.h (revision 11695) +@@ -11,6 +11,7 @@ + #include "petscsys.h" + + #include "./SolverEnum.h" ++#include "../../toolkitsenums.h" + + class Parameters; + +@@ -20,11 +21,8 @@ + int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); + int PetscMatrixToMatlabMatrix(mxArray** pdataref,Mat matrix); + int PetscVectorToMatlabVector(mxArray** pdataref,Vec vector); +-int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix); +-int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector); + #endif + +-int PetscDetermineLocalSize(int global_size); + Vec NewVec(int size,bool fromlocalsize=false); + Mat NewMat(int M,int N); + Mat NewMat(int M,int N,double sparsity); +@@ -48,5 +46,7 @@ + void MatToSerial(double** poutmatrix,Mat matrix); + void VecDuplicatePatch(Vec* output, Vec input); + Vec SerialToVec(double* vector,int vector_size); ++InsertMode ISSMToPetscInsertMode(InsMode mode); ++NormType ISSMToPetscNormMode(NormMode mode); + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/petscincludes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/petscincludes.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/petscincludes.h (revision 11695) +@@ -5,6 +5,8 @@ + #ifndef _PETSC_INCLUDES_H_ + #define _PETSC_INCLUDES_H_ + ++#ifdef _HAVE_PETSC_ ++ + /*Petsc includes: */ + #include + #include +@@ -15,3 +17,4 @@ + #include "patches/petscpatches.h" + + #endif ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 11695) +@@ -5,10 +5,21 @@ + #ifndef _TOOLKITS_H_ + #define _TOOLKITS_H_ + ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#ifdef _HAVE_PETSC_ + #include "./petsc/petscincludes.h" ++#endif ++ + #include "./mpi/mpiincludes.h" + #include "./metis/metisincludes.h" + #include "./triangle/triangleincludes.h" + #include "./matlab/matlabincludes.h" ++#include "./double/double.h" ++#include "./toolkitsenums.h" + + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11695) +@@ -78,8 +78,6 @@ + ./objects/ExternalResults/IntExternalResult.cpp\ + ./objects/ExternalResults/StringExternalResult.h\ + ./objects/ExternalResults/StringExternalResult.cpp\ +- ./objects/ExternalResults/PetscVecExternalResult.h\ +- ./objects/ExternalResults/PetscVecExternalResult.cpp\ + ./objects/Elements/Tria.h\ + ./objects/Elements/Tria.cpp\ + ./objects/Elements/TriaHook.h\ +@@ -136,8 +134,6 @@ + ./objects/Params/DoubleParam.h\ + ./objects/Params/FileParam.cpp\ + ./objects/Params/FileParam.h\ +- ./objects/Params/PetscMatParam.cpp\ +- ./objects/Params/PetscMatParam.h\ + ./objects/Params/StringArrayParam.cpp\ + ./objects/Params/StringArrayParam.h\ + ./objects/Params/DoubleMatParam.cpp\ +@@ -148,10 +144,12 @@ + ./objects/Params/DoubleMatArrayParam.h\ + ./objects/Params/DoubleVecParam.cpp\ + ./objects/Params/DoubleVecParam.h\ +- ./objects/Params/PetscVecParam.cpp\ +- ./objects/Params/PetscVecParam.h\ + ./objects/Params/StringParam.cpp\ + ./objects/Params/StringParam.h\ ++ ./objects/Params/MatrixParam.h\ ++ ./objects/Params/MatrixParam.cpp\ ++ ./objects/Params/VectorParam.h\ ++ ./objects/Params/VectorParam.cpp\ + ./Container/Container.h\ + ./Container/Constraints.h\ + ./Container/Constraints.cpp\ +@@ -194,7 +192,7 @@ + ./shared/Numerics/extrema.cpp\ + ./shared/Numerics/XZvectorsToCoordinateSystem.cpp\ + ./shared/Numerics/UnitConversion.cpp\ +- ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ ++ ./shared/Numerics/OptionsFromAnalysis.cpp\ + ./shared/Exceptions/exceptions.h\ + ./shared/Exceptions/Exceptions.cpp\ + ./shared/Exceptions/exprintf.cpp\ +@@ -208,39 +206,9 @@ + ./shared/Elements/GetGlobalDofList.cpp\ + ./shared/Elements/GetNumberOfDofs.cpp\ + ./shared/String/sharedstring.h\ +- ./toolkits/petsc\ +- ./toolkits/petsc/patches\ +- ./toolkits/petsc/patches/SolverEnum.h\ +- ./toolkits/petsc/patches/petscpatches.h\ +- ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ +- ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ +- ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ +- ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ +- ./toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp\ +- ./toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp\ +- ./toolkits/petsc/patches/PetscDetermineLocalSize.cpp\ +- ./toolkits/petsc/patches/VecTranspose.cpp\ +- ./toolkits/petsc/patches/VecToMPISerial.cpp\ +- ./toolkits/petsc/patches/MatToSerial.cpp\ +- ./toolkits/petsc/patches/VecMerge.cpp\ +- ./toolkits/petsc/patches/NewVec.cpp\ +- ./toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp\ +- ./toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp\ +- ./toolkits/petsc/patches/NewMat.cpp\ +- ./toolkits/petsc/patches/SerialToVec.cpp\ +- ./toolkits/petsc/patches/VecFree.cpp\ +- ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ +- ./toolkits/petsc/patches/KSPFree.cpp\ +- ./toolkits/petsc/patches/ISFree.cpp\ +- ./toolkits/petsc/patches/MatFree.cpp\ +- ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ +- ./toolkits/petsc/patches/VecPartition.cpp\ +- ./toolkits/petsc/patches/MatPartition.cpp\ +- ./toolkits/petsc/patches/MatInvert.cpp\ +- ./toolkits/petsc/patches/MatMultPatch.cpp\ +- ./toolkits/petsc/petscincludes.h\ + ./toolkits/mpi/mpiincludes.h\ + ./toolkits/mpi/patches/mpipatches.h\ ++ ./toolkits/mpi/patches/DetermineLocalSize.cpp\ + ./toolkits/mpi/patches/MPI_Upperrow.cpp\ + ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ + ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ +@@ -248,6 +216,7 @@ + ./toolkits/metis/patches/metispatches.h\ + ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ + ./toolkits/triangle/triangleincludes.h\ ++ ./toolkitsenums.h\ + ./toolkits.h\ + ./io/io.h\ + ./io/Disk/diskio.h\ +@@ -267,8 +236,6 @@ + ./modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp\ + ./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\ + ./modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp\ +- ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ +- ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ + ./modules/NodesDofx/NodesDofx.h\ + ./modules/NodesDofx/NodesDofx.cpp\ + ./modules/NodalValuex/NodalValuex.h\ +@@ -343,9 +310,7 @@ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h\ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.cpp\ + ./modules/Solverx/Solverx.cpp\ +- ./modules/Solverx/SolverxPetsc.cpp\ + ./modules/Solverx/Solverx.h\ +- ./modules/Solverx/DofTypesToIndexSet.cpp\ + ./modules/VecMergex/VecMergex.cpp\ + ./modules/VecMergex/VecMergex.h\ + ./modules/Mergesolutionfromftogx/Mergesolutionfromftogx.cpp\ +@@ -730,11 +695,52 @@ + ./toolkits/matlab/MatlabNArrayToNArray.cpp\ + ./toolkits/matlab/MatlabMatrixToMatrix.cpp\ + ./toolkits/matlab/MatlabVectorToVector.cpp\ ++ ./toolkits/double/MatlabVectorToDoubleVector.cpp\ ++ ./toolkits/double/double.h\ ++ ./toolkits/double/MatlabMatrixToDoubleMatrix.cpp\ + ./io/Matlab/matlabio.h\ + ./io/Matlab/WriteMatlabData.cpp\ + ./io/Matlab/FetchMatlabData.cpp\ + ./io/Matlab/OptionParse.cpp + #}}} ++#Petsc sources {{{1 ++petsc_sources= ./toolkits/petsc\ ++ ./toolkits/petsc/patches\ ++ ./toolkits/petsc/patches/SolverEnum.h\ ++ ./toolkits/petsc/patches/petscpatches.h\ ++ ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ ++ ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ ++ ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ ++ ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ ++ ./toolkits/petsc/patches/VecTranspose.cpp\ ++ ./toolkits/petsc/patches/VecToMPISerial.cpp\ ++ ./toolkits/petsc/patches/MatToSerial.cpp\ ++ ./toolkits/petsc/patches/VecMerge.cpp\ ++ ./toolkits/petsc/patches/NewVec.cpp\ ++ ./toolkits/petsc/patches/PetscOptionsDetermineSolverType.cpp\ ++ ./toolkits/petsc/patches/PetscOptionsInsertMultipleString.cpp\ ++ ./toolkits/petsc/patches/NewMat.cpp\ ++ ./toolkits/petsc/patches/SerialToVec.cpp\ ++ ./toolkits/petsc/patches/VecFree.cpp\ ++ ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ ++ ./toolkits/petsc/patches/KSPFree.cpp\ ++ ./toolkits/petsc/patches/ISFree.cpp\ ++ ./toolkits/petsc/patches/MatFree.cpp\ ++ ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ ++ ./toolkits/petsc/patches/VecPartition.cpp\ ++ ./toolkits/petsc/patches/MatPartition.cpp\ ++ ./toolkits/petsc/patches/MatInvert.cpp\ ++ ./toolkits/petsc/patches/MatMultPatch.cpp\ ++ ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\ ++ ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\ ++ ./toolkits/petsc/petscincludes.h\ ++ ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ ++ ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ ++ ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ ++ ./modules/Solverx/SolverxPetsc.cpp\ ++ ./modules/Solverx/DofTypesToIndexSet.cpp ++ ++#}}} + #Serialsources {{{1 + serial_sources= ./objects/Options/Option.cpp\ + ./objects/Options/Option.h\ +@@ -834,6 +840,11 @@ + issm_psources += $(dakota_psources) + endif + ++if PETSC ++issm_sources += $(petsc_sources) ++issm_psources += $(petsc_psources) ++endif ++ + if TRANSIENT + issm_sources += $(transient_sources) + issm_psources += $(transient_psources) +@@ -897,6 +908,7 @@ + #}}} + + #ISSM serial library {{{1 ++if SERIAL + libISSM_a_SOURCES = $(issm_sources) + libISSM_a_SOURCES += $(serial_sources) + libISSM_a_SOURCES += $(bamg_sources) +@@ -909,11 +921,14 @@ + else + libISSM_a_CXXFLAGS += -DMX_COMPAT_32 + endif ++endif + #}}} + #ISSM parallel library {{{1 ++if PARALLEL + libpISSM_a_SOURCES = $(issm_sources) + libpISSM_a_SOURCES += $(issm_psources) + libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) ++endif + #}}} + #Overload library, to overload any non-standard symbols. {{{1 + libOverload_a_SOURCES = ./shared/String/stricmp.c +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.cpp (revision 11695) +@@ -228,7 +228,7 @@ + } + /*}}}*/ + /*FUNCTION Matice::GetVectorFromInputs{{{1*/ +-void Matice::GetVectorFromInputs(Vec vector,int input_enum){ ++void Matice::GetVectorFromInputs(Vector* vector,int input_enum){ + + /*Intermediaries*/ + Element *element= NULL; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Material.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Material.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Material.h (revision 11695) +@@ -21,7 +21,7 @@ + /*Numerics*/ + virtual void InputDuplicate(int original_enum,int new_enum)=0; + virtual void Configure(Elements* elements)=0; +- virtual void GetVectorFromInputs(Vec vector,int input_enum)=0; ++ virtual void GetVectorFromInputs(Vector* vector,int input_enum)=0; + + }; + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matice.h (revision 11695) +@@ -59,7 +59,7 @@ + /*Material virtual functions resolution: {{{1*/ + void InputDuplicate(int original_enum,int new_enum); + void Configure(Elements* elements); +- void GetVectorFromInputs(Vec vector,int input_enum); ++ void GetVectorFromInputs(Vector* vector,int input_enum); + /*}}}*/ + /*Matice Numerics: {{{1*/ + void SetCurrentConfiguration(Elements* elementsin,Loads* loadsin,Nodes* nodesin,Vertices* verticesin,Materials* materialsin,Parameters* parametersin); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Materials/Matpar.h (revision 11695) +@@ -70,7 +70,7 @@ + /*Material virtual functions resolution: {{{1*/ + void InputDuplicate(int original_enum,int new_enum){_error_("not implemented yet");}; + void Configure(Elements* elements); +- void GetVectorFromInputs(Vec vector,int input_enum){return;} ++ void GetVectorFromInputs(Vector* vector,int input_enum){return;} + /*}}}*/ + /*Numerics: {{{1*/ + double GetG(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscMatParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscMatParam.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscMatParam.cpp (revision 11695) +@@ -1,242 +0,0 @@ +-/*!\file PetscMatParam.c +- * \brief: implementation of the PetscMatParam object +- */ +- +-/*header files: */ +-/*{{{1*/ +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include +-#include +-#include "../objects.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../shared/shared.h" +-#include "../../Container/Container.h" +-#include "../../include/include.h" +-/*}}}*/ +- +-/*PetscMatParam constructors and destructor*/ +-/*FUNCTION PetscMatParam::PetscMatParam(){{{1*/ +-PetscMatParam::PetscMatParam(){ +- return; +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::PetscMatParam(int enum_type,IssmPetscMat value){{{1*/ +-PetscMatParam::PetscMatParam(int in_enum_type,Mat in_value){ +- +- enum_type=in_enum_type; +- +- value=NULL; +- +- if(in_value){ +- MatDuplicate(in_value,MAT_COPY_VALUES,&value); +- } +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::~PetscMatParam(){{{1*/ +-PetscMatParam::~PetscMatParam(){ +- MatFree(&value); +-} +-/*}}}*/ +- +-/*Object virtual functions definitions:*/ +-/*FUNCTION PetscMatParam::Echo {{{1*/ +-void PetscMatParam::Echo(void){ +- +- printf("PetscMatParam:\n"); +- printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); +- +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::DeepEcho{{{1*/ +-void PetscMatParam::DeepEcho(void){ +- +- int i; +- printf("PetscMatParam:\n"); +- printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); +- MatView(value,PETSC_VIEWER_STDOUT_WORLD); +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::Id{{{1*/ +-int PetscMatParam::Id(void){ return -1; } +-/*}}}*/ +-/*FUNCTION PetscMatParam::MyRank{{{1*/ +-int PetscMatParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION PetscMatParam::Marshall{{{1*/ +-void PetscMatParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int M,N; +- double* serial_mat=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of PetscMatParam: */ +- enum_value=PetscMatParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall PetscMatParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- if(value){ +- MatGetSize(value,&M,&N); +- MatToSerial(&serial_mat,value); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); +- } +- else{ +- M=0; +- N=0; +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); +- } +- +- /*Free ressources:*/ +- xfree((void**)&serial_mat); +- +- /*return:*/ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::MarshallSize{{{1*/ +-int PetscMatParam::MarshallSize(){ +- +- int M=0; +- int N=0; +- if(value)MatGetSize(value,&M,&N); +- +- return sizeof(M)+ +- sizeof(N)+ +- M*N*sizeof(double)+ +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::Demarshall{{{1*/ +-void PetscMatParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i,j; +- int M,N; +- double* serial_mat=NULL; +- int* idxm=NULL; +- int* idxn=NULL; +- double sparsity=.001; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); +- if(M!=0 && N!=0){ +- serial_mat=(double*)xmalloc(M*N*sizeof(double)); +- memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); +- value=NewMat(M,N,sparsity); +- idxm=(int*)xmalloc(M*sizeof(int)); +- idxn=(int*)xmalloc(N*sizeof(int)); +- for(i=0;ienum_type,this->value); +- +-} +-/*}}}*/ +- +-/*PetscMatParam virtual functions definitions: */ +-/*FUNCTION PetscMatParam::GetParameterValue{{{1*/ +-void PetscMatParam::GetParameterValue(Mat* poutput){ +- Mat output=NULL; +- +- if(value){ +- MatDuplicate(value,MAT_COPY_VALUES,&output); +- } +- *poutput=output; +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::GetParameterName{{{1*/ +-void PetscMatParam::GetParameterName(char**pname){ +- EnumToStringx(pname,this->enum_type); +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::SetMatlabField{{{1*/ +-#ifdef _SERIAL_ +-void PetscMatParam::SetMatlabField(mxArray* dataref){ +- +- char* name=NULL; +- int M,N; +- double* doublemat=NULL; +- mxArray* pfield=NULL; +- +- MatToSerial(&doublemat,value); +- MatGetSize(value,&M,&N); +- this->GetParameterName(&name); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,N); +- mxSetPr(pfield,doublemat); +- mxSetField( dataref, 0, name, pfield); +-} +-#endif +-/*}}}*/ +-/*FUNCTION PetscMatParam::SetValue{{{1*/ +-void PetscMatParam::SetValue(Mat matrix){ +- +- /*avoid leak: */ +- MatFree(&value); +- +- /*copy: */ +- MatDuplicate(matrix,MAT_COPY_VALUES,&value); +-} +-/*}}}*/ +-/*FUNCTION PetscMatParam::UnitConversion{{{1*/ +-void PetscMatParam::UnitConversion(int direction_enum){ +- /*do nothing, no unit conversion*/ +-} +-/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscVecParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscVecParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscVecParam.h (revision 11695) +@@ -1,90 +0,0 @@ +-/*! \file PetscVecParam.h +- * \brief: header file for triavertexinput object +- */ +- +- +-#ifndef _PETSCVECPARAM_H_ +-#define _PETSCVECPARAM_H_ +- +-/*Headers:*/ +-/*{{{1*/ +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#ifdef _SERIAL_ +-#include +-#endif +- +-#include "./Param.h" +-#include "../../include/include.h" +-#include "../../shared/shared.h" +-/*}}}*/ +- +-class PetscVecParam: public Param{ +- +- private: +- /*just hold 3 values for 3 vertices: */ +- int enum_type; +- Vec value; +- +- public: +- /*PetscVecParam constructors, destructors: {{{1*/ +- PetscVecParam(); +- PetscVecParam(int enum_type,Vec value); +- ~PetscVecParam(); +- /*}}}*/ +- /*Object virtual functions definitions:{{{1 */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif +- int ObjectEnum(); +- Object* copy(); +- /*}}}*/ +- /*Param vritual function definitions: {{{1*/ +- int InstanceEnum(){return enum_type;} +- void GetParameterValue(bool* pbool){_error_("PetscVec param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(int* pinteger){_error_("PetscVec param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(int** pintarray,int* pM){_error_("PetscVec param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("PetscVec param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double* pdouble){_error_("PetscVec param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(char** pstring){_error_("PetscVec param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(char*** pstringarray,int* pM){_error_("PetscVec param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double** pdoublearray,int* pM){_error_("PetscVec param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("PetscVec param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("PetscVec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("PetscVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* poutput); +- void GetParameterValue(FILE** pfid){_error_("PetscVec of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} +- +- void SetValue(bool boolean){_error_("PetscVec of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +- void SetValue(int integer){_error_("PetscVec of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} +- void SetValue(double scalar){_error_("PetscVec of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} +- void SetValue(char* string){_error_("PetscVec of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} +- void SetValue(char** stringarray,int M){_error_("PetscVec of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} +- void SetValue(double* doublearray,int M){_error_("PetscVec of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} +- void SetValue(double* pdoublearray,int M,int N){_error_("PetscVec of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} +- void SetValue(int* intarray,int M){_error_("PetscVec of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(int* pintarray,int M,int N){_error_("PetscVec of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec); +- void SetValue(Mat mat){_error_("PetscVec of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} +- void SetValue(FILE* fid){_error_("PetscVec of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} +- void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("PetscVec param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} +- void UnitConversion(int direction_enum); +- +- void GetParameterName(char**pname); +- #ifdef _SERIAL_ +- void SetMatlabField(mxArray* dataref); +- #endif +- +- /*}}}*/ +-}; +-#endif /* _PETSCVECPARAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscMatParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscMatParam.h (revision 11695) +@@ -1,90 +0,0 @@ +-/*! \file PetscMatParam.h +- * \brief: header file for triavertexinput object +- */ +- +- +-#ifndef _PETSCMATPARAM_H_ +-#define _PETSCMATPARAM_H_ +- +-/*Headers:*/ +-/*{{{1*/ +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#ifdef _SERIAL_ +-#include +-#endif +- +-#include "./Param.h" +-#include "../../include/include.h" +-#include "../../shared/shared.h" +-/*}}}*/ +- +-class PetscMatParam: public Param{ +- +- private: +- /*just hold 3 values for 3 vertices: */ +- int enum_type; +- Mat value; +- +- public: +- /*PetscMatParam constructors, destructors: {{{1*/ +- PetscMatParam(); +- PetscMatParam(int enum_type,Mat value); +- ~PetscMatParam(); +- /*}}}*/ +- /*Object virtual functions definitions:{{{1 */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- #ifdef _SERIAL_ +- void Marshall(char** pmarshalled_dataset); +- int MarshallSize(); +- void Demarshall(char** pmarshalled_dataset); +- #endif +- int ObjectEnum(); +- Object* copy(); +- /*}}}*/ +- /*Param vritual function definitions: {{{1*/ +- int InstanceEnum(){return enum_type;} +- void GetParameterValue(bool* pbool){_error_("PetscMat param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(int* pinteger){_error_("PetscMat param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(int** pintarray,int* pM){_error_("PetscMat param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("PetscMat param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double* pdouble){_error_("PetscMat param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(char** pstring){_error_("PetscMat param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(char*** pstringarray,int* pM){_error_("PetscMat param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double** pdoublearray,int* pM){_error_("PetscMat param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("PetscMat param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("PetscMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("PetscMat param of enum %i (%s) cannot return a vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* poutput); +- void GetParameterValue(FILE** pfid){_error_("PetscMat param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} +- +- void SetValue(bool boolean){_error_("PetscMat param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +- void SetValue(int integer){_error_("PetscMat param of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} +- void SetValue(double scalar){_error_("PetscMat param of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} +- void SetValue(char* string){_error_("PetscMat param of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} +- void SetValue(char** stringarray,int M){_error_("PetscMat param of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} +- void SetValue(double* doublearray,int M){_error_("PetscMat param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} +- void SetValue(double* pdoublearray,int M,int N){_error_("PetscMat param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} +- void SetValue(int* intarray,int M){_error_("PetscMat param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(int* pintarray,int M,int N){_error_("PetscMat param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("PetscMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat); +- void SetValue(FILE* fid){_error_("PetscMat param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} +- void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("PetscMat param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} +- void UnitConversion(int direction_enum); +- +- void GetParameterName(char**pname); +- #ifdef _SERIAL_ +- void SetMatlabField(mxArray* dataref); +- #endif +- +- /*}}}*/ +-}; +-#endif /* _PETSCMATPARAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscVecParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscVecParam.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/PetscVecParam.cpp (revision 11695) +@@ -1,237 +0,0 @@ +-/*!\file PetscVecParam.c +- * \brief: implementation of the PetscVecParam object +- */ +- +-/*header files: */ +-/*{{{1*/ +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include +-#include +-#include "../objects.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../shared/shared.h" +-#include "../../Container/Container.h" +-#include "../../include/include.h" +-/*}}}*/ +- +-/*PetscVecParam constructors and destructor*/ +-/*FUNCTION PetscVecParam::PetscVecParam(){{{1*/ +-PetscVecParam::PetscVecParam(){ +- return; +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::PetscVecParam(int enum_type,IssmPetscVec value){{{1*/ +-PetscVecParam::PetscVecParam(int in_enum_type,Vec in_value){ +- +- enum_type=in_enum_type; +- +- value=NULL; +- +- if(in_value){ +- VecDuplicate(in_value,&value); +- VecCopy(in_value,value); +- } +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::~PetscVecParam(){{{1*/ +-PetscVecParam::~PetscVecParam(){ +- VecFree(&value); +-} +-/*}}}*/ +- +-/*Object virtual functions definitions:*/ +-/*FUNCTION PetscVecParam::Echo {{{1*/ +-void PetscVecParam::Echo(void){ +- +- printf("PetscVecParam:\n"); +- printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); +- +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::DeepEcho{{{1*/ +-void PetscVecParam::DeepEcho(void){ +- +- int i; +- printf("PetscVecParam:\n"); +- printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); +- VecView(value,PETSC_VIEWER_STDOUT_WORLD); +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::Id{{{1*/ +-int PetscVecParam::Id(void){ return -1; } +-/*}}}*/ +-/*FUNCTION PetscVecParam::MyRank{{{1*/ +-int PetscVecParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ +-#ifdef _SERIAL_ +-/*FUNCTION PetscVecParam::Marshall{{{1*/ +-void PetscVecParam::Marshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int enum_value=0; +- int M; +- double* serial_value=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*get enum value of PetscVecParam: */ +- enum_value=PetscVecParamEnum; +- +- /*marshall enum: */ +- memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); +- +- /*marshall PetscVecParam data: */ +- memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- if(value){ +- VecGetSize(value,&M); +- VecToMPISerial(&serial_value,value); +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); +- } +- else{ +- M=0; +- memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); +- } +- /*Free ressources:*/ +- xfree((void**)&serial_value); +- +- /*return:*/ +- *pmarshalled_dataset=marshalled_dataset; +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::MarshallSize{{{1*/ +-int PetscVecParam::MarshallSize(){ +- +- int M=0; +- if(value)VecGetSize(value,&M); +- +- return sizeof(M)+M*sizeof(double) +- +sizeof(enum_type)+ +- +sizeof(int); //sizeof(int) for enum value +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::Demarshall{{{1*/ +-void PetscVecParam::Demarshall(char** pmarshalled_dataset){ +- +- char* marshalled_dataset=NULL; +- int i; +- int M; +- double* serial_vec=NULL; +- int* idxm=NULL; +- +- /*recover marshalled_dataset: */ +- marshalled_dataset=*pmarshalled_dataset; +- +- /*this time, no need to get enum type, the pointer directly points to the beginning of the +- *object data (thanks to DataSet::Demarshall):*/ +- memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); +- +- /*data: */ +- +- memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); +- if(M){ +- serial_vec=(double*)xmalloc(M*sizeof(double)); +- memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); +- +- value=NewVec(M); +- idxm=(int*)xmalloc(M*sizeof(int)); +- for(i=0;ienum_type,this->value); +- +-} +-/*}}}*/ +- +-/*PetscVecParam virtual functions definitions: */ +-/*FUNCTION PetscVecParam::GetParameterValue{{{1*/ +-void PetscVecParam::GetParameterValue(Vec* poutput){ +- Vec output=NULL; +- +- if(value){ +- VecDuplicate(value,&output); +- VecCopy(value,output); +- } +- *poutput=output; +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::GetParameterName{{{1*/ +-void PetscVecParam::GetParameterName(char**pname){ +- EnumToStringx(pname,this->enum_type); +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::SetMatlabField{{{1*/ +-#ifdef _SERIAL_ +-void PetscVecParam::SetMatlabField(mxArray* dataref){ +- +- mxArray* pfield=NULL; +- char* name=NULL; +- double* doublevec=NULL; +- int M; +- +- VecToMPISerial(&doublevec,value); +- VecGetSize(value,&M); +- this->GetParameterName(&name); +- +- pfield=mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(pfield,M); +- mxSetN(pfield,1); +- mxSetPr(pfield,doublevec); +- +- mxSetField( dataref, 0, name, pfield); +-} +-#endif +-/*}}}*/ +-/*FUNCTION PetscVecParam::SetValue{{{1*/ +-void PetscVecParam::SetValue(Vec vector){ +- +- /*avoid leak: */ +- VecFree(&value); +- +- /*copy: */ +- VecDuplicate(vector,&value); +- VecCopy(vector,value); +-} +-/*}}}*/ +-/*FUNCTION PetscVecParam::UnitConversion{{{1*/ +-void PetscVecParam::UnitConversion(int direction_enum){ +- /*do nothing, no unit conversion*/ +-} +-/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleVecParam.h (revision 11695) +@@ -61,8 +61,8 @@ + void GetParameterValue(double** pdoublearray,int* pM); + void GetParameterValue(double** pdoublearray,int* pM, int* pN); + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("DoubleVec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("DoubleVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("DoubleVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("DoubleVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("DoubleVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("DoubleVec param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("DoubleVec param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -74,8 +74,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("DoubleVec param of enum %i (%s) cannot hold a double mat array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("DoubleVec param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));}; + void SetValue(int* pintarray,int M,int N){_error_("DoubleVec param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("DoubleVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("DoubleVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("DoubleVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("DoubleVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("DoubleVec param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("DoubleVec param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleParam.h (revision 11695) +@@ -61,8 +61,8 @@ + void GetParameterValue(double** pdoublearray,int* pM); + void GetParameterValue(double** pdoublearray,int* pM, int* pN); + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Double param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("Double param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("Double param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("Double param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("Double param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("Double param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){this->value=(double)boolean;} +@@ -74,8 +74,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("Double param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("Double param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("Double param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("Double param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("Double param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("Double param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("Double param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("Double param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Double param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h (revision 11695) +@@ -63,8 +63,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("DoubleMatArray param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("DoubleMatArray param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims); +- void GetParameterValue(Vec* pvec){_error_("DoubleMatArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("DoubleMatArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("DoubleMatArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("DoubleMatArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("DoubleMatArray param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("DoubleMatArray param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -76,8 +76,8 @@ + void SetValue(double* doublearray,int M,int N){_error_("DoubleMatArray param of enum %i (%s) cannot hold a double mat array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("DoubleMatArray param of enum %i (%s) cannot hold a int vec array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M,int N){_error_("DoubleMatArray param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("DoubleMatArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("Bool param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array); + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/DoubleMatParam.h (revision 11695) +@@ -62,8 +62,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("DoubleMat param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM,int* pN); + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("DoubleMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("DoubleMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("DoubleMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("DoubleMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("DoubleMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("DoubleMat param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("DoubleMat param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -75,8 +75,8 @@ + void SetValue(double* doublearray,int M,int N); + void SetValue(int* intarray,int M){_error_("DoubleMat param of enum %i (%s) cannot hold a int vec array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M,int N){_error_("DoubleMat param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));}; +- void SetValue(Vec vec){_error_("DoubleMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("DoubleMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("DoubleMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("DoubleMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("DoubleMat param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("DoubleMat param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/Param.h (revision 11695) +@@ -40,8 +40,8 @@ + virtual void GetParameterValue(double** pdoublearray,int* pM)=0; + virtual void GetParameterValue(double** pdoublearray,int* pM,int* pN)=0; + virtual void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims)=0; +- virtual void GetParameterValue(Vec* pvec)=0; +- virtual void GetParameterValue(Mat* pmat)=0; ++ virtual void GetParameterValue(Vector** pvec)=0; ++ virtual void GetParameterValue(Matrix** pmat)=0; + virtual void GetParameterValue(FILE** pfid)=0; + + virtual void SetValue(bool boolean)=0; +@@ -53,8 +53,8 @@ + virtual void SetValue(double* pdoublearray,int M,int N)=0; + virtual void SetValue(int* intarray,int M)=0; + virtual void SetValue(int* pintarray,int M,int N)=0; +- virtual void SetValue(Vec vec)=0; +- virtual void SetValue(Mat mat)=0; ++ virtual void SetValue(Vector* vec)=0; ++ virtual void SetValue(Matrix* mat)=0; + virtual void SetValue(FILE* fid)=0; + virtual void SetValue(double** array, int M, int* mdim_array, int* ndim_array)=0; + virtual void UnitConversion(int direction_enum)=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/FileParam.h (revision 11695) +@@ -60,8 +60,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("FileParam of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("FileParam of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("File param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("FileParam of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("FileParam of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("FileParam of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("FileParam of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){*pfid=value;}; + + void SetValue(bool boolean){_error_("FileParam of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} +@@ -73,8 +73,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("FileParam of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("FileParam of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("FileParam of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("FileParam of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("FileParam of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("FileParam of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("FileParam of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("File param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("File param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntVecParam.h (revision 11695) +@@ -62,8 +62,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("IntVec param of enum %i (%s) cannot return a double array (maybe in serial?)",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("IntVec param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("IntVec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("IntVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("IntVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("IntVec param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("IntVec param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("IntVec param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("IntVec param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -75,8 +75,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("IntVec param of enum %i (%s) cannot hold a double mat array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M); + void SetValue(int* pintarray,int M,int N){_error_("IntVec param of enum %i (%s) cannot hold a int mat array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("IntVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("IntVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("IntVec param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("IntVec param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("IntVec param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("IntVec param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntParam.h (revision 11695) +@@ -61,8 +61,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("Int param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Int param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Int param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("Int param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("Int param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("Int param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("Int param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("Int param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){this->value=(int)boolean;} +@@ -74,8 +74,8 @@ + void SetValue(char** stringarray,int M){_error_("Int param of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} + void SetValue(double* doublearray,int M){_error_("Int param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(double* pdoublearray,int M,int N){_error_("Int param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("Int param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("Int param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("Int param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("Int param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("Int param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Int param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/BoolParam.h (revision 11695) +@@ -60,8 +60,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("Bool param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Bool param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Bool param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("Bool param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("Bool param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("Bool param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("Bool param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("Bool param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){this->value=boolean;} +@@ -73,8 +73,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("Bool param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("Bool param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("Bool param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("Bool param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("Bool param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("Bool param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("Bool param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("Bool param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Bool param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/IntMatParam.h (revision 11695) +@@ -62,8 +62,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("IntMat param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM,int* pN){_error_("IntMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));}; + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("IntMat param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("IntMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("IntMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("IntMat param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("IntMat param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("IntMat param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("IntMat param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -75,8 +75,8 @@ + void SetValue(double* doublearray,int M,int N){_error_("IntMat param of enum %i (%s) cannot hold a double vec array",enum_type,EnumToStringx(enum_type));}; + void SetValue(int* intarray,int M){_error_("IntMat param of enum %i (%s) cannot hold a int vec array",enum_type,EnumToStringx(enum_type));}; + void SetValue(int* intarray,int M,int N); +- void SetValue(Vec vec){_error_("IntMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("IntMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("IntMat param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("IntMat param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("IntMat param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("IntMat param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.cpp (revision 11695) +@@ -0,0 +1,227 @@ ++/*!\file VectorParam.c ++ * \brief: implementation of the VectorParam object ++ */ ++ ++/*header files: */ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++/*}}}*/ ++ ++/*VectorParam constructors and destructor*/ ++/*FUNCTION VectorParam::VectorParam(){{{1*/ ++VectorParam::VectorParam(){ ++ return; ++} ++/*}}}*/ ++/*FUNCTION VectorParam::VectorParam(int enum_type,IssmVector value){{{1*/ ++VectorParam::VectorParam(int in_enum_type,Vector* in_value){ ++ ++ enum_type=in_enum_type; ++ ++ value=NULL; ++ ++ if(in_value){ ++ value=in_value->Duplicate(); ++ in_value->Copy(value); ++ } ++} ++/*}}}*/ ++/*FUNCTION VectorParam::~VectorParam(){{{1*/ ++VectorParam::~VectorParam(){ ++ xdelete(&value); ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION VectorParam::Echo {{{1*/ ++void VectorParam::Echo(void){ ++ ++ printf("VectorParam:\n"); ++ printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); ++ ++} ++/*}}}*/ ++/*FUNCTION VectorParam::DeepEcho{{{1*/ ++void VectorParam::DeepEcho(void){ ++ ++ int i; ++ printf("VectorParam:\n"); ++ printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); ++ value->Echo(); ++} ++/*}}}*/ ++/*FUNCTION VectorParam::Id{{{1*/ ++int VectorParam::Id(void){ return -1; } ++/*}}}*/ ++/*FUNCTION VectorParam::MyRank{{{1*/ ++int VectorParam::MyRank(void){ ++ extern int my_rank; ++ return my_rank; ++} ++/*}}}*/ ++#ifdef _SERIAL_ ++/*FUNCTION VectorParam::Marshall{{{1*/ ++void VectorParam::Marshall(char** pmarshalled_dataset){ ++ ++ char* marshalled_dataset=NULL; ++ int enum_value=0; ++ int M; ++ double* serial_value=NULL; ++ ++ /*recover marshalled_dataset: */ ++ marshalled_dataset=*pmarshalled_dataset; ++ ++ /*get enum value of VectorParam: */ ++ enum_value=VectorParamEnum; ++ ++ /*marshall enum: */ ++ memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); ++ ++ /*marshall VectorParam data: */ ++ memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); ++ if(value){ ++ value->GetSize(&M); ++ serial_value=value->ToMPISerial(); ++ memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); ++ memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); ++ } ++ else{ ++ M=0; ++ memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); ++ } ++ /*Free ressources:*/ ++ xfree((void**)&serial_value); ++ ++ /*return:*/ ++ *pmarshalled_dataset=marshalled_dataset; ++} ++/*}}}*/ ++/*FUNCTION VectorParam::MarshallSize{{{1*/ ++int VectorParam::MarshallSize(){ ++ ++ int M=0; ++ if(value)value->GetSize(&M); ++ ++ return sizeof(M)+M*sizeof(double) ++ +sizeof(enum_type)+ ++ +sizeof(int); //sizeof(int) for enum value ++} ++/*}}}*/ ++/*FUNCTION VectorParam::Demarshall{{{1*/ ++void VectorParam::Demarshall(char** pmarshalled_dataset){ ++ ++ char* marshalled_dataset=NULL; ++ int i; ++ double* serial_vec=NULL; ++ int M; ++ ++ /*recover marshalled_dataset: */ ++ marshalled_dataset=*pmarshalled_dataset; ++ ++ /*this time, no need to get enum type, the pointer directly points to the beginning of the ++ *object data (thanks to DataSet::Demarshall):*/ ++ memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); ++ ++ /*data: */ ++ ++ memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); ++ if(M){ ++ serial_vec=(double*)xmalloc(M*sizeof(double)); ++ memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); ++ ++ value=new Vector(serial_vec,M); ++ } ++ else{ ++ value=NULL; ++ } ++ ++ /*Free ressources:*/ ++ xfree((void**)&serial_vec); ++ ++ /*return: */ ++ *pmarshalled_dataset=marshalled_dataset; ++} ++/*}}}*/ ++#endif ++/*FUNCTION VectorParam::ObjectEnum{{{1*/ ++int VectorParam::ObjectEnum(void){ ++ ++ return VectorParamEnum; ++ ++} ++/*}}}*/ ++/*FUNCTION VectorParam::copy{{{1*/ ++Object* VectorParam::copy() { ++ ++ return new VectorParam(this->enum_type,this->value); ++ ++} ++/*}}}*/ ++ ++/*VectorParam virtual functions definitions: */ ++/*FUNCTION VectorParam::GetParameterValue{{{1*/ ++void VectorParam::GetParameterValue(Vector** poutput){ ++ Vector* output=NULL; ++ ++ if(value){ ++ output=value->Duplicate(); ++ value->Copy(output); ++ } ++ *poutput=output; ++} ++/*}}}*/ ++/*FUNCTION VectorParam::GetParameterName{{{1*/ ++void VectorParam::GetParameterName(char**pname){ ++ EnumToStringx(pname,this->enum_type); ++} ++/*}}}*/ ++/*FUNCTION VectorParam::SetMatlabField{{{1*/ ++#ifdef _SERIAL_ ++void VectorParam::SetMatlabField(mxArray* dataref){ ++ ++ mxArray* pfield=NULL; ++ char* name=NULL; ++ double* doublevec=NULL; ++ int M; ++ ++ doublevec=value->ToMPISerial(); ++ value->GetSize(&M); ++ this->GetParameterName(&name); ++ ++ pfield=mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(pfield,M); ++ mxSetN(pfield,1); ++ mxSetPr(pfield,doublevec); ++ ++ mxSetField( dataref, 0, name, pfield); ++} ++#endif ++/*}}}*/ ++/*FUNCTION VectorParam::SetValue{{{1*/ ++void VectorParam::SetValue(Vector* vector){ ++ ++ /*avoid leak: */ ++ xdelete(&value); ++ ++ /*copy: */ ++ value=vector->Duplicate(); ++ vector->Copy(value); ++} ++/*}}}*/ ++/*FUNCTION VectorParam::UnitConversion{{{1*/ ++void VectorParam::UnitConversion(int direction_enum){ ++ /*do nothing, no unit conversion*/ ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.cpp (revision 11695) +@@ -0,0 +1,227 @@ ++/*!\file MatrixParam.c ++ * \brief: implementation of the MatrixParam object ++ */ ++ ++/*header files: */ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++/*}}}*/ ++ ++/*MatrixParam constructors and destructor*/ ++/*FUNCTION MatrixParam::MatrixParam(){{{1*/ ++MatrixParam::MatrixParam(){ ++ return; ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::MatrixParam(int enum_type,Matrix* value){{{1*/ ++MatrixParam::MatrixParam(int in_enum_type,Matrix* in_value){ ++ ++ enum_type=in_enum_type; ++ value=NULL; ++ ++ if(in_value){ ++ value=in_value->Duplicate(); ++ } ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::~MatrixParam(){{{1*/ ++MatrixParam::~MatrixParam(){ ++ xdelete(&value); ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION MatrixParam::Echo {{{1*/ ++void MatrixParam::Echo(void){ ++ ++ printf("MatrixParam:\n"); ++ printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); ++ ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::DeepEcho{{{1*/ ++void MatrixParam::DeepEcho(void){ ++ ++ int i; ++ printf("MatrixParam:\n"); ++ printf(" enum: %i (%s)\n",this->enum_type,EnumToStringx(this->enum_type)); ++ this->value->Echo(); ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::Id{{{1*/ ++int MatrixParam::Id(void){ return -1; } ++/*}}}*/ ++/*FUNCTION MatrixParam::MyRank{{{1*/ ++int MatrixParam::MyRank(void){ ++ extern int my_rank; ++ return my_rank; ++} ++/*}}}*/ ++#ifdef _SERIAL_ ++/*FUNCTION MatrixParam::Marshall{{{1*/ ++void MatrixParam::Marshall(char** pmarshalled_dataset){ ++ ++ char* marshalled_dataset=NULL; ++ int enum_value=0; ++ int M,N; ++ double* serial_mat=NULL; ++ ++ /*recover marshalled_dataset: */ ++ marshalled_dataset=*pmarshalled_dataset; ++ ++ /*get enum value of MatrixParam: */ ++ enum_value=MatrixParamEnum; ++ ++ /*marshall enum: */ ++ memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); ++ ++ /*marshall MatrixParam data: */ ++ memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); ++ if(value){ ++ value->GetSize(&M,&N); ++ serial_mat=value->ToSerial(); ++ memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); ++ memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); ++ memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); ++ } ++ else{ ++ M=0; ++ N=0; ++ memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); ++ memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); ++ } ++ ++ /*Free ressources:*/ ++ xfree((void**)&serial_mat); ++ ++ /*return:*/ ++ *pmarshalled_dataset=marshalled_dataset; ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::MarshallSize{{{1*/ ++int MatrixParam::MarshallSize(){ ++ ++ int M=0; ++ int N=0; ++ if(value)value->GetSize(&M,&N); ++ ++ return sizeof(M)+ ++ sizeof(N)+ ++ M*N*sizeof(double)+ ++ +sizeof(enum_type)+ ++ +sizeof(int); //sizeof(int) for enum value ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::Demarshall{{{1*/ ++void MatrixParam::Demarshall(char** pmarshalled_dataset){ ++ ++ char* marshalled_dataset=NULL; ++ int M,N; ++ double* serial_mat=NULL; ++ ++ /*recover marshalled_dataset: */ ++ marshalled_dataset=*pmarshalled_dataset; ++ ++ /*this time, no need to get enum type, the pointer directly points to the beginning of the ++ *object data (thanks to DataSet::Demarshall):*/ ++ memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); ++ ++ /*data: */ ++ memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); ++ memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); ++ if(M!=0 && N!=0){ ++ serial_mat=(double*)xmalloc(M*N*sizeof(double)); ++ memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); ++ value=new Matrix(serial_mat,M,N,.001); ++ } ++ else{ ++ value=NULL; ++ } ++ ++ /*Free ressources:*/ ++ xfree((void**)&serial_mat); ++ ++ /*return: */ ++ *pmarshalled_dataset=marshalled_dataset; ++} ++/*}}}*/ ++#endif ++/*FUNCTION MatrixParam::ObjectEnum{{{1*/ ++int MatrixParam::ObjectEnum(void){ ++ ++ return MatrixParamEnum; ++ ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::copy{{{1*/ ++Object* MatrixParam::copy() { ++ ++ return new MatrixParam(this->enum_type,this->value); ++ ++} ++/*}}}*/ ++ ++/*MatrixParam virtual functions definitions: */ ++/*FUNCTION MatrixParam::GetParameterValue{{{1*/ ++void MatrixParam::GetParameterValue(Matrix** poutput){ ++ Matrix* output=NULL; ++ ++ if(value){ ++ output=value->Duplicate(); ++ } ++ *poutput=output; ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::GetParameterName{{{1*/ ++void MatrixParam::GetParameterName(char**pname){ ++ EnumToStringx(pname,this->enum_type); ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::SetMatlabField{{{1*/ ++#ifdef _SERIAL_ ++void MatrixParam::SetMatlabField(mxArray* dataref){ ++ ++ char* name=NULL; ++ int M,N; ++ double* doublemat=NULL; ++ mxArray* pfield=NULL; ++ ++ doublemat=value->ToSerial(); ++ value->GetSize(&M,&N); ++ this->GetParameterName(&name); ++ ++ pfield=mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(pfield,M); ++ mxSetN(pfield,N); ++ mxSetPr(pfield,doublemat); ++ mxSetField( dataref, 0, name, pfield); ++} ++#endif ++/*}}}*/ ++/*FUNCTION MatrixParam::SetValue{{{1*/ ++void MatrixParam::SetValue(Matrix* matrix){ ++ ++ /*avoid leak: */ ++ xdelete(&value); ++ ++ /*copy: */ ++ value=matrix->Duplicate(); ++} ++/*}}}*/ ++/*FUNCTION MatrixParam::UnitConversion{{{1*/ ++void MatrixParam::UnitConversion(int direction_enum){ ++ /*do nothing, no unit conversion*/ ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/VectorParam.h (revision 11695) +@@ -0,0 +1,90 @@ ++/*! \file VectorParam.h ++ * \brief: header file for triavertexinput object ++ */ ++ ++ ++#ifndef _VECTORPARAM_H_ ++#define _VECTORPARAM_H_ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#ifdef _SERIAL_ ++#include ++#endif ++ ++#include "./Param.h" ++#include "../../include/include.h" ++#include "../../shared/shared.h" ++/*}}}*/ ++ ++class VectorParam: public Param{ ++ ++ private: ++ /*just hold 3 values for 3 vertices: */ ++ int enum_type; ++ Vector* value; ++ ++ public: ++ /*VectorParam constructors, destructors: {{{1*/ ++ VectorParam(); ++ VectorParam(int enum_type,Vector* value); ++ ~VectorParam(); ++ /*}}}*/ ++ /*Object virtual functions definitions:{{{1 */ ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int MyRank(); ++ #ifdef _SERIAL_ ++ void Marshall(char** pmarshalled_dataset); ++ int MarshallSize(); ++ void Demarshall(char** pmarshalled_dataset); ++ #endif ++ int ObjectEnum(); ++ Object* copy(); ++ /*}}}*/ ++ /*Param vritual function definitions: {{{1*/ ++ int InstanceEnum(){return enum_type;} ++ void GetParameterValue(bool* pbool){_error_("Vector param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(int* pinteger){_error_("Vector param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(int** pintarray,int* pM){_error_("Vector param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Vector param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double* pdouble){_error_("Vector param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(char** pstring){_error_("Vector param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(char*** pstringarray,int* pM){_error_("Vector param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double** pdoublearray,int* pM){_error_("Vector param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Vector param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Vector param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("Vector param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** poutput); ++ void GetParameterValue(FILE** pfid){_error_("Vector of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} ++ ++ void SetValue(bool boolean){_error_("Vector of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} ++ void SetValue(int integer){_error_("Vector of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double scalar){_error_("Vector of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} ++ void SetValue(char* string){_error_("Vector of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} ++ void SetValue(char** stringarray,int M){_error_("Vector of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double* doublearray,int M){_error_("Vector of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double* pdoublearray,int M,int N){_error_("Vector of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(int* intarray,int M){_error_("Vector of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(int* pintarray,int M,int N){_error_("Vector of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec); ++ void SetValue(Matrix* mat){_error_("Vector of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(FILE* fid){_error_("Vector of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Vector param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} ++ void UnitConversion(int direction_enum); ++ ++ void GetParameterName(char**pname); ++ #ifdef _SERIAL_ ++ void SetMatlabField(mxArray* dataref); ++ #endif ++ ++ /*}}}*/ ++}; ++#endif /* _VECTORPARAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/MatrixParam.h (revision 11695) +@@ -0,0 +1,90 @@ ++/*! \file MatrixParam.h ++ * \brief: header file for MatrixParam object ++ */ ++ ++ ++#ifndef _MATRIXPARAM_H_ ++#define _MATRIXPARAM_H_ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#ifdef _SERIAL_ ++#include ++#endif ++ ++#include "./Param.h" ++#include "../../include/include.h" ++#include "../../shared/shared.h" ++/*}}}*/ ++ ++class MatrixParam: public Param{ ++ ++ private: ++ /*just hold 3 values for 3 vertices: */ ++ int enum_type; ++ Matrix* value; ++ ++ public: ++ /*MatrixParam constructors, destructors: {{{1*/ ++ MatrixParam(); ++ MatrixParam(int enum_type,Matrix* value); ++ ~MatrixParam(); ++ /*}}}*/ ++ /*Object virtual functions definitions:{{{1 */ ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int MyRank(); ++ #ifdef _SERIAL_ ++ void Marshall(char** pmarshalled_dataset); ++ int MarshallSize(); ++ void Demarshall(char** pmarshalled_dataset); ++ #endif ++ int ObjectEnum(); ++ Object* copy(); ++ /*}}}*/ ++ /*Param vritual function definitions: {{{1*/ ++ int InstanceEnum(){return enum_type;} ++ void GetParameterValue(bool* pbool){_error_("Matrix param of enum %i (%s) cannot return a bool",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(int* pinteger){_error_("Matrix param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(int** pintarray,int* pM){_error_("Matrix param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Matrix param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double* pdouble){_error_("Matrix param of enum %i (%s) cannot return a double",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(char** pstring){_error_("Matrix param of enum %i (%s) cannot return a string",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(char*** pstringarray,int* pM){_error_("Matrix param of enum %i (%s) cannot return a string array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double** pdoublearray,int* pM){_error_("Matrix param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("Matrix param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Matrix param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("Matrix param of enum %i (%s) cannot return a vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** poutput); ++ void GetParameterValue(FILE** pfid){_error_("Matrix param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} ++ ++ void SetValue(bool boolean){_error_("Matrix param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} ++ void SetValue(int integer){_error_("Matrix param of enum %i (%s) cannot hold an integer",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double scalar){_error_("Matrix param of enum %i (%s) cannot hold a scalar",enum_type,EnumToStringx(enum_type));} ++ void SetValue(char* string){_error_("Matrix param of enum %i (%s) cannot hold a string",enum_type,EnumToStringx(enum_type));} ++ void SetValue(char** stringarray,int M){_error_("Matrix param of enum %i (%s) cannot hold a string array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double* doublearray,int M){_error_("Matrix param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double* pdoublearray,int M,int N){_error_("Matrix param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(int* intarray,int M){_error_("Matrix param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(int* pintarray,int M,int N){_error_("Matrix param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("Matrix param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat); ++ void SetValue(FILE* fid){_error_("Matrix param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} ++ void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("Matrix param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} ++ void UnitConversion(int direction_enum); ++ ++ void GetParameterName(char**pname); ++ #ifdef _SERIAL_ ++ void SetMatlabField(mxArray* dataref); ++ #endif ++ ++ /*}}}*/ ++}; ++#endif /* _MATRIXPARAM_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringArrayParam.h (revision 11695) +@@ -63,8 +63,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("StringArray param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("StringArray param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("Vec param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("StringArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("StringArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("StringArray param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("StringArray param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("StringArray param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("StringArray param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -76,8 +76,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("StringArray param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("StringArray param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("StringArray param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("StringArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("StringArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("StringArray param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("StringArray param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("StringArray param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("StringArray param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Params/StringParam.h (revision 11695) +@@ -61,8 +61,8 @@ + void GetParameterValue(double** pdoublearray,int* pM){_error_("String param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double** pdoublearray,int* pM, int* pN){_error_("String param of enum %i (%s) cannot return a double array",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(double*** parray, int* pM,int** pmdims, int** pndims){_error_("String param of enum %i (%s) cannot return a matrix array",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Vec* pvec){_error_("String param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} +- void GetParameterValue(Mat* pmat){_error_("String param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Vector** pvec){_error_("String param of enum %i (%s) cannot return a Vec",enum_type,EnumToStringx(enum_type));} ++ void GetParameterValue(Matrix** pmat){_error_("String param of enum %i (%s) cannot return a Mat",enum_type,EnumToStringx(enum_type));} + void GetParameterValue(FILE** pfid){_error_("Bool param of enum %i (%s) cannot return a FILE",enum_type,EnumToStringx(enum_type));} + + void SetValue(bool boolean){_error_("String param of enum %i (%s) cannot hold a boolean",enum_type,EnumToStringx(enum_type));} +@@ -74,8 +74,8 @@ + void SetValue(double* pdoublearray,int M,int N){_error_("String param of enum %i (%s) cannot hold a double array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* intarray,int M){_error_("String param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} + void SetValue(int* pintarray,int M,int N){_error_("String param of enum %i (%s) cannot hold a int array",enum_type,EnumToStringx(enum_type));} +- void SetValue(Vec vec){_error_("String param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} +- void SetValue(Mat mat){_error_("String param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Vector* vec){_error_("String param of enum %i (%s) cannot hold a Vec",enum_type,EnumToStringx(enum_type));} ++ void SetValue(Matrix* mat){_error_("String param of enum %i (%s) cannot hold a Mat",enum_type,EnumToStringx(enum_type));} + void SetValue(FILE* fid){_error_("String param of enum %i (%s) cannot hold a FILE",enum_type,EnumToStringx(enum_type));} + void SetValue(double** array, int M, int* mdim_array, int* ndim_array){_error_("String param of enum %i (%s) cannot hold an array of matrices",enum_type,EnumToStringx(enum_type));} + void UnitConversion(int direction_enum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11695) +@@ -16,6 +16,7 @@ + #include "../../shared/shared.h" + #include "../../Container/Container.h" + #include "../../include/include.h" ++#include "../../toolkits/toolkits.h" + #include "./Vector.h" + /*}}}*/ + +@@ -48,7 +49,35 @@ + #endif + } + /*}}}*/ +-/*FUNCTION Vector::~Vector(){{{1*/ ++/*FUNCTION Vector::Vector(double* serial_vec,int M){{{1*/ ++Vector::Vector(double* serial_vec,int pM){ ++ ++ int i,j; ++ ++ #ifdef _HAVE_PETSC_ ++ int* idxm=NULL; ++ ++ this->vector=NewVec(pM); ++ ++ idxm=(int*)xmalloc(M*sizeof(int)); ++ for(i=0;ivector,M,idxm,serial_vec,INSERT_VALUES); ++ ++ VecAssemblyBegin(this->vector); ++ VecAssemblyEnd(this->vector); ++ ++ xfree((void**)&idxm); ++ ++ #else ++ this->M=pM; ++ this->vector=(double*)xcalloc(pM,sizeof(double)); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->avector=(adouble*)xmalloc(pM*sizeof(adouble)); ++ #endif ++} ++/*}}}*/ ++ /*FUNCTION Vector::~Vector(){{{1*/ + Vector::~Vector(){ + + #ifdef _HAVE_PETSC_ +@@ -62,6 +91,7 @@ + } + /*}}}*/ + ++ + /*Vector specific routines: */ + /*FUNCTION Vector::Echo{{{1*/ + void Vector::Echo(void){ +@@ -115,17 +145,42 @@ + } + /*}}}*/ + /*FUNCTION Vector::SetValues{{{1*/ +-void Vector::SetValues(int ssize, int* list, double* values, int mode){ ++void Vector::SetValues(int ssize, int* list, double* values, InsMode mode){ + + + #ifdef _HAVE_PETSC_ +- VecSetValues(this->vector,ssize,list,values,(InsertMode)mode); ++ VecSetValues(this->vector,ssize,list,values,ISSMToPetscInsertMode(mode)); + #else + _error_("not implemented yet!"); + #endif + + } + /*}}}*/ ++/*FUNCTION Vector::SetValue{{{1*/ ++void Vector::SetValue(int dof, double value, InsMode mode){ ++ ++ ++ #ifdef _HAVE_PETSC_ ++ VecSetValues(this->vector,1,&dof,&value,ISSMToPetscInsertMode(mode)); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Vector::GetValue{{{1*/ ++void Vector::GetValue(double* pvalue,int dof){ ++ ++ ++ #ifdef _HAVE_PETSC_ ++ VecGetValues(this->vector,1,&dof,pvalue); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ ++} ++/*}}}*/ ++ + /*FUNCTION Vector::GetSize{{{1*/ + void Vector::GetSize(int* pM){ + +@@ -225,11 +280,11 @@ + } + /*}}}*/ + /*FUNCTION Vector::Norm{{{1*/ +-double Vector::Norm(int norm_type){ ++double Vector::Norm(NormMode norm_type){ + + double norm=0; + #ifdef _HAVE_PETSC_ +- VecNorm(this->vector,(NormType)norm_type,&norm); ++ VecNorm(this->vector,ISSMToPetscNormMode(norm_type),&norm); + #else + _error_("not implemented yet!"); + #endif +@@ -246,3 +301,25 @@ + #endif + } + /*}}}*/ ++/*FUNCTION Vector::Scale{{{1*/ ++double Vector::Dot(Vector* vector){ ++ ++ double dot; ++ #ifdef _HAVE_PETSC_ ++ VecDot(this->vector,vector->vector,&dot); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ return dot; ++} ++/*}}}*/ ++/*FUNCTION Vector::PointwiseDivide{{{1*/ ++void Vector::PointwiseDivide(Vector* x,Vector* y){ ++ ++ #ifdef _HAVE_PETSC_ ++ VecPointwiseDivide(this->vector,x->vector,y->vector); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11695) +@@ -16,7 +16,9 @@ + #include "../../shared/shared.h" + #include "../../Container/Container.h" + #include "../../include/include.h" ++#include "../../toolkits/toolkits.h" + #include "./Matrix.h" ++ + /*}}}*/ + + /*Matrix constructors and destructor*/ +@@ -68,6 +70,39 @@ + #endif + } + /*}}}*/ ++/*FUNCTION Matrix::Matrix(double* serial_mat, int M,int N,double sparsity){{{1*/ ++Matrix::Matrix(double* serial_mat, int pM,int pN,double sparsity){ ++ ++ this->M=pM; ++ this->N=pN; ++ ++ #ifdef _HAVE_PETSC_ ++ int i; ++ int* idxm=NULL; ++ int* idxn=NULL; ++ ++ this->matrix=NewMat(pM,pN,sparsity); ++ ++ idxm=(int*)xmalloc(M*sizeof(int)); ++ idxn=(int*)xmalloc(N*sizeof(int)); ++ for(i=0;imatrix,M,idxm,N,idxn,serial_mat,INSERT_VALUES); ++ ++ MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); ++ MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); ++ ++ xfree((void**)&idxm); ++ xfree((void**)&idxn); ++ #else ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ #endif ++ #ifdef _HAVE_ADOLC_ ++ this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ #endif ++} ++/*}}}*/ + /*FUNCTION Matrix::Matrix(int M,int N,int connectivity,int numberofdofspernode){{{1*/ + Matrix::Matrix(int pM,int pN,int connectivity,int numberofdofspernode){ + +@@ -159,11 +194,11 @@ + } + /*}}}*/ + /*FUNCTION Matrix::Norm{{{1*/ +-double Matrix::Norm(int norm_type){ ++double Matrix::Norm(NormMode norm_type){ + + double norm=0; + #ifdef _HAVE_PETSC_ +- MatNorm(this->matrix,(NormType)norm_type,&norm); ++ MatNorm(this->matrix,ISSMToPetscNormMode(norm_type),&norm); + #else + _error_("not implemented yet!"); + #endif +@@ -200,3 +235,30 @@ + #endif + } + /*}}}*/ ++/*FUNCTION Matrix::Duplicate{{{1*/ ++Matrix* Matrix::Duplicate(void){ ++ ++ Matrix* output=NULL; ++ ++ output=new Matrix(); ++ ++ #ifdef _HAVE_PETSC ++ MatDuplicate(this->matrix,MAT_COPY_VALUES,&output->matrix); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Matrix::ToSerial{{{1*/ ++double* Matrix::ToSerial(void){ ++ ++ double* output=NULL; ++ ++ #ifdef _HAVE_PETSC ++ MatToSerial(&output,this->matrix); ++ #else ++ _error_("not implemented yet!"); ++ #endif ++ return output; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11695) +@@ -13,7 +13,6 @@ + #else + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif +-#include "../Object.h" + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +@@ -21,7 +20,6 @@ + #include "adolc.h" + #endif + +- + #ifdef _SERIAL_ + #include "mex.h" + #endif +@@ -46,6 +44,7 @@ + /*Vector constructors, destructors {{{1*/ + Vector(); + Vector(int M,bool fromlocalsize=false); ++ Vector(double* serial_vec,int pM); + ~Vector(); + /*}}}*/ + /*Vector specific routines {{{1*/ +@@ -54,7 +53,9 @@ + mxArray* ToMatlabVector(void); + #endif + void Assemble(void); +- void SetValues(int ssize, int* list, double* values, int mode); ++ void SetValues(int ssize, int* list, double* values, InsMode mode); ++ void SetValue(int dof, double value, InsMode mode); ++ void GetValue(double* pvalue, int dof); + void GetSize(int* pM); + void GetLocalSize(int* pM); + Vector* Duplicate(void); +@@ -63,8 +64,10 @@ + void AYPX(Vector* X, double a); + double* ToMPISerial(void); + void Copy(Vector* to); +- double Norm(int norm_type); ++ double Norm(NormMode norm_type); + void Scale(double scale_factor); ++ void PointwiseDivide(Vector* x,Vector* y); ++ double Dot(Vector* vector); + /*}}}*/ + }; + #endif //#ifndef _VECTOR_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11695) +@@ -13,7 +13,6 @@ + #else + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif +-#include "../Object.h" + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + +@@ -47,6 +46,7 @@ + Matrix(); + Matrix(int M,int N); + Matrix(int M,int N,double sparsity); ++ Matrix(double* serial_mat,int M,int N,double sparsity); + Matrix(int M,int N,int connectivity,int numberofdofspernode); + ~Matrix(); + /*}}}*/ +@@ -56,10 +56,12 @@ + mxArray* ToMatlabMatrix(void); + #endif + void Assemble(void); +- double Norm(int norm_type); ++ double Norm(NormMode norm_type); + void GetSize(int* pM,int* pN); + void GetLocalSize(int* pM,int* pN); + void MatMult(Vector* X,Vector* AX); ++ Matrix* Duplicate(void); ++ double* ToSerial(void); + /*}}}*/ + + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.cpp (revision 11695) +@@ -272,7 +272,7 @@ + int Vertex::Sid(void){ return sid; } + /*}}}*/ + /*FUNCTION Vertex::UpdateVertexPosition {{{1*/ +-void Vertex::UpdatePosition(Vec vz,Parameters* parameters,double* thickness,double* bed){ ++void Vertex::UpdatePosition(Vector* vz,Parameters* parameters,double* thickness,double* bed){ + + double oldz,newz; + double dt,velz; +@@ -287,6 +287,6 @@ + this->z = newz; + + /*put vz in vector*/ +- VecSetValue(vz,this->dof,velz,INSERT_VALUES); ++ vz->SetValue(this->dof,velz,INS_VAL); + } + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 11695) +@@ -26,7 +26,7 @@ + } + /*}}}*/ + /*FUNCTION PetscVecExternalResult::PetscVecExternalResult(int enum_type,IssmPetscVec value){{{1*/ +-PetscVecExternalResult::PetscVecExternalResult(int in_id, int in_enum_type,Vec in_value,int in_step, double in_time){ ++PetscVecExternalResult::PetscVecExternalResult(int in_id, int in_enum_type,Vector* in_value,int in_step, double in_time){ + + id=in_id; + enum_type=in_enum_type; +@@ -34,8 +34,8 @@ + value=NULL; + + if(in_value){ +- VecDuplicate(in_value,&value); +- VecCopy(in_value,value); ++ value=in_value->Duplicate(); ++ in_value->Copy(value); + } + else value=NULL; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 11695) +@@ -32,14 +32,14 @@ + private: + int id; + int enum_type; +- Vec value; ++ Vector* value; + int step; + double time; + + public: + /*PetscVecExternalResult constructors, destructors: {{{1*/ + PetscVecExternalResult(); +- PetscVecExternalResult(int id,int enum_type,Vec value, int step, double time); ++ PetscVecExternalResult(int id,int enum_type,Vector* value, int step, double time); + ~PetscVecExternalResult(); + /*}}}*/ + /*Object virtual functions definitions:{{{1 */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/FemModel.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/FemModel.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/FemModel.cpp (revision 11695) +@@ -143,11 +143,13 @@ + this->nodes->SetCurrentConfiguration(elements,loads, nodes,vertices, materials,parameters); + this->loads->SetCurrentConfiguration(elements, loads, nodes,vertices, materials,parameters); + ++ #ifdef _HAVE_PETSC_ + /*take care of petsc options, that depend on this analysis type (present only after model processor)*/ + if(this->parameters->Exist(PetscOptionsStringsEnum)){ + PetscOptionsFromAnalysis(this->parameters,analysis_type); + _printf_(VerboseSolver()," petsc Options set for analysis type: %s\n",EnumToStringx(analysis_type)); + } ++ #endif + + } + /*}}}1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 11695) +@@ -50,8 +50,8 @@ + /*}}}*/ + /*TriaP1ElementResult management: {{{1*/ + int InstanceEnum(); +- void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs); +- void GetElementVectorFromResults(Vec vector,int dof); ++ void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs); ++ void GetElementVectorFromResults(Vector* vector,int dof); + /*}}}*/ + + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 11695) +@@ -194,17 +194,17 @@ + } + /*}}}*/ + /*FUNCTION PentaP1ElementResult::GetVectorFromResults{{{1*/ +-void PentaP1ElementResult::GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){ ++void PentaP1ElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){ + + double data[6]; + + if(numdofs!=6)_error_("Result %s is a PentaP1ElementResult and cannot write vector of %i dofs",numdofs); + for(int i=0;i<6;i++) data[i]=this->values[i]/(double)connectivitylist[i]; +- VecSetValues(vector,numdofs,doflist,(const double*)&data,ADD_VALUES); ++ vector->SetValues(numdofs,doflist,&data[0],ADD_VAL); + + } /*}}}*/ + /*FUNCTION PentaP1ElementResult::GetElementVectorFromResults{{{1*/ +-void PentaP1ElementResult::GetElementVectorFromResults(Vec vector,int dof){ ++void PentaP1ElementResult::GetElementVectorFromResults(Vector* vector,int dof){ + + _error_("Result %s is a PentaP1ElementResult and should not write vector of size numberofelemenrs",EnumToStringx(enum_type)); + } /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp (revision 11695) +@@ -184,12 +184,12 @@ + } + /*}}}*/ + /*FUNCTION BoolElementResult::GetVectorFromResults{{{1*/ +-void BoolElementResult::GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){ ++void BoolElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){ + + _error_("cannot return vector on vertices"); + } /*}}}*/ + /*FUNCTION BoolElementResult::GetElementVectorFromResults{{{1*/ +-void BoolElementResult::GetElementVectorFromResults(Vec vector,int dof){ ++void BoolElementResult::GetElementVectorFromResults(Vector* vector,int dof){ + +- VecSetValue(vector,dof,(double)value,INSERT_VALUES); ++ vector->SetValue(dof,value,INS_VAL); + } /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 11695) +@@ -51,8 +51,8 @@ + /*}}}*/ + /*PentaP1ElementResult management: {{{1*/ + int InstanceEnum(); +- void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs); +- void GetElementVectorFromResults(Vec vector,int dof); ++ void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs); ++ void GetElementVectorFromResults(Vector* vector,int dof); + /*}}}*/ + + }; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h (revision 11695) +@@ -52,8 +52,8 @@ + /*}}}*/ + /*DoubleElementResult management: {{{1*/ + int InstanceEnum(); +- void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){_error_("not implemented");}; +- void GetElementVectorFromResults(Vec vector,int dof){_error_("not implemented");}; ++ void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){_error_("not implemented");}; ++ void GetElementVectorFromResults(Vector* vector,int dof){_error_("not implemented");}; + /*}}}*/ + }; + #endif /* _DOUBLEELEMENTRESULT_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h (revision 11695) +@@ -52,8 +52,8 @@ + /*}}}*/ + /*BoolElementResult management: {{{1*/ + int InstanceEnum(); +- void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs); +- void GetElementVectorFromResults(Vec vector,int dof); ++ void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs); ++ void GetElementVectorFromResults(Vector* vector,int dof); + /*}}}*/ + }; + #endif /* _BOOLELEMENTRESULT_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 11695) +@@ -183,17 +183,16 @@ + } + /*}}}*/ + /*FUNCTION TriaP1ElementResult::GetVectorFromResults{{{1*/ +-void TriaP1ElementResult::GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdofs){ ++void TriaP1ElementResult::GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdofs){ + + double data[3]; + + if(numdofs!=3)_error_("Result %s is a TriaP1ElementResult and cannot write vector of %i dofs",numdofs); + for(int i=0;i<3;i++) data[i]=this->values[i]/(double)connectivitylist[i]; +- VecSetValues(vector,numdofs,doflist,(const double*)&data,ADD_VALUES); ++ vector->SetValues(numdofs,doflist,&data[0],ADD_VAL); + + } /*}}}*/ + /*FUNCTION TriaP1ElementResult::GetElementVectorFromResults{{{1*/ +-void TriaP1ElementResult::GetElementVectorFromResults(Vec vector,int dof){ +- ++void TriaP1ElementResult::GetElementVectorFromResults(Vector* vector,int dof){ + _error_("Result %s is a TriaP1ElementResult and should not write vector of size numberofelemenrs",EnumToStringx(enum_type)); + } /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/ElementResult.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/ElementResult.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/ElementResults/ElementResult.h (revision 11695) +@@ -24,8 +24,8 @@ + virtual int NumberOfNodalValues(void)=0; + virtual void PatchFill(int row, Patch* patch)=0; + virtual int InstanceEnum()=0; +- virtual void GetVectorFromResults(Vec vector,int* doflist,int* connectivitylist,int numdof)=0; +- virtual void GetElementVectorFromResults(Vec vector,int dof)=0; ++ virtual void GetVectorFromResults(Vector* vector,int* doflist,int* connectivitylist,int numdof)=0; ++ virtual void GetElementVectorFromResults(Vector* vector,int dof)=0; + + }; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.h (revision 11695) +@@ -86,7 +86,7 @@ + void DofInSSet(int dof); + void DofInFSet(int dof); + int GetDof(int dofindex,int setenum); +- void CreateVecSets(Vec pv_g,Vec pv_f,Vec pv_s); ++ void CreateVecSets(Vector* pv_g,Vector* pv_f,Vector* pv_s); + int GetConnectivity(); + void GetDofList(int* poutdoflist,int approximation_enum,int setenum); + void GetLocalDofList(int* poutdoflist,int approximation_enum,int setenum); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Element.h (revision 11695) +@@ -45,8 +45,8 @@ + + virtual double SurfaceArea(void)=0; + virtual void InputDepthAverageAtBase(int enum_type,int average_enum_type,int object_enum)=0; +- virtual void ComputeBasalStress(Vec sigma_b)=0; +- virtual void ComputeStrainRate(Vec eps)=0; ++ virtual void ComputeBasalStress(Vector* sigma_b)=0; ++ virtual void ComputeStrainRate(Vector* eps)=0; + virtual void PatchSize(int* pnumrows, int* pnumvertices,int* pnumnodes)=0; + virtual void PatchFill(int* pcount, Patch* patch)=0; + virtual void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results)=0; +@@ -61,19 +61,19 @@ + + virtual int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units)=0; + virtual void InputScale(int enum_type,double scale_factor)=0; +- virtual void GetVectorFromInputs(Vec vector, int name_enum)=0; +- virtual void GetVectorFromResults(Vec vector,int id,int interp)=0; ++ virtual void GetVectorFromInputs(Vector* vector, int name_enum)=0; ++ virtual void GetVectorFromResults(Vector* vector,int id,int interp)=0; + virtual void InputArtificialNoise(int enum_type,double min,double max)=0; + virtual bool InputConvergence(double* eps, int* enums,int num_enums,int* criterionenums,double* criterionvalues,int num_criterionenums)=0; +- virtual void AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part)=0; ++ virtual void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part)=0; + virtual int* GetHorizontalNeighboorSids(void)=0; + virtual double TimeAdapt()=0; + virtual void MigrateGroundingLine(double* old_floating_ice,double* sheet_ungrounding)=0; +- virtual void PotentialSheetUngrounding(Vec potential_sheet_ungrounding)=0; ++ virtual void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding)=0; + virtual void PositiveDegreeDay(void)=0; +- virtual int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf)=0; ++ virtual int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf)=0; + virtual void ResetCoordinateSystem()=0; +- virtual void SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius)=0; ++ virtual void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius)=0; + + #ifdef _HAVE_RESPONSES_ + virtual void MinVel(double* pminvel, bool process_units)=0; +@@ -93,7 +93,7 @@ + #endif + + #ifdef _HAVE_CONTROL_ +- virtual void Gradj(Vec gradient,int control_type,int control_index)=0; ++ virtual void Gradj(Vector* gradient,int control_type,int control_index)=0; + virtual double ThicknessAbsMisfit(bool process_units ,int weight_index)=0; + virtual double SurfaceAbsVelMisfit(bool process_units ,int weight_index)=0; + virtual double SurfaceRelVelMisfit(bool process_units ,int weight_index)=0; +@@ -103,10 +103,10 @@ + virtual double ThicknessAbsGradient(bool process_units,int weight_index)=0; + virtual double RheologyBbarAbsGradient(bool process_units,int weight_index)=0; + virtual double DragCoefficientAbsGradient(bool process_units,int weight_index)=0; +- virtual void ControlInputGetGradient(Vec gradient,int enum_type,int control_index)=0; ++ virtual void ControlInputGetGradient(Vector* gradient,int enum_type,int control_index)=0; + virtual void ControlInputSetGradient(double* gradient,int enum_type,int control_index)=0; + virtual void ControlInputScaleGradient(int enum_type, double scale)=0; +- virtual void GetVectorFromControlInputs(Vec gradient,int control_enum,int control_index,const char* data)=0; ++ virtual void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data)=0; + virtual void SetControlInputsFromVector(double* vector,int control_enum,int control_index)=0; + virtual void InputControlUpdate(double scalar,bool save_parameter)=0; + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11695) +@@ -278,7 +278,7 @@ + + /*Other*/ + /*FUNCTION Tria::AverageOntoPartition {{{1*/ +-void Tria::AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part){ ++void Tria::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part){ + + bool already=false; + int i,j; +@@ -311,8 +311,8 @@ + } + } + if(!already){ +- VecSetValue(partition_contributions,partition[i],mean*area,ADD_VALUES); +- VecSetValue(partition_areas,partition[i],area,ADD_VALUES); ++ partition_contributions->SetValue(partition[i],mean*area,ADD_VAL); ++ partition_areas->SetValue(partition[i],area,ADD_VAL); + }; + } + } +@@ -924,12 +924,12 @@ + } + /*}}}*/ + /*FUNCTION Tria::ComputeBasalStress {{{1*/ +-void Tria::ComputeBasalStress(Vec eps){ ++void Tria::ComputeBasalStress(Vector* eps){ + _error_("Not Implemented yet"); + } + /*}}}*/ + /*FUNCTION Tria::ComputeStrainRate {{{1*/ +-void Tria::ComputeStrainRate(Vec eps){ ++void Tria::ComputeStrainRate(Vector* eps){ + _error_("Not Implemented yet"); + } + /*}}}*/ +@@ -1323,7 +1323,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetVectorFromInputs{{{1*/ +-void Tria::GetVectorFromInputs(Vec vector,int input_enum){ ++void Tria::GetVectorFromInputs(Vector* vector,int input_enum){ + + int doflist1[NUMVERTICES]; + +@@ -1342,7 +1342,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetVectorFromResults{{{1*/ +-void Tria::GetVectorFromResults(Vec vector,int offset,int interp){ ++void Tria::GetVectorFromResults(Vector* vector,int offset,int interp){ + + /*Get result*/ + ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(offset); +@@ -2205,7 +2205,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::PotentialSheetUngrounding{{{1*/ +-void Tria::PotentialSheetUngrounding(Vec potential_sheet_ungrounding){ ++void Tria::PotentialSheetUngrounding(Vector* potential_sheet_ungrounding){ + + int i; + double h[NUMVERTICES],ba[NUMVERTICES]; +@@ -2227,7 +2227,7 @@ + bed_hydro=-density*h[i]; + if (bed_hydro>ba[i]){ + /*Vertex that could potentially unground, flag it*/ +- VecSetValue(potential_sheet_ungrounding,nodes[i]->Sid(),1,INSERT_VALUES); ++ potential_sheet_ungrounding->SetValue(nodes[i]->Sid(),1,INS_VAL); + } + } + } +@@ -2285,7 +2285,7 @@ + } + /*}}}1*/ + /*FUNCTION Tria::SmearFunction {{{1*/ +-void Tria::SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ ++void Tria::SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ + _error_("not implemented yet"); + + } +@@ -2506,7 +2506,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::UpdatePotentialSheetUngrounding{{{1*/ +-int Tria::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ ++int Tria::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ + + int i; + int nflipped=0; +@@ -2514,7 +2514,7 @@ + /*Go through nodes, and whoever is on the potential_sheet_ungrounding, ends up in nodes_on_iceshelf: */ + for(i=0;i<3;i++){ + if (vertices_potentially_ungrounding[nodes[i]->Sid()]){ +- VecSetValue(vec_nodes_on_iceshelf,nodes[i]->Sid(),1,INSERT_VALUES); ++ vec_nodes_on_iceshelf->SetValue(nodes[i]->Sid(),1,INS_VAL); + + /*If node was not on ice shelf, we flipped*/ + if(nodes_on_iceshelf[nodes[i]->Sid()]==0){ +@@ -3169,7 +3169,7 @@ + values[i*NDOF2+1]=vy; + } + +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -3208,7 +3208,7 @@ + values[i*NDOF2+1]=vy; + } + +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -3376,7 +3376,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::ControlInputGetGradient{{{1*/ +-void Tria::ControlInputGetGradient(Vec gradient,int enum_type,int control_index){ ++void Tria::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){ + + int doflist1[NUMVERTICES]; + Input* input=NULL; +@@ -3435,7 +3435,7 @@ + + }/*}}}*/ + /*FUNCTION Tria::Gradj {{{1*/ +-void Tria::Gradj(Vec gradient,int control_type,int control_index){ ++void Tria::Gradj(Vector* gradient,int control_type,int control_index){ + /*dJ/dalpha = ∂L/∂alpha = ∂J/∂alpha + ∂/∂alpha(KU-F)*/ + + /*If on water, grad = 0: */ +@@ -3494,7 +3494,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GradjBGradient{{{1*/ +-void Tria::GradjBGradient(Vec gradient,int weight_index,int control_index){ ++void Tria::GradjBGradient(Vector* gradient,int weight_index,int control_index){ + + int i,ig; + int doflist1[NUMVERTICES]; +@@ -3527,14 +3527,14 @@ + /*Build gradje_g_gaussian vector (actually -dJ/ddrag): */ + for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]); + } +- VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; + } + /*}}}*/ + /*FUNCTION Tria::GradjBMacAyeal{{{1*/ +-void Tria::GradjBMacAyeal(Vec gradient,int control_index){ ++void Tria::GradjBMacAyeal(Vector* gradient,int control_index){ + + /*Intermediaries*/ + int i,ig; +@@ -3584,14 +3584,14 @@ + )*Jdet*gauss->weight*basis[i]; + } + +- VecSetValues(gradient,NUMVERTICES,doflist,(const double*)grad,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist,grad,ADD_VAL); + + /*clean-up*/ + delete gauss; + } + /*}}}*/ + /*FUNCTION Tria::GradjDragMacAyeal {{{1*/ +-void Tria::GradjDragMacAyeal(Vec gradient,int control_index){ ++void Tria::GradjDragMacAyeal(Vector* gradient,int control_index){ + + int i,ig; + int analysis_type; +@@ -3671,7 +3671,7 @@ + //} + /*End Analytical gradient*/ + +- VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3679,7 +3679,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GradjDragGradient{{{1*/ +-void Tria::GradjDragGradient(Vec gradient, int weight_index,int control_index){ ++void Tria::GradjDragGradient(Vector* gradient, int weight_index,int control_index){ + + int i,ig; + int doflist1[NUMVERTICES]; +@@ -3716,14 +3716,14 @@ + _assert_(!isnan(grade_g[i])); + } + } +- VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; + } + /*}}}*/ + /*FUNCTION Tria::GradjDhDtBalancedthickness{{{1*/ +-void Tria::GradjDhDtBalancedthickness(Vec gradient,int control_index){ ++void Tria::GradjDhDtBalancedthickness(Vector* gradient,int control_index){ + + /*Intermediaries*/ + int doflist1[NUMVERTICES]; +@@ -3735,11 +3735,11 @@ + GetInputListOnVertices(&lambda[0],AdjointEnum); + for(int i=0;iSetValues(NUMVERTICES,doflist1,gradient_g,INS_VAL); + } + /*}}}*/ + /*FUNCTION Tria::GradjVxBalancedthickness{{{1*/ +-void Tria::GradjVxBalancedthickness(Vec gradient,int control_index){ ++void Tria::GradjVxBalancedthickness(Vector* gradient,int control_index){ + + /*Intermediaries*/ + int i,ig; +@@ -3775,14 +3775,14 @@ + for(i=0;iweight*basis[i]; + } + +- VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; + } + /*}}}*/ + /*FUNCTION Tria::GradjVyBalancedthickness{{{1*/ +-void Tria::GradjVyBalancedthickness(Vec gradient,int control_index){ ++void Tria::GradjVyBalancedthickness(Vector* gradient,int control_index){ + + /*Intermediaries*/ + int i,ig; +@@ -3817,7 +3817,7 @@ + + for(i=0;iweight*basis[i]; + } +- VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -4911,7 +4911,7 @@ + } + /*}}}*/ + /*FUNCTION Tria::GetVectorFromControlInputs{{{1*/ +-void Tria::GetVectorFromControlInputs(Vec vector,int control_enum,int control_index,const char* data){ ++void Tria::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){ + + int doflist1[NUMVERTICES]; + Input *input=NULL; +@@ -5213,7 +5213,7 @@ + values[i]=watercolumn; + } + +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.h (revision 11695) +@@ -75,9 +75,9 @@ + void InputUpdateFromIoModel(int index, IoModel* iomodel); + /*}}}*/ + /*Element virtual functions definitions: {{{1*/ +- void AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part); +- void ComputeBasalStress(Vec sigma_b); +- void ComputeStrainRate(Vec eps); ++ void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part); ++ void ComputeBasalStress(Vector* sigma_b); ++ void ComputeStrainRate(Vector* eps); + void ComputeStressTensor(); + void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); +@@ -92,8 +92,8 @@ + bool IsNodeOnShelfFromFlags(double* flags); + bool IsOnWater(); + void GetSolutionFromInputs(Vector* solution); +- void GetVectorFromInputs(Vec vector, int name_enum); +- void GetVectorFromResults(Vec vector,int offset,int interp); ++ void GetVectorFromInputs(Vector* vector, int name_enum); ++ void GetVectorFromResults(Vector* vector,int offset,int interp); + void InputArtificialNoise(int enum_type,double min, double max); + bool InputConvergence(double* eps, int* enums,int num_enums,int* criterionenums,double* criterionvalues,int num_criterionenums); + void InputCreate(double scalar,int name,int code); +@@ -106,7 +106,7 @@ + void MaterialUpdateFromTemperature(void){_error_("not implemented yet");}; + void MigrateGroundingLine(double* oldfloating,double* sheet_ungrounding); + int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); +- void PotentialSheetUngrounding(Vec potential_sheet_ungrounding); ++ void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding); + void PositiveDegreeDay(void); + void RequestedOutput(int output_enum,int step,double time); + void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results); +@@ -116,10 +116,10 @@ + void ResetCoordinateSystem(void){_error_("not implemented yet");}; + double SurfaceArea(void); + void Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type); +- int UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf); ++ int UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf); + double TimeAdapt(); + int* GetHorizontalNeighboorSids(void); +- void SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius); ++ void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius); + + #ifdef _HAVE_RESPONSES_ + double IceVolume(void); +@@ -142,18 +142,18 @@ + #ifdef _HAVE_CONTROL_ + double DragCoefficientAbsGradient(bool process_units,int weight_index); + void GradientIndexing(int* indexing,int control_index); +- void Gradj(Vec gradient,int control_type,int control_index); +- void GradjBGradient(Vec gradient,int weight_index,int control_index); +- void GradjBMacAyeal(Vec gradient,int control_index); +- void GradjDragMacAyeal(Vec gradient,int control_index); +- void GradjDragStokes(Vec gradient,int control_index); +- void GradjDragGradient(Vec gradient,int weight_index,int control_index); +- void GradjDhDtBalancedthickness(Vec gradient,int control_index); +- void GradjVxBalancedthickness(Vec gradient,int control_index); +- void GradjVyBalancedthickness(Vec gradient,int control_index); +- void GetVectorFromControlInputs(Vec gradient,int control_enum,int control_index,const char* data); ++ void Gradj(Vector* gradient,int control_type,int control_index); ++ void GradjBGradient(Vector* gradient,int weight_index,int control_index); ++ void GradjBMacAyeal(Vector* gradient,int control_index); ++ void GradjDragMacAyeal(Vector* gradient,int control_index); ++ void GradjDragStokes(Vector* gradient,int control_index); ++ void GradjDragGradient(Vector* gradient,int weight_index,int control_index); ++ void GradjDhDtBalancedthickness(Vector* gradient,int control_index); ++ void GradjVxBalancedthickness(Vector* gradient,int control_index); ++ void GradjVyBalancedthickness(Vector* gradient,int control_index); ++ void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data); + void SetControlInputsFromVector(double* vector,int control_enum,int control_index); +- void ControlInputGetGradient(Vec gradient,int enum_type,int control_index); ++ void ControlInputGetGradient(Vector* gradient,int enum_type,int control_index); + void ControlInputScaleGradient(int enum_type,double scale); + void ControlInputSetGradient(double* gradient,int enum_type,int control_index); + double RheologyBbarAbsGradient(bool process_units,int weight_index); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.cpp (revision 11695) +@@ -301,7 +301,7 @@ + + /*Other*/ + /*FUNCTION Penta::AverageOntoPartition {{{1*/ +-void Penta::AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part){ ++void Penta::AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part){ + _error_("Not supported yet!"); + } + /*}}}*/ +@@ -382,7 +382,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::ComputeBasalStress {{{1*/ +-void Penta::ComputeBasalStress(Vec sigma_b){ ++void Penta::ComputeBasalStress(Vector* sigma_b){ + + int i,j,ig; + int dofv[3]={0,1,2}; +@@ -416,7 +416,7 @@ + + if(!IsOnBed()){ + //put zero +- VecSetValue(sigma_b,id-1,0.0,INSERT_VALUES); ++ sigma_b->SetValue(id-1,0.0,INS_VAL); + return; + } + +@@ -468,11 +468,11 @@ + value=value/surface; + + /*Add value to output*/ +- VecSetValue(sigma_b,id-1,value,INSERT_VALUES); ++ sigma_b->SetValue(id-1,value,INS_VAL); + } + /*}}}*/ + /*FUNCTION Penta::ComputeStrainRate {{{1*/ +-void Penta::ComputeStrainRate(Vec eps){ ++void Penta::ComputeStrainRate(Vector* eps){ + + _error_("Not implemented yet"); + +@@ -1217,7 +1217,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetVectorFromInputs{{{1*/ +-void Penta::GetVectorFromInputs(Vec vector,int input_enum){ ++void Penta::GetVectorFromInputs(Vector* vector,int input_enum){ + + int doflist1[NUMVERTICES]; + +@@ -1236,7 +1236,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetVectorFromResults{{{1*/ +-void Penta::GetVectorFromResults(Vec vector,int offset,int interp){ ++void Penta::GetVectorFromResults(Vector* vector,int offset,int interp){ + + /*Get result*/ + ElementResult* elementresult=(ElementResult*)this->results->GetObjectByOffset(offset); +@@ -2415,7 +2415,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::PotentialSheetUngrounding{{{1*/ +-void Penta::PotentialSheetUngrounding(Vec potential_sheet_ungrounding){ ++void Penta::PotentialSheetUngrounding(Vector* potential_sheet_ungrounding){ + + int i; + double h[NUMVERTICES],ba[NUMVERTICES]; +@@ -2437,7 +2437,7 @@ + bed_hydro=-density*h[i]; + if (bed_hydro>ba[i]){ + /*Vertex that could potentially unground, flag it*/ +- VecSetValue(potential_sheet_ungrounding,nodes[i]->Sid(),1,INSERT_VALUES); ++ potential_sheet_ungrounding->SetValue(nodes[i]->Sid(),1,INS_VAL); + } + } + } +@@ -2935,7 +2935,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::UpdatePotentialSheetUngrounding{{{1*/ +-int Penta::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ ++int Penta::UpdatePotentialSheetUngrounding(double* vertices_potentially_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf){ + + int i; + int nflipped=0; +@@ -2943,7 +2943,7 @@ + /*Go through nodes, and whoever is on the potential_sheet_ungrounding, ends up in nodes_on_iceshelf: */ + for(i=0;iSid()]){ +- VecSetValue(vec_nodes_on_iceshelf,nodes[i]->Sid(),1,INSERT_VALUES); ++ vec_nodes_on_iceshelf->SetValue(nodes[i]->Sid(),1,INS_VAL); + + /*If node was not on ice shelf, we flipped*/ + if(nodes_on_iceshelf[nodes[i]->Sid()]==0){ +@@ -3003,7 +3003,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::SmearFunction {{{1*/ +-void Penta::SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ ++void Penta::SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius){ + _error_("not implemented yet"); + } + /*}}}1*/ +@@ -4202,7 +4202,7 @@ + } + + /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -4233,7 +4233,7 @@ + } + + /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -4393,7 +4393,7 @@ + + #ifdef _HAVE_CONTROL_ + /*FUNCTION Penta::ControlInputGetGradient{{{1*/ +-void Penta::ControlInputGetGradient(Vec gradient,int enum_type,int control_index){ ++void Penta::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){ + + int doflist1[NUMVERTICES]; + Input* input=NULL; +@@ -4718,7 +4718,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::Gradj {{{1*/ +-void Penta::Gradj(Vec gradient,int control_type,int control_index){ ++void Penta::Gradj(Vector* gradient,int control_type,int control_index){ + /*dJ/dalpha = ∂L/∂alpha = ∂J/∂alpha + ∂/∂alpha(KU-F)*/ + + int i,approximation; +@@ -4809,7 +4809,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GradjDragMacAyeal {{{1*/ +-void Penta::GradjDragMacAyeal(Vec gradient,int control_index){ ++void Penta::GradjDragMacAyeal(Vector* gradient,int control_index){ + + /*Gradient is 0 if on shelf or not on bed*/ + if(IsFloating() || !IsOnBed()) return; +@@ -4821,7 +4821,7 @@ + + } /*}}}*/ + /*FUNCTION Penta::GradjDragPattyn {{{1*/ +-void Penta::GradjDragPattyn(Vec gradient,int control_index){ ++void Penta::GradjDragPattyn(Vector* gradient,int control_index){ + + int i,j,ig; + int analysis_type; +@@ -4884,7 +4884,7 @@ + grade_g[i]+=grade_g_gaussian[i]; + } + } +- VecSetValues(gradient,NUMVERTICES,doflist1,(const double*)grade_g,ADD_VALUES); ++ gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -4892,7 +4892,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GradjDragStokes {{{1*/ +-void Penta::GradjDragStokes(Vec gradient,int control_index){ ++void Penta::GradjDragStokes(Vector* gradient,int control_index){ + + int i,j,ig; + int analysis_type; +@@ -4977,14 +4977,14 @@ + for( i=0; iSetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); + + delete friction; + delete gauss; + } + /*}}}*/ + /*FUNCTION Penta::GradjBbarMacAyeal {{{1*/ +-void Penta::GradjBbarMacAyeal(Vec gradient,int control_index){ ++void Penta::GradjBbarMacAyeal(Vector* gradient,int control_index){ + + /*This element should be collapsed into a tria element at its base*/ + if (!IsOnBed()) return; +@@ -5002,7 +5002,7 @@ + + } /*}}}*/ + /*FUNCTION Penta::GradjBbarPattyn {{{1*/ +-void Penta::GradjBbarPattyn(Vec gradient,int control_index){ ++void Penta::GradjBbarPattyn(Vector* gradient,int control_index){ + + /*Gradient is computed on bed only (Bbar)*/ + if (!IsOnBed()) return; +@@ -5019,7 +5019,7 @@ + this->matice->inputs->DeleteInput(MaterialsRheologyBbarEnum); + } /*}}}*/ + /*FUNCTION Penta::GradjBbarStokes {{{1*/ +-void Penta::GradjBbarStokes(Vec gradient,int control_index){ ++void Penta::GradjBbarStokes(Vector* gradient,int control_index){ + + /*Gradient is computed on bed only (Bbar)*/ + if (!IsOnBed()) return; +@@ -5395,7 +5395,7 @@ + } + /*}}}*/ + /*FUNCTION Penta::GetVectorFromControlInputs{{{1*/ +-void Penta::GetVectorFromControlInputs(Vec vector,int control_enum,int control_index,const char* data){ ++void Penta::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){ + + int doflist1[NUMVERTICES]; + +@@ -7873,7 +7873,7 @@ + } + + /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -7909,7 +7909,7 @@ + } + + /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -7942,7 +7942,7 @@ + } + + /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +@@ -7987,7 +7987,7 @@ + } + + /*Add value to global vector*/ +- solution->SetValues(numdof,doflist,values,INSERT_VALUES); ++ solution->SetValues(numdof,doflist,values,INS_VAL); + + /*Free ressources:*/ + delete gauss; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Penta.h (revision 11695) +@@ -78,10 +78,10 @@ + void InputUpdateFromIoModel(int index, IoModel* iomodel); + /*}}}*/ + /*Element virtual functions definitions: {{{1*/ +- void AverageOntoPartition(Vec partition_contributions,Vec partition_areas,double* vertex_response,double* qmu_part); ++ void AverageOntoPartition(Vector* partition_contributions,Vector* partition_areas,double* vertex_response,double* qmu_part); + void BasalFrictionCreateInput(void); +- void ComputeBasalStress(Vec sigma_b); +- void ComputeStrainRate(Vec eps); ++ void ComputeBasalStress(Vector* sigma_b); ++ void ComputeStrainRate(Vector* eps); + void ComputeStressTensor(); + void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); +@@ -92,8 +92,8 @@ + int GetNodeIndex(Node* node); + void GetSolutionFromInputs(Vector* solution); + double GetZcoord(GaussPenta* gauss); +- void GetVectorFromInputs(Vec vector,int name_enum); +- void GetVectorFromResults(Vec vector,int offset,int interp); ++ void GetVectorFromInputs(Vector* vector,int name_enum); ++ void GetVectorFromResults(Vector* vector,int offset,int interp); + + int Sid(); + void InputArtificialNoise(int enum_type,double min, double max); +@@ -106,7 +106,7 @@ + + void InputToResult(int enum_type,int step,double time); + void MigrateGroundingLine(double* old_floating_ice,double* sheet_ungrounding); +- void PotentialSheetUngrounding(Vec potential_sheet_ungrounding); ++ void PotentialSheetUngrounding(Vector* potential_sheet_ungrounding); + void RequestedOutput(int output_enum,int step,double time); + void ListResultsInfo(int** results_enums,int** results_size,double** results_times,int** results_steps,int* num_results); + void PatchFill(int* pcount, Patch* patch); +@@ -116,12 +116,12 @@ + void ResetCoordinateSystem(void); + double SurfaceArea(void); + void Update(int index, IoModel* iomodel,int analysis_counter,int analysis_type); +- int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vec vec_nodes_on_iceshelf,double* nodes_on_iceshelf); ++ int UpdatePotentialSheetUngrounding(double* potential_sheet_ungrounding,Vector* vec_nodes_on_iceshelf,double* nodes_on_iceshelf); + int NodalValue(double* pvalue, int index, int natureofdataenum,bool process_units); + double TimeAdapt(); + int* GetHorizontalNeighboorSids(void); + void ViscousHeatingCreateInput(void); +- void SmearFunction(Vec smearedvector,double (*WeightFunction)(double distance,double radius),double radius); ++ void SmearFunction(Vector* smearedvector,double (*WeightFunction)(double distance,double radius),double radius); + + #ifdef _HAVE_RESPONSES_ + double IceVolume(void); +@@ -143,16 +143,16 @@ + #ifdef _HAVE_CONTROL_ + double DragCoefficientAbsGradient(bool process_units,int weight_index); + void GradientIndexing(int* indexing,int control_index); +- void Gradj(Vec gradient,int control_type,int control_index); +- void GradjDragMacAyeal(Vec gradient,int control_index); +- void GradjDragPattyn(Vec gradient,int control_index); +- void GradjDragStokes(Vec gradient,int control_index); +- void GradjBbarMacAyeal(Vec gradient,int control_index); +- void GradjBbarPattyn(Vec gradient,int control_index); +- void GradjBbarStokes(Vec gradient,int control_index); +- void GetVectorFromControlInputs(Vec gradient,int control_enum,int control_index,const char* data); ++ void Gradj(Vector* gradient,int control_type,int control_index); ++ void GradjDragMacAyeal(Vector* gradient,int control_index); ++ void GradjDragPattyn(Vector* gradient,int control_index); ++ void GradjDragStokes(Vector* gradient,int control_index); ++ void GradjBbarMacAyeal(Vector* gradient,int control_index); ++ void GradjBbarPattyn(Vector* gradient,int control_index); ++ void GradjBbarStokes(Vector* gradient,int control_index); ++ void GetVectorFromControlInputs(Vector* gradient,int control_enum,int control_index,const char* data); + void SetControlInputsFromVector(double* vector,int control_enum,int control_index); +- void ControlInputGetGradient(Vec gradient,int enum_type,int control_index); ++ void ControlInputGetGradient(Vector* gradient,int enum_type,int control_index); + void ControlInputScaleGradient(int enum_type,double scale); + void ControlInputSetGradient(double* gradient,int enum_type,int control_index); + double RheologyBbarAbsGradient(bool process_units,int weight_index); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 11695) +@@ -134,8 +134,8 @@ + #include "./Params/IntMatParam.h" + #include "./Params/FileParam.h" + #include "./Params/Param.h" +-#include "./Params/PetscMatParam.h" +-#include "./Params/PetscVecParam.h" ++#include "./Params/MatrixParam.h" ++#include "./Params/VectorParam.h" + #include "./Params/StringArrayParam.h" + #include "./Params/StringParam.h" + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.h (revision 11695) +@@ -79,7 +79,7 @@ + double MinAbs(void); + void Extrude(void){_error_("not supported yet");}; + void VerticallyIntegrate(Input* thickness_input); +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values); + /*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp (revision 11695) +@@ -354,7 +354,7 @@ + //gradient->Extrude(); + }/*}}}*/ + /*FUNCTION ControlInput::GetGradient{{{1*/ +-void ControlInput::GetGradient(Vec gradient_vec,int* doflist){ ++void ControlInput::GetGradient(Vector* gradient_vec,int* doflist){ + if(gradient) gradient->GetVectorFromInputs(gradient_vec,doflist); + }/*}}}*/ + /*FUNCTION ControlInput::ScaleGradient{{{1*/ +@@ -405,12 +405,12 @@ + _assert_(gradient); + return gradient->SpawnResult(step,time); + }/*}}}*/ +-/*FUNCTION ControlInput::GetVectorFromInputs(Vec vector,int* doflist){{{1*/ +-void ControlInput::GetVectorFromInputs(Vec vector,int* doflist){ ++/*FUNCTION ControlInput::GetVectorFromInputs(Vector* vector,int* doflist){{{1*/ ++void ControlInput::GetVectorFromInputs(Vector* vector,int* doflist){ + values->GetVectorFromInputs(vector,doflist); + }/*}}}*/ +-/*FUNCTION ControlInput::GetVectorFromInputs(Vec vector,int* doflist,const char* data){{{1*/ +-void ControlInput::GetVectorFromInputs(Vec vector,int* doflist,const char* data){ ++/*FUNCTION ControlInput::GetVectorFromInputs(Vector* vector,int* doflist,const char* data){{{1*/ ++void ControlInput::GetVectorFromInputs(Vector* vector,int* doflist,const char* data){ + if(strcmp(data,"value")==0){ + _assert_(values); + values->GetVectorFromInputs(vector,doflist); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/Input.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/Input.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/Input.h (revision 11695) +@@ -55,7 +55,7 @@ + virtual void Constrain(double cm_min, double cm_max)=0; + virtual void VerticallyIntegrate(Input* thickness_input)=0; + virtual void Extrude()=0; +- virtual void GetVectorFromInputs(Vec vector,int* doflist)=0; ++ virtual void GetVectorFromInputs(Vector* vector,int* doflist)=0; + virtual void GetValuesPtr(double** pvalues,int* pnum_values)=0; + + virtual Input* SpawnTriaInput(int* indices)=0; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/ControlInput.h (revision 11695) +@@ -86,11 +86,11 @@ + double MinAbs(void){_error_("not implemented yet");}; + void Extrude(void); + void VerticallyIntegrate(Input* thickness_input); +- void GetVectorFromInputs(Vec vector,int* doflist,const char* data); +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist,const char* data); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values){_error_("not implemented yet");}; + ElementResult* SpawnGradient(int step, double time); +- void GetGradient(Vec gradient_vec,int* doflist); ++ void GetGradient(Vector* gradient_vec,int* doflist); + void ScaleGradient(double scale); + void SetGradient(Input* gradient_in); + void UpdateValue(double scalar); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DatasetInput.h (revision 11695) +@@ -81,10 +81,10 @@ + double MinAbs(void){_error_("not implemented yet");}; + void Extrude(void){_error_("not implemented yet");}; + void VerticallyIntegrate(Input* thickness_input){_error_("not implemented yet");}; +- void GetVectorFromInputs(Vec vector,int* doflist){_error_("not implemented yet");}; ++ void GetVectorFromInputs(Vector* vector,int* doflist){_error_("not implemented yet");}; + void GetValuesPtr(double** pvalues,int* pnum_values){_error_("not implemented yet");}; + ElementResult* SpawnGradient(int step, double time){_error_("not implemented yet");}; +- void GetGradient(Vec gradient_vec,int* doflist){_error_("not implemented yet");}; ++ void GetGradient(Vector* gradient_vec,int* doflist){_error_("not implemented yet");}; + void ScaleGradient(double scale){_error_("not implemented yet");}; + void SetGradient(Input* gradient_in){_error_("not implemented yet");}; + void UpdateValue(double scalar){_error_("not implemented yet");}; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.cpp (revision 11695) +@@ -230,7 +230,7 @@ + } + /*}}}*/ + /*FUNCTION IntInput::GetVectorFromInputs{{{1*/ +-void IntInput::GetVectorFromInputs(Vec vector,int* doflist){ ++void IntInput::GetVectorFromInputs(Vector* vector,int* doflist){ + + _error_(" not supporte yet!"); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp (revision 11695) +@@ -232,7 +232,7 @@ + } + /*}}}*/ + /*FUNCTION BoolInput::GetVectorFromInputs{{{1*/ +-void BoolInput::GetVectorFromInputs(Vec vector,int* doflist){ ++void BoolInput::GetVectorFromInputs(Vector* vector,int* doflist){ + + _error_(" not supporte yet!"); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/IntInput.h (revision 11695) +@@ -80,7 +80,7 @@ + double MinAbs(void){_error_("Min not implemented for integers");}; + void Extrude(void){_error_("not supported yet");}; + void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values); + /*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/BoolInput.h (revision 11695) +@@ -80,7 +80,7 @@ + void Constrain(double cm_min, double cm_max); + void Extrude(void); + void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values); + /*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp (revision 11695) +@@ -390,10 +390,10 @@ + } + /*}}}*/ + /*FUNCTION TriaP1Input::GetVectorFromInputs{{{1*/ +-void TriaP1Input::GetVectorFromInputs(Vec vector,int* doflist){ ++void TriaP1Input::GetVectorFromInputs(Vector* vector,int* doflist){ + + const int numvertices=3; +- VecSetValues(vector,numvertices,doflist,(const double*)this->values,INSERT_VALUES); ++ vector->SetValues(numvertices,doflist,this->values,INS_VAL); + + } /*}}}*/ + /*FUNCTION TriaP1Input::GetValuesPtr{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h (revision 11695) +@@ -81,7 +81,7 @@ + double MinAbs(void); + void Extrude(void){_error_("not supported yet");}; + void VerticallyIntegrate(Input* thickness_input){_error_("not supported yet");}; +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values); + /*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp (revision 11695) +@@ -439,7 +439,7 @@ + } + /*}}}*/ + /*FUNCTION TransientInput::GetVectorFromInputs{{{1*/ +-void TransientInput::GetVectorFromInputs(Vec vector,int* doflist){ ++void TransientInput::GetVectorFromInputs(Vector* vector,int* doflist){ + + double time; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp (revision 11695) +@@ -659,10 +659,10 @@ + } + /*}}}*/ + /*FUNCTION PentaP1Input::GetVectorFromInputs{{{1*/ +-void PentaP1Input::GetVectorFromInputs(Vec vector,int* doflist){ ++void PentaP1Input::GetVectorFromInputs(Vector* vector,int* doflist){ + + const int numvertices=6; +- VecSetValues(vector,numvertices,doflist,(const double*)this->values,INSERT_VALUES); ++ vector->SetValues(numvertices,doflist,this->values,INS_VAL); + + } /*}}}*/ + /*FUNCTION PentaP1Input::GetValuesPtr{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp (revision 11695) +@@ -309,7 +309,7 @@ + } + /*}}}*/ + /*FUNCTION DoubleInput::GetVectorFromInputs{{{1*/ +-void DoubleInput::GetVectorFromInputs(Vec vector,int* doflist){ ++void DoubleInput::GetVectorFromInputs(Vector* vector,int* doflist){ + + _error_(" not supporte yet!"); + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/TransientInput.h (revision 11695) +@@ -83,7 +83,7 @@ + double MinAbs(void); + void Extrude(void){_error_("not supported yet");} + void VerticallyIntegrate(Input* thickness_forcing){_error_("not supported yet");}; +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values){_error_("not supported yet");}; + void GetTimeValues(double* values,double time){_error_("not implemented yet");}; + Input* GetTimeInput(double time); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h (revision 11695) +@@ -81,7 +81,7 @@ + double MinAbs(void); + void Extrude(void); + void VerticallyIntegrate(Input* thickness_input); +- void GetVectorFromInputs(Vec vector,int* doflist); ++ void GetVectorFromInputs(Vector* vector,int* doflist); + void GetValuesPtr(double** pvalues,int* pnum_values); + /*}}}*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.h (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Vertex.h (revision 11695) +@@ -9,6 +9,8 @@ + /*{{{1*/ + #include "./Object.h" + class IoModel; ++class Vector; ++class Parameters; + #include "../shared/Exceptions/exceptions.h" + #include "../toolkits/toolkits.h" + #include "../include/include.h" +@@ -62,7 +64,7 @@ + /*Vertex management: {{{1*/ + int Sid(void); + int Connectivity(void); +- void UpdatePosition(Vec vz,Parameters* parameters,double* thickness,double* bed); ++ void UpdatePosition(Vector* vz,Parameters* parameters,double* thickness,double* bed); + /*}}}*/ + }; + #endif /* _VERTEX_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Node.cpp (revision 11695) +@@ -567,7 +567,7 @@ + } + /*}}}*/ + /*FUNCTION Node::CreateVecSets {{{1*/ +-void Node::CreateVecSets(Vec pv_g,Vec pv_f,Vec pv_s){ ++void Node::CreateVecSets(Vector* pv_g,Vector* pv_f,Vector* pv_s){ + + double gvalue=1.0; //all nodes are in the g set; + double value; +@@ -577,15 +577,15 @@ + for(i=0;iindexing.gsize;i++){ + + /*g set: */ +- VecSetValues(pv_g,1,&indexing.gdoflist[i],&gvalue,INSERT_VALUES); ++ pv_g->SetValue(indexing.gdoflist[i],gvalue,INS_VAL); + + /*f set: */ + value=(double)this->indexing.f_set[i]; +- VecSetValues(pv_f,1,&indexing.gdoflist[i],&value,INSERT_VALUES); ++ pv_f->SetValue(indexing.gdoflist[i],value,INS_VAL); + + /*s set: */ + value=(double)this->indexing.s_set[i]; +- VecSetValues(pv_s,1,&indexing.gdoflist[i],&value,INSERT_VALUES); ++ pv_s->SetValue(indexing.gdoflist[i],value,INS_VAL); + + } + +@@ -612,7 +612,7 @@ + } + + /*Add values into constraint vector: */ +- ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); ++ ys->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INS_VAL); + } + + /*Free ressources:*/ +@@ -896,7 +896,7 @@ + } + + /*Add values into ug: */ +- ug->SetValues(this->indexing.fsize,indices,values,INSERT_VALUES); ++ ug->SetValues(this->indexing.fsize,indices,values,INS_VAL); + } + } + else if(setenum==SsetEnum){ +@@ -914,7 +914,7 @@ + } + + /*Add values into ug: */ +- ug->SetValues(this->indexing.ssize,indices,values,INSERT_VALUES); ++ ug->SetValues(this->indexing.ssize,indices,values,INS_VAL); + } + } + else _error_("VecMerge can only merge from the s or f-set onto the g-set!"); +@@ -944,7 +944,7 @@ + } + + /*Add values into ug: */ +- vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INSERT_VALUES); ++ vector->SetValues(this->indexing.fsize,this->indexing.fdoflist,values,INS_VAL); + } + } + else if(setenum==SsetEnum){ +@@ -960,7 +960,7 @@ + } + + /*Add values into ug: */ +- vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INSERT_VALUES); ++ vector->SetValues(this->indexing.ssize,this->indexing.sdoflist,values,INS_VAL); + } + } + else _error_("VecReduce can only merge from the s or f-set onto the g-set!"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.cpp (revision 11695) +@@ -34,7 +34,7 @@ + char* interptype=NULL; + + /* output: */ +- Vec flags=NULL; ++ Vector* flags=NULL; + int nods; + + //contours +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp (revision 11695) +@@ -15,7 +15,7 @@ + Parameters* parameters=NULL; + int name_enum; + int type_enum; +- Vec ug=NULL; ++ Vector* ug=NULL; + + /* output datasets: elements and loads*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp (revision 11695) +@@ -54,7 +54,7 @@ + int nods_prime; + + /* output: */ +- Vec data_prime=NULL; ++ Vector* data_prime=NULL; + + /*Boot module: */ + MODULEBOOT(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp (revision 11695) +@@ -13,7 +13,7 @@ + Loads *loads = NULL; + Materials *materials = NULL; + Parameters *parameters = NULL; +- Vec gradient = NULL; ++ Vector* gradient = NULL; + + /* output datasets: elements and loads*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp (revision 11695) +@@ -16,7 +16,7 @@ + double multithread; + + /* output: */ +- Vec flags=NULL; ++ Vector* flags=NULL; + + /*Boot module: */ + MODULEBOOT(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.cpp (revision 11695) +@@ -32,9 +32,9 @@ + char* interptype=NULL; + + /* output: */ +- Vec in_nod=NULL; ++ Vector* in_nod=NULL; + int nods; +- Vec in_elem=NULL; ++ Vector* in_elem=NULL; + int nel; + + //contours +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Orth/Orth.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Orth/Orth.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Orth/Orth.cpp (revision 11695) +@@ -7,11 +7,11 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Vec gradj=NULL; +- Vec oldgradj=NULL; ++ Vector* gradj=NULL; ++ Vector* oldgradj=NULL; + + /* output datasets: */ +- Vec newgradj=NULL; ++ Vector* newgradj=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -30,9 +30,9 @@ + WriteMatlabData(NEWGRADJ,newgradj); + + /*Free ressources: */ +- VecFree(&gradj); +- VecFree(&oldgradj); +- VecFree(&newgradj); ++ xdelete(&gradj); ++ xdelete(&oldgradj); ++ xdelete(&newgradj); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ComputeBasalStress/ComputeBasalStress.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ComputeBasalStress/ComputeBasalStress.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ComputeBasalStress/ComputeBasalStress.cpp (revision 11695) +@@ -16,7 +16,7 @@ + int numberofnodes; + + /* output datasets: */ +- Vec sigma_g=NULL; ++ Vector* sigma_g=NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -50,7 +50,7 @@ + delete materials; + delete loads; + delete parameters; +- VecFree(&sigma_g); ++ xdelete(&sigma_g); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp (revision 11695) +@@ -36,7 +36,7 @@ + int interpolationenum; + + /* output: */ +- Vec data_mesh=NULL; ++ Vector* data_mesh=NULL; + + /*Boot module: */ + MODULEBOOT(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Gradj/Gradj.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Gradj/Gradj.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Gradj/Gradj.cpp (revision 11695) +@@ -17,7 +17,7 @@ + Parameters *parameters = NULL; + + /* output datasets: */ +- Vec gradient = NULL; ++ Vector* gradient = NULL; + + /*Boot module: */ + MODULEBOOT(); +@@ -53,7 +53,7 @@ + delete loads; + delete materials; + delete parameters; +- VecFree(&gradient); ++ xdelete(&gradient); + + /*end module: */ + MODULEEND(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp (revision 11695) +@@ -60,7 +60,7 @@ + int nods_prime; + + /* output: */ +- Vec data_prime=NULL; ++ Vector* data_prime=NULL; + + /*Boot module: */ + MODULEBOOT(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp (revision 11695) +@@ -16,7 +16,7 @@ + int numberofnodes; + + /* output datasets: */ +- Vec sigma_g=NULL; ++ Vector* sigma_g=NULL; + + /*Boot module: */ + MODULEBOOT(); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 11695) +@@ -75,7 +75,6 @@ + UpdateConstraints\ + SurfaceArea\ + SystemMatrices\ +- Test\ + TimeAdapt\ + TriaSearch\ + TriMesh\ +@@ -205,9 +204,6 @@ + GroundinglineMigration_SOURCES = GroundinglineMigration/GroundinglineMigration.cpp\ + GroundinglineMigration/GroundinglineMigration.h + +-Test_SOURCES = Test/Test.cpp\ +- Test/Test.h +- + HoleFiller_SOURCES = HoleFiller/HoleFiller.cpp\ + HoleFiller/HoleFiller.h + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Solver/Solver.cpp (revision 11695) +@@ -14,16 +14,14 @@ + Vector* df = NULL; + Parameters *parameters = NULL; + int analysis_type; +- char option[100]; +- #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) +- PetscTruth flag; +- #else +- PetscBool flag; +- #endif +- +- /*Matlab solver: */ ++ char* options=NULL; ++ char* token=NULL; ++ char* option=NULL; ++ ++ /*For use of matlab solver: */ + mxArray* array[2]; + ++ /*Start module: */ + MODULEBOOT(); + + /*checks on arguments on the matlab side: */ +@@ -33,16 +31,12 @@ + FetchMatlabData(¶meters,PARAMETERS); + + /*In serial mode, we have not set any petsc options, do it now: */ +- #ifdef _SERIAL_ +- parameters->FindParam(&analysis_type,AnalysisTypeEnum); +- PetscOptionsFromAnalysis(parameters,analysis_type); +- #endif + +- /*Retrieve solver type: */ +- PetscOptionsGetString(PETSC_NULL,"-ksp_type",&option[0],100,&flag); ++ options=OptionsFromAnalysis(parameters,analysis_type); ++ token=strstr(options,"--ksp_type"); + + /*Fetch rest of data only if not running the matlab solver: */ +- if (strcmp(option,"matlab")!=0){ ++ if ((token==NULL) || (strncmp(token+10,"matlab",6)!=0)){ + + /*Input datasets: */ + FetchMatlabData(&Kff,KFF); +@@ -57,7 +51,7 @@ + WriteMatlabData(UF,uf); + } + else{ +- /*Matlab solver: */ ++ /*Call Matlab solver: */ + if (VerboseModule()) printf(" Solving\n"); + array[0]=KFF; + array[1]=PF; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/PetscVecParamEnum.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/PetscVecParamEnum.m (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/PetscVecParamEnum.m (revision 11695) +@@ -1,11 +0,0 @@ +-function macro=PetscVecParamEnum() +-%PETSCVECPARAMENUM - Enum of PetscVecParam +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% macro=PetscVecParamEnum() +- +-macro=StringToEnum('PetscVecParam'); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/PetscMatParamEnum.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/PetscMatParamEnum.m (revision 11694) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/PetscMatParamEnum.m (revision 11695) +@@ -1,11 +0,0 @@ +-function macro=PetscMatParamEnum() +-%PETSCMATPARAMENUM - Enum of PetscMatParam +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% macro=PetscMatParamEnum() +- +-macro=StringToEnum('PetscMatParam'); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/VectorParamEnum.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/VectorParamEnum.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/VectorParamEnum.m (revision 11695) +@@ -0,0 +1,11 @@ ++function macro=VectorParamEnum() ++%VECTORPARAMENUM - Enum of VectorParam ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=VectorParamEnum() ++ ++macro=StringToEnum('VectorParam'); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MatrixParamEnum.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MatrixParamEnum.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/enum/MatrixParamEnum.m (revision 11695) +@@ -0,0 +1,11 @@ ++function macro=MatrixParamEnum() ++%MATRIXPARAMENUM - Enum of MatrixParam ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=MatrixParamEnum() ++ ++macro=StringToEnum('MatrixParam'); Index: /issm/oecreview/Archive/11681-11700/ISSM-11695-11696.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11695-11696.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11695-11696.diff (revision 11991) @@ -0,0 +1,90 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11695) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11696) +@@ -18,6 +18,7 @@ + [SERIAL_VALUE=$withval],[SERIAL_VALUE="yes"]) + AC_MSG_CHECKING(for serial compilation) + AM_CONDITIONAL([NOSERIAL], [test $SERIAL_VALUE = no]) ++ AM_CONDITIONAL([SERIAL], [test $SERIAL_VALUE = yes]) + AC_MSG_RESULT($SERIAL_VALUE) + dnl }}} + dnl Parallel build {{{1 +@@ -27,6 +28,7 @@ + [PARALLEL_VALUE=$withval],[PARALLEL_VALUE="yes"]) + AC_MSG_CHECKING(for parallel compilation) + AM_CONDITIONAL([NOPARALLEL], [test $PARALLEL_VALUE = no]) ++ AM_CONDITIONAL([PARALLEL], [test $PARALLEL_VALUE = yes]) + AC_MSG_RESULT($PARALLEL_VALUE) + ISSMEXT=".exe" + AC_SUBST([ISSMEXT]) +@@ -504,33 +506,34 @@ + AS_HELP_STRING([--with-petsc-dir = DIR], + [petsc root directory, necessary for parallel build]), + [PETSC_ROOT=$withval],[PETSC_ROOT=""]) ++ ++ dnl Used to be necessary, not anymore. ++ dnl if test "$PARALLEL_VALUE" = "yes" ; then ++ dnl if test "$PETSC_ROOT" = "" ; then ++ dnl AC_MSG_ERROR([missing --with-petsc-dir argument for parallel compilation!]) ++ dnl fi ++ dnl fi + +- if test "$PARALLEL_VALUE" = "yes" ; then +- if test "$PETSC_ROOT" = "" ; then +- AC_MSG_ERROR([missing --with-petsc-dir argument for parallel compilation!]) +- fi +- fi +- +- dnl if test "$PARALLEL_VALUE" = "yes" ; then ++ if test -d "$PETSC_ROOT"; then + AC_MSG_CHECKING(for petsc version) + PETSC_MAJOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MAJOR" | sed 's/#define PETSC_VERSION_MAJOR//' | sed 's/ //g'` + PETSC_MINOR=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_MINOR" | sed 's/#define PETSC_VERSION_MINOR//' | sed 's/ //g'` + AC_DEFINE_UNQUOTED([_PETSC_MAJOR_],$PETSC_MAJOR,[ Petsc version major]) + AC_DEFINE_UNQUOTED([_PETSC_MINOR_],$PETSC_MINOR,[ Petsc version minor]) + AC_MSG_RESULT($PETSC_MAJOR.$PETSC_MINOR) +- dnl fi ++ fi + +- + AC_ARG_WITH([petsc-arch], + AS_HELP_STRING([--with-petsc-arch = DIR], + [petsc arch , necessary for parallel build]), + [PETSC_ARCH=$withval],[PETSC_ARCH=""]) + +- if test "$PARALLEL_VALUE" = "yes" ; then +- if test "$PETSC_ARCH" = "" ; then +- AC_MSG_ERROR([missing --with-petsc-arch argument for parallel compilation!]) +- fi +- fi ++ dnl Used to be necessary, not anymore. ++ dnl if test "$PARALLEL_VALUE" = "yes" ; then ++ dnl if test "$PETSC_ARCH" = "" ; then ++ dnl AC_MSG_ERROR([missing --with-petsc-arch argument for parallel compilation!]) ++ dnl fi ++ dnl fi + + AC_MSG_CHECKING(for Petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH) + +@@ -572,11 +575,15 @@ + HAVE_PETSC=no + fi + +- if test $HAVE_PETSC = no; then +- AC_MSG_ERROR([could not find petsc. user should specify --with-petsc-dir and --with-petsc-arch options. Petsc is needed to run ISSM!]) +- else +- AC_MSG_RESULT($HAVE_PETSC) +- fi ++ dnl used to e necessary, not anymore. ++ dnl if test $HAVE_PETSC = no; then ++ dnl AC_MSG_ERROR([could not find petsc. user should specify --with-petsc-dir and --with-petsc-arch options. Petsc is needed to run ISSM!]) ++ dnl else ++ dnl AC_MSG_RESULT($HAVE_PETSC) ++ dnl fi ++ ++ AM_CONDITIONAL([PETSC], [test x$HAVE_PETSC = xyes]) ++ AC_MSG_RESULT($HAVE_PETSC) + dnl }}} + dnl tao{{{1 + AC_ARG_WITH([tao-dir], Index: /issm/oecreview/Archive/11681-11700/ISSM-11696-11697.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11696-11697.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11696-11697.diff (revision 11991) @@ -0,0 +1,71 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11696) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11697) +@@ -8,20 +8,20 @@ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ ++ --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-numthreads=8 \ ++ --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-petsc-arch=$ISSM_ARCH \ + --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ +- --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ + --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-fortran-lib="/usr/local/lib/libgfortran.a" \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ +- --with-math-lib="/usr/lib/libm.dylib" \ +- --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +- --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ +- --with-numthreads=8 ++ --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh (revision 11696) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-ad.sh (revision 11697) +@@ -7,17 +7,10 @@ + --with-serial=no\ + --prefix=$ISSM_TIER \ + --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ + --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ +- --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++ --without-blas-lapack-dir \ + --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ +- --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ +- --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ + --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-math-lib="/usr/lib/libm.dylib" \ +@@ -40,5 +33,11 @@ + --without-groundingline + + #--without-prognostic \ +- +- ++#--with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++#--with-petsc-arch=$ISSM_ARCH \ ++#--with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install \ ++#--with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++#--with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++#--with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++#--with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++#--with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ Index: /issm/oecreview/Archive/11681-11700/ISSM-11697-11698.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11697-11698.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11697-11698.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11697) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/cron/configs/macosx64_larour_validation (revision 11698) +@@ -93,7 +93,7 @@ + #by Matlab and nightlyrun.m + #ex: "'id',[101 102 103]" + +-NROPTIONS="'id',101:151" ++NROPTIONS="'id',[101:136 138:151]" + + #------------------------# + # 7: Matlab# Index: /issm/oecreview/Archive/11681-11700/ISSM-11698-11699.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11698-11699.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11698-11699.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11698) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp (revision 11699) +@@ -45,7 +45,7 @@ + Kfs->MatMult(y_s,Kfsy_s); + } + +- pf->AXPY(Kfsy_s,-1); ++ pf->AXPY(Kfsy_s,-1.); + } + + Index: /issm/oecreview/Archive/11681-11700/ISSM-11699-11700.diff =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-11699-11700.diff (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-11699-11700.diff (revision 11991) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11699) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp (revision 11700) +@@ -7,12 +7,12 @@ + void mexFunction( int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){ + + /*input datasets: */ +- Vector* ug=NULL; +- Nodes* nodes=NULL; +- Parameters* parameters=NULL; ++ Vector *ug = NULL; ++ Nodes *nodes = NULL; ++ Parameters *parameters = NULL; + + /* output datasets: */ +- Vector* uf=NULL; ++ Vector *uf = NULL; + + /*Boot module: */ + MODULEBOOT(); Index: /issm/oecreview/Archive/11681-11700/ISSM-DocReview-11681-11700.tex =================================================================== --- /issm/oecreview/Archive/11681-11700/ISSM-DocReview-11681-11700.tex (revision 11991) +++ /issm/oecreview/Archive/11681-11700/ISSM-DocReview-11681-11700.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11681-11700/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11681-11700/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11681-11700/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11681-11700 Index: /issm/oecreview/Archive/11681-11700/Makefile =================================================================== --- /issm/oecreview/Archive/11681-11700/Makefile (revision 11991) +++ /issm/oecreview/Archive/11681-11700/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11681-11700 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11681-11700/log.tex =================================================================== --- /issm/oecreview/Archive/11681-11700/log.tex (revision 11991) +++ /issm/oecreview/Archive/11681-11700/log.tex (revision 11991) @@ -0,0 +1,31 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11684-11685.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp \\ Export determination: 6. \\Rationale: Using new delete routines to fix segfault \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11685-11686.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp \\ Export determination: 6. \\Rationale: Using new delete routines to fix segfault +M /issm/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp M /issm/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp M /issm/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp M /issm/trunk-jpl/src/mex/Reduceload/Reduceload.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp M /issm/trunk-jpl/src/mex/Solver/Solver.cpp M /issm/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp M /issm/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp Added xdeletes instead of deletes for vectors and matrices \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11686-11687.diff: \\ Function name: \\M /issm/trunk-jpl/src/mex/CreateNodalConstraints/CreateNodalConstraints.cpp M /issm/trunk-jpl/src/mex/InputUpdateFromSolution/InputUpdateFromSolution.cpp M /issm/trunk-jpl/src/mex/Mergesolutionfromftog/Mergesolutionfromftog.cpp M /issm/trunk-jpl/src/mex/Reduceload/Reduceload.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp M /issm/trunk-jpl/src/mex/Reducevectorgtos/Reducevectorgtos.cpp M /issm/trunk-jpl/src/mex/Solver/Solver.cpp M /issm/trunk-jpl/src/mex/SystemMatrices/SystemMatrices.cpp M /issm/trunk-jpl/src/mex/UpdateDynamicConstraints/UpdateDynamicConstraints.cpp \\ Export determination: 6. \\Rationale: Added xdeletes instead of deletes for vectors and matrices +M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp Fixed seg fault (obvious) \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11687-11688.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp \\ Export determination: 6. \\Rationale: Fixed seg fault (obvious) +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp Fixed infinite loop \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11688-11689.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: Fixed infinite loop +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp minor \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11689-11690.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp minor \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11690-11691.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp Changed to xdelete \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11691-11692.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp \\ Export determination: 6. \\Rationale: Changed to xdelete +M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp temporary fix \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11692-11693.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp \\ Export determination: 6. \\Rationale: temporary fix +M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp Do not delete Matrix and Object. Matlab API bug \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11693-11694.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp \\ Export determination: 6. \\Rationale: Do not delete Matrix and Object. Matlab API bug +M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp Improved quick fix, going back to Mathieu's bug fix \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11694-11695.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp \\ Export determination: 6. \\Rationale: Improved quick fix, going back to Mathieu's bug fix +M /issm/trunk-jpl/src/c/Container/Elements.cpp M /issm/trunk-jpl/src/c/Container/Parameters.cpp M /issm/trunk-jpl/src/c/Container/Parameters.h M /issm/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/matlabio.h M /issm/trunk-jpl/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp M /issm/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp M /issm/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h M /issm/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp M /issm/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp M /issm/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.cpp M /issm/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.h M /issm/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp M /issm/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h M /issm/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp M /issm/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h M /issm/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h M /issm/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h M /issm/trunk-jpl/src/c/modules/Gradjx/Gradjx.cpp M /issm/trunk-jpl/src/c/modules/Gradjx/Gradjx.h M /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp M /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h M /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h M /issm/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h M /issm/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h M /issm/trunk-jpl/src/c/modules/Orthx/Orthx.cpp M /issm/trunk-jpl/src/c/modules/Orthx/Orthx.h M /issm/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp M /issm/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h M /issm/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp M /issm/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp M /issm/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.h M /issm/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp M /issm/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/ElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp M /issm/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h M /issm/trunk-jpl/src/c/objects/FemModel.cpp M /issm/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/BoolInput.h M /issm/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/ControlInput.h M /issm/trunk-jpl/src/c/objects/Inputs/DatasetInput.h M /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.h M /issm/trunk-jpl/src/c/objects/Inputs/Input.h M /issm/trunk-jpl/src/c/objects/Inputs/IntInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/IntInput.h M /issm/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp M /issm/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h M /issm/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/TransientInput.h M /issm/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp M /issm/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h M /issm/trunk-jpl/src/c/objects/Materials/Material.h M /issm/trunk-jpl/src/c/objects/Materials/Matice.cpp M /issm/trunk-jpl/src/c/objects/Materials/Matice.h M /issm/trunk-jpl/src/c/objects/Materials/Matpar.h M /issm/trunk-jpl/src/c/objects/Node.cpp M /issm/trunk-jpl/src/c/objects/Node.h M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/objects/Params/BoolParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleMatParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleVecParam.h M /issm/trunk-jpl/src/c/objects/Params/FileParam.h M /issm/trunk-jpl/src/c/objects/Params/IntMatParam.h M /issm/trunk-jpl/src/c/objects/Params/IntParam.h M /issm/trunk-jpl/src/c/objects/Params/IntVecParam.h A /issm/trunk-jpl/src/c/objects/Params/MatrixParam.cpp A /issm/trunk-jpl/src/c/objects/Params/MatrixParam.h M /issm/trunk-jpl/src/c/objects/Params/Param.h D /issm/trunk-jpl/src/c/objects/Params/PetscMatParam.cpp D /issm/trunk-jpl/src/c/objects/Params/PetscMatParam.h D /issm/trunk-jpl/src/c/objects/Params/PetscVecParam.cpp D /issm/trunk-jpl/src/c/objects/Params/PetscVecParam.h M /issm/trunk-jpl/src/c/objects/Params/StringArrayParam.h M /issm/trunk-jpl/src/c/objects/Params/StringParam.h A /issm/trunk-jpl/src/c/objects/Params/VectorParam.cpp A /issm/trunk-jpl/src/c/objects/Params/VectorParam.h M /issm/trunk-jpl/src/c/objects/Vertex.cpp M /issm/trunk-jpl/src/c/objects/Vertex.h M /issm/trunk-jpl/src/c/objects/objects.h M /issm/trunk-jpl/src/c/shared/Exp/IsInPoly.cpp M /issm/trunk-jpl/src/c/shared/Exp/exp.h M /issm/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp A /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp M /issm/trunk-jpl/src/c/shared/Numerics/PetscOptionsFromAnalysis.cpp M /issm/trunk-jpl/src/c/shared/Numerics/numerics.h M /issm/trunk-jpl/src/c/solutions/convergence.cpp M /issm/trunk-jpl/src/c/solutions/gradient\_core.cpp M /issm/trunk-jpl/src/c/solutions/issm.cpp A /issm/trunk-jpl/src/c/toolkits/double A /issm/trunk-jpl/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp A /issm/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp A /issm/trunk-jpl/src/c/toolkits/double/double.h A /issm/trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/MPI\_Boundariesfromrange.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/MPI\_Lowerrow.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/MPI\_Upperrow.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h A /issm/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscInsertMode.cpp A /issm/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatToSerial.cpp D /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp D /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/NewVec.cpp D /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscDetermineLocalSize.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/VecToMPISerial.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/petscpatches.h M /issm/trunk-jpl/src/c/toolkits/petsc/petscincludes.h M /issm/trunk-jpl/src/c/toolkits/plapack/plapackincludes.h M /issm/trunk-jpl/src/c/toolkits/toolkits.h A /issm/trunk-jpl/src/c/toolkits/toolkitsenums.h A /issm/trunk-jpl/src/m/enum/MatrixParamEnum.m D /issm/trunk-jpl/src/m/enum/PetscMatParamEnum.m D /issm/trunk-jpl/src/m/enum/PetscVecParamEnum.m A /issm/trunk-jpl/src/m/enum/VectorParamEnum.m M /issm/trunk-jpl/src/mex/ComputeBasalStress/ComputeBasalStress.cpp M /issm/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.cpp M /issm/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.cpp M /issm/trunk-jpl/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp M /issm/trunk-jpl/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp M /issm/trunk-jpl/src/mex/Gradj/Gradj.cpp M /issm/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp M /issm/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp M /issm/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp M /issm/trunk-jpl/src/mex/Makefile.am M /issm/trunk-jpl/src/mex/Orth/Orth.cpp M /issm/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp M /issm/trunk-jpl/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp M /issm/trunk-jpl/src/mex/Solver/Solver.cpp Completed separation of Petsc from ISSM. Matrix and Vector are now the vehicles for Mat and Vec objects when running with Petsc, or double* when running with a custom made type of matrix (still to be finished). \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11695-11696.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Container/Elements.cpp M /issm/trunk-jpl/src/c/Container/Parameters.cpp M /issm/trunk-jpl/src/c/Container/Parameters.h M /issm/trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp M /issm/trunk-jpl/src/c/io/Matlab/matlabio.h M /issm/trunk-jpl/src/c/modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp M /issm/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.cpp M /issm/trunk-jpl/src/c/modules/ComputeBasalStressx/ComputeBasalStressx.h M /issm/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.cpp M /issm/trunk-jpl/src/c/modules/ComputeStrainRatex/ComputeStrainRatex.h M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.cpp M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshx.h M /issm/trunk-jpl/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp M /issm/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.cpp M /issm/trunk-jpl/src/c/modules/ContourToNodesx/ContourToNodesx.h M /issm/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.cpp M /issm/trunk-jpl/src/c/modules/ControlInputGetGradientx/ControlInputGetGradientx.h M /issm/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.cpp M /issm/trunk-jpl/src/c/modules/ControlInputSetGradientx/ControlInputSetGradientx.h M /issm/trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h M /issm/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromInputsx/GetVectorFromInputsx.h M /issm/trunk-jpl/src/c/modules/Gradjx/Gradjx.cpp M /issm/trunk-jpl/src/c/modules/Gradjx/Gradjx.h M /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp M /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.h M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.cpp M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorDakotax/InputUpdateFromVectorDakotax.h M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.cpp M /issm/trunk-jpl/src/c/modules/InputUpdateFromVectorx/InputUpdateFromVectorx.h M /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.h M /issm/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dx.h M /issm/trunk-jpl/src/c/modules/InterpFromMesh2dx/InterpFromMesh2dxt.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.cpp M /issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh3dx/InterpFromMeshToMesh3dx.h M /issm/trunk-jpl/src/c/modules/Orthx/Orthx.cpp M /issm/trunk-jpl/src/c/modules/Orthx/Orthx.h M /issm/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.cpp M /issm/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsx.h M /issm/trunk-jpl/src/c/modules/PointCloudFindNeighborsx/PointCloudFindNeighborsxt.cpp M /issm/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp M /issm/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.h M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.h M /issm/trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp M /issm/trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp M /issm/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/BoolElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/DoubleElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/ElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/PentaP1ElementResult.h M /issm/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.cpp M /issm/trunk-jpl/src/c/objects/ElementResults/TriaP1ElementResult.h M /issm/trunk-jpl/src/c/objects/Elements/Element.h M /issm/trunk-jpl/src/c/objects/Elements/Penta.cpp M /issm/trunk-jpl/src/c/objects/Elements/Penta.h M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/Elements/Tria.h M /issm/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.cpp M /issm/trunk-jpl/src/c/objects/ExternalResults/PetscVecExternalResult.h M /issm/trunk-jpl/src/c/objects/FemModel.cpp M /issm/trunk-jpl/src/c/objects/Inputs/BoolInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/BoolInput.h M /issm/trunk-jpl/src/c/objects/Inputs/ControlInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/ControlInput.h M /issm/trunk-jpl/src/c/objects/Inputs/DatasetInput.h M /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/DoubleInput.h M /issm/trunk-jpl/src/c/objects/Inputs/Input.h M /issm/trunk-jpl/src/c/objects/Inputs/IntInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/IntInput.h M /issm/trunk-jpl/src/c/objects/Inputs/PentaP1Input.cpp M /issm/trunk-jpl/src/c/objects/Inputs/PentaP1Input.h M /issm/trunk-jpl/src/c/objects/Inputs/TransientInput.cpp M /issm/trunk-jpl/src/c/objects/Inputs/TransientInput.h M /issm/trunk-jpl/src/c/objects/Inputs/TriaP1Input.cpp M /issm/trunk-jpl/src/c/objects/Inputs/TriaP1Input.h M /issm/trunk-jpl/src/c/objects/Materials/Material.h M /issm/trunk-jpl/src/c/objects/Materials/Matice.cpp M /issm/trunk-jpl/src/c/objects/Materials/Matice.h M /issm/trunk-jpl/src/c/objects/Materials/Matpar.h M /issm/trunk-jpl/src/c/objects/Node.cpp M /issm/trunk-jpl/src/c/objects/Node.h M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/objects/Params/BoolParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleMatArrayParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleMatParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleParam.h M /issm/trunk-jpl/src/c/objects/Params/DoubleVecParam.h M /issm/trunk-jpl/src/c/objects/Params/FileParam.h M /issm/trunk-jpl/src/c/objects/Params/IntMatParam.h M /issm/trunk-jpl/src/c/objects/Params/IntParam.h M /issm/trunk-jpl/src/c/objects/Params/IntVecParam.h A /issm/trunk-jpl/src/c/objects/Params/MatrixParam.cpp A /issm/trunk-jpl/src/c/objects/Params/MatrixParam.h M /issm/trunk-jpl/src/c/objects/Params/Param.h D /issm/trunk-jpl/src/c/objects/Params/PetscMatParam.cpp D /issm/trunk-jpl/src/c/objects/Params/PetscMatParam.h D /issm/trunk-jpl/src/c/objects/Params/PetscVecParam.cpp D /issm/trunk-jpl/src/c/objects/Params/PetscVecParam.h M /issm/trunk-jpl/src/c/objects/Params/StringArrayParam.h M /issm/trunk-jpl/src/c/objects/Params/StringParam.h A /issm/trunk-jpl/src/c/objects/Params/VectorParam.cpp A /issm/trunk-jpl/src/c/objects/Params/VectorParam.h M /issm/trunk-jpl/src/c/objects/Vertex.cpp M /issm/trunk-jpl/src/c/objects/Vertex.h M /issm/trunk-jpl/src/c/objects/objects.h M /issm/trunk-jpl/src/c/shared/Exp/IsInPoly.cpp M /issm/trunk-jpl/src/c/shared/Exp/exp.h M /issm/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp A /issm/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp M /issm/trunk-jpl/src/c/shared/Numerics/PetscOptionsFromAnalysis.cpp M /issm/trunk-jpl/src/c/shared/Numerics/numerics.h M /issm/trunk-jpl/src/c/solutions/convergence.cpp M /issm/trunk-jpl/src/c/solutions/gradient\_core.cpp M /issm/trunk-jpl/src/c/solutions/issm.cpp A /issm/trunk-jpl/src/c/toolkits/double A /issm/trunk-jpl/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp A /issm/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp A /issm/trunk-jpl/src/c/toolkits/double/double.h A /issm/trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/MPI\_Boundariesfromrange.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/MPI\_Lowerrow.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/MPI\_Upperrow.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h A /issm/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscInsertMode.cpp A /issm/trunk-jpl/src/c/toolkits/petsc/patches/ISSMToPetscNormMode.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatToSerial.cpp D /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToDoubleMatrix.cpp D /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToDoubleVector.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/NewMat.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/NewVec.cpp D /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscDetermineLocalSize.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/VecToMPISerial.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/petscpatches.h M /issm/trunk-jpl/src/c/toolkits/petsc/petscincludes.h M /issm/trunk-jpl/src/c/toolkits/plapack/plapackincludes.h M /issm/trunk-jpl/src/c/toolkits/toolkits.h A /issm/trunk-jpl/src/c/toolkits/toolkitsenums.h A /issm/trunk-jpl/src/m/enum/MatrixParamEnum.m D /issm/trunk-jpl/src/m/enum/PetscMatParamEnum.m D /issm/trunk-jpl/src/m/enum/PetscVecParamEnum.m A /issm/trunk-jpl/src/m/enum/VectorParamEnum.m M /issm/trunk-jpl/src/mex/ComputeBasalStress/ComputeBasalStress.cpp M /issm/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.cpp M /issm/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.cpp M /issm/trunk-jpl/src/mex/ControlInputGetGradient/ControlInputGetGradient.cpp M /issm/trunk-jpl/src/mex/GetVectorFromInputs/GetVectorFromInputs.cpp M /issm/trunk-jpl/src/mex/Gradj/Gradj.cpp M /issm/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.cpp M /issm/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.cpp M /issm/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp M /issm/trunk-jpl/src/mex/Makefile.am M /issm/trunk-jpl/src/mex/Orth/Orth.cpp M /issm/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.cpp M /issm/trunk-jpl/src/mex/ResetCoordinateSystem/ResetCoordinateSystem.cpp M /issm/trunk-jpl/src/mex/Solver/Solver.cpp \\ Export determination: 6. \\Rationale: Completed separation of Petsc from ISSM. Matrix and Vector are now the vehicles for Mat and Vec objects when running with Petsc, or double* when running with a custom made type of matrix (still to be finished). +M /issm/trunk-jpl/m4/issm\_options.m4 More leeway in terms of running without petsc support \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11696-11697.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: More leeway in terms of running without petsc support +M /issm/trunk-jpl/configs/config-macosx64-larour-ad.sh M /issm/trunk-jpl/configs/config-macosx64-larour.sh run without petsc \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11697-11698.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-macosx64-larour-ad.sh M /issm/trunk-jpl/configs/config-macosx64-larour.sh \\ Export determination: 6. \\Rationale: run without petsc +M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation Skip bamg \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11698-11699.diff: \\ Function name: \\M /issm/trunk-jpl/cron/configs/macosx64\_larour\_validation \\ Export determination: 6. \\Rationale: Skip bamg +M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp minor \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11699-11700.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Reduceloadx/Reduceloadx.cpp \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/mex/Reducevectorgtof/Reducevectorgtof.cpp cosmetics \\\\ Index: /issm/oecreview/Archive/11681-11700/r1.tex =================================================================== --- /issm/oecreview/Archive/11681-11700/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11681-11700/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11681 Index: /issm/oecreview/Archive/11681-11700/r2.tex =================================================================== --- /issm/oecreview/Archive/11681-11700/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11681-11700/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11700 Index: /issm/oecreview/Archive/11700-11718/Date.tex =================================================================== --- /issm/oecreview/Archive/11700-11718/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11700-11718/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11700-11718/ISSM-11700-11701.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11700-11701.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11700-11701.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11700) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11701) +@@ -34,7 +34,7 @@ + PetscOptionsFromAnalysis(parameters,analysis_type); + #endif + +- SolverxPetsc(&uf->vector, Kff->matrix, pf->vector, uf0_vector, df->vector, parameters); ++ SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); + VecGetSize(uf->vector,&uf->M); + #else + _error_("not supported yet!"); Index: /issm/oecreview/Archive/11700-11718/ISSM-11701-11702.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11701-11702.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11701-11702.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 11701) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 11702) +@@ -64,7 +64,7 @@ + } + + /*ok, grab the option string: */ +- outstring=(char*)xmalloc(strlen(strings[found]+1)*sizeof(char)); ++ outstring=(char*)xmalloc((strlen(strings[found])+1)*sizeof(char)); + strcpy(outstring,strings[found]); + + /*Free ressources*/ Index: /issm/oecreview/Archive/11700-11718/ISSM-11702-11703.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11702-11703.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11702-11703.diff (revision 11991) @@ -0,0 +1,87 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11702) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11703) +@@ -12,7 +12,7 @@ + #include "../include/include.h" + #include "../solvers/solvers.h" + +-#if defined (_HAVE_TAO_) && (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ == 2) ++#if defined (_HAVE_TAO_) && defined (_HAVE_PETSC_) && (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ == 2) + #include + + /*Local prototype*/ +@@ -32,9 +32,9 @@ + TaoSolver tao; + double *dummy = NULL; + int *control_list = NULL; +- Vec X = NULL; +- Vec XL = NULL; +- Vec XU = NULL; ++ Vector *X = NULL; ++ Vector *XL = NULL; ++ Vector *XU = NULL; + + /*Initialize TAO*/ + int argc; char **args=NULL; +@@ -67,10 +67,10 @@ + GetVectorFromControlInputsx(&X, femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); + GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); +- TaoSetInitialVector(tao,X); +- TaoSetVariableBounds(tao,XL,XU); +- VecFree(&XL); +- VecFree(&XU); ++ TaoSetInitialVector(tao,X->vector); ++ TaoSetVariableBounds(tao,XL->vector,XU->vector); ++ xdelete(&XL); ++ xdelete(&XU); + + user.femmodel=femmodel; + TaoSetObjectiveAndGradientRoutine(tao,FormFunctionGradient,(void*)&user); +@@ -79,7 +79,7 @@ + _printf_(VerboseControl(),"%s\n"," Starting optimization"); + TaoSolve(tao); + TaoView(tao,PETSC_VIEWER_STDOUT_WORLD); +- TaoGetSolutionVector(tao,&X); ++ TaoGetSolutionVector(tao,&X->vector); + SetControlInputsFromVectorx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,X); + for(int i=0;ielements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,control_list[i]); +@@ -94,11 +94,11 @@ + + /*Clean up and return*/ + xfree((void**)&control_list); +- VecFree(&X); ++ xdelete(&X); + TaoDestroy(&tao); + TaoFinalize(); + } +-int FormFunctionGradient(TaoSolver tao, Vec X, double *fcn,Vec G,void *userCtx){ ++int FormFunctionGradient(TaoSolver tao, Vec Xpetsc, double *fcn,Vec G,void *userCtx){ + + /*Retreive arguments*/ + int solution_type,num_cost_functions; +@@ -106,8 +106,12 @@ + FemModel *femmodel = user->femmodel; + int *cost_functions = NULL; + double *cost_functionsd= NULL; +- Vec gradient = NULL; ++ Vector *gradient = NULL; ++ Vector *X = NULL; + ++ /*Convert input to Vec*/ ++ X=new Vector(Xpetsc); ++ + /*Set new variable*/ + //VecView(X,PETSC_VIEWER_STDOUT_WORLD); + SetControlInputsFromVectorx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,X); +@@ -135,7 +139,7 @@ + + /*Compute gradient*/ + Gradjx(&gradient,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); +- VecCopy(gradient,G); VecFree(&gradient); ++ VecCopy(gradient->vector,G); xdelete(&gradient); + VecScale(G,-1.); + + /*Clean-up and return*/ Index: /issm/oecreview/Archive/11700-11718/ISSM-11703-11704.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11703-11704.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11703-11704.diff (revision 11991) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11703) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11704) +@@ -77,6 +77,20 @@ + #endif + } + /*}}}*/ ++#ifdef _HAVE_PETSC_ ++/*FUNCTION Vector::Vector(Vec petsc_vec){{{1*/ ++Vector::Vector(Vec petsc_vec){ ++ ++ /*Get Vector size*/ ++ VecGetSize(petsc_vec,&this->M); ++ ++ /*copy vector*/ ++ VecDuplicate(petsc_vec,&this->vector); ++ VecCopy(petsc_vec,this->vector); ++ ++} ++/*}}}*/ ++#endif + /*FUNCTION Vector::~Vector(){{{1*/ + Vector::~Vector(){ + +@@ -91,7 +105,6 @@ + } + /*}}}*/ + +- + /*Vector specific routines: */ + /*FUNCTION Vector::Echo{{{1*/ + void Vector::Echo(void){ +@@ -239,7 +252,6 @@ + #else + _error_("not implemented yet!"); + #endif +- + } + /*}}}*/ + /*FUNCTION Vector::AYPX{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11703) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11704) +@@ -45,6 +45,9 @@ + Vector(); + Vector(int M,bool fromlocalsize=false); + Vector(double* serial_vec,int pM); ++ #ifdef _HAVE_PETSC_ ++ Vector(Vec petsc_vec); ++ #endif + ~Vector(); + /*}}}*/ + /*Vector specific routines {{{1*/ Index: /issm/oecreview/Archive/11700-11718/ISSM-11704-11705.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11704-11705.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11704-11705.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11704) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11705) +@@ -82,7 +82,7 @@ + void xdelete(Matrix** pv){ + + if (pv && *pv){ +- #ifdef _HAVE_PARALLEL_ ++ #ifdef _PARALLEL_ + /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ +@@ -99,7 +99,7 @@ + void xdelete(Vector** pv){ + + if (pv && *pv){ +- #ifdef _HAVE_PARALLEL_ ++ #ifdef _PARALLEL_ + /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we + * don't actually free memory in Matlab, we let the memory manager do that. We only + * free in parallel: */ Index: /issm/oecreview/Archive/11700-11718/ISSM-11705-11706.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11705-11706.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11705-11706.diff (revision 11991) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11705) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/controltao_core.cpp (revision 11706) +@@ -115,6 +115,7 @@ + /*Set new variable*/ + //VecView(X,PETSC_VIEWER_STDOUT_WORLD); + SetControlInputsFromVectorx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,X); ++ xdelete(&X); + + /*Recover some parameters*/ + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); Index: /issm/oecreview/Archive/11700-11718/ISSM-11706-11707.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11706-11707.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11706-11707.diff (revision 11991) @@ -0,0 +1,12 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp (revision 11706) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/UpdateVertexPositionsx/UpdateVertexPositionsx.cpp (revision 11707) +@@ -39,6 +39,6 @@ + /*Free ressources:*/ + xfree((void**)&thickness); + xfree((void**)&bed); +- delete vz; ++ xdelete(&vz); + return 1; + } Index: /issm/oecreview/Archive/11700-11718/ISSM-11708-11709.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11708-11709.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11708-11709.diff (revision 11991) @@ -0,0 +1,86 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 11708) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/vim/addons/vim/syntax/c.vim (revision 11709) +@@ -405,7 +405,7 @@ + "ISSM containers: + syn keyword cType Constraints DataSet Elements Inputs Loads Materials Nodes Parameters Results Vertices + "Petsc +-syn keyword cType Vec Mat ++syn keyword cType Vec Mat + "other ISSM's syntax + syn keyword cType mxArray ErrorException + +@@ -426,6 +426,7 @@ + syn keyword cType SpcDynamic + syn keyword cType GaussTria + syn keyword cType GaussPenta ++syn keyword cType Load + syn keyword cType Friction + syn keyword cType Icefront + syn keyword cType Numericalflux +@@ -433,7 +434,6 @@ + syn keyword cType Penpair + syn keyword cType Pengrid + syn keyword cType Element +-syn keyword cType Load + syn keyword cType Penta + syn keyword cType PentaHook + syn keyword cType PentaRef +@@ -501,6 +501,8 @@ + syn keyword cType Matpar + syn keyword cType ElementMatrix + syn keyword cType ElementVector ++syn keyword cType Vector ++syn keyword cType Matrix + syn keyword cType BoolParam + syn keyword cType DoubleMatParam + syn keyword cType DoubleTransientMatParam +@@ -512,8 +514,8 @@ + syn keyword cType IntMatParam + syn keyword cType FileParam + syn keyword cType Param +-syn keyword cType PetscMatParam +-syn keyword cType PetscVecParam ++syn keyword cType MatrixParam ++syn keyword cType VectorParam + syn keyword cType StringArrayParam + syn keyword cType StringParam + syn keyword cType Contour +@@ -608,6 +610,7 @@ + syn keyword cConstant InversionGradientScalingEnum + syn keyword cConstant InversionIscontrolEnum + syn keyword cConstant InversionTaoEnum ++syn keyword cConstant InversionIncompleteAdjointEnum + syn keyword cConstant InversionMaxParametersEnum + syn keyword cConstant InversionMaxiterPerStepEnum + syn keyword cConstant InversionMinParametersEnum +@@ -687,8 +690,7 @@ + syn keyword cConstant SteadystateReltolEnum + syn keyword cConstant SteadystateRequestedOutputsEnum + syn keyword cConstant SurfaceEnum +-syn keyword cConstant SurfaceforcingsAblationRateEnum +-syn keyword cConstant SurfaceforcingsAccumulationRateEnum ++syn keyword cConstant SurfaceforcingsPrecipitationEnum + syn keyword cConstant SurfaceforcingsMassBalanceEnum + syn keyword cConstant ThermalMaxiterEnum + syn keyword cConstant ThermalPenaltyFactorEnum +@@ -696,6 +698,7 @@ + syn keyword cConstant ThermalPenaltyThresholdEnum + syn keyword cConstant ThermalSpctemperatureEnum + syn keyword cConstant ThermalStabilizationEnum ++syn keyword cConstant ThermalIsenthalpyEnum + syn keyword cConstant ThicknessEnum + syn keyword cConstant TimesteppingCflCoefficientEnum + syn keyword cConstant TimesteppingFinalTimeEnum +@@ -790,8 +793,8 @@ + syn keyword cConstant PenpairEnum + syn keyword cConstant PentaEnum + syn keyword cConstant PentaP1InputEnum +-syn keyword cConstant PetscMatParamEnum +-syn keyword cConstant PetscVecParamEnum ++syn keyword cConstant MatrixParamEnum ++syn keyword cConstant VectorParamEnum + syn keyword cConstant RiftfrontEnum + syn keyword cConstant SegmentEnum + syn keyword cConstant SegmentRiftfrontEnum Index: /issm/oecreview/Archive/11700-11718/ISSM-11710-11711.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11710-11711.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11710-11711.diff (revision 11991) @@ -0,0 +1,152 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/install.sh (revision 11710) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/install.sh (revision 11711) +@@ -5,17 +5,21 @@ + # ( enter the CVS password: "cvsanon" ) + + #Some cleanup +-rm -rf install ++rm -rf install bin exe + + #add cvs repository + export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack' + ++echo loging into MITgcm cvs: provide password, which is cvsanon ++cvs login ++ + #Download code from server +-cvs co -P MITgcm_code ++cvs co -P MITgcm + + #move + mv MITgcm install + ++ + #compile code + cd install + mkdir bin exe +@@ -23,3 +27,6 @@ + ../tools/genmake2 -mods=../../code + make depend + make -j 8 ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/notes +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/notes (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/notes (revision 11711) +@@ -0,0 +1,112 @@ ++Explanations of the code: {{{1 ++doc: call Dimitris. ++ ++Main code of MITgcm in 3 dir: ++ ++eesupp: running the code on parallel clusters. infrastructure for running MPI, shared memory, non-physics part of the code. ++ src: main.F: eeboo (wrapper initialization) ++ check_threads ++ the_model_main ++ eedie (wrapper termination) ++ inc ++ ++ ++model: here is the model main. ++ src: the_model_main.F includes the base MITgcm code. ++ inc: ++ ++pkg: do various physics. packages will not be compiled. ++ kpp: vertical mixing parametization ++ gmred: isopicnel mixing parameterization. ++ ++ thice: ++ seaice: sea ice models ++ ++ shelfice: interacting with ice sheets ++ icefront ++ ++ cal: calendar correspondance between model time step and calendar time. ++ ++ diagnostics: any physical variable that you want to look at. get output variables into output of the model. ++ ++ debug: other kind of diagnostics, various levels of debug. ++ ++ frazil: frazil ice. ++ ++ atmospherics packages: fizhi, cheapaml ++ ++ exch2: fancier way of exchanging data and tiling. ++ ++ ++jobs: forget about it. ++ ++ ++lsopt: forget it. ++ ++optim: forget it. ++ ++ ++utils: ++ matlab: bunch of matlab scripts. ++ ++tools: build_options: platform dependent run files to be run with gene_make to generate the correct Makefile. ++}}} ++How to run : {{{1 ++All the verification tests are downloaded if you checkout the MITgcm repository instead of the ++MITgcm_code: ++cvs co -P MITgcm ++ ++The verification tests are downloaded in MITgcm/verification. They can be run using ++the testreport utility. Only a subset of the tests can be run if needed, by supplying ++an option flag to tesstreport. ++ ++ ++For our work, the relevant tests are: ++labsea: sea ice ++ismip: shelf ice ++ ++If you run a test like lab_sea: ++ ++./code/packages.conf: list of packages that we want to compile for this specific run. ++For each package, you at least need to modify code/size.h ++ ++You can find the runtime parameters in: ++input/data: runtime parameters for model source ++input/eedata:runtime parameters for eesupp source ++input/data.: runtime parameters for all packages ++intput/data.pkg: runtime parameters for packages that need to be run. subset of packages.conf ++ ++The build directory holds the source and objects for the current test, with symlinks ++ ++If errors appear during the run, go into: ++./run and find the STDERR file. ++ ++To supply different Makefile templates for testreport: ++testreport -ef -opt Makefile_amd64_gfortran ++ ++You can use matlab to plot the results: ++use readbin from the labsea experiment or MITgcm/tools/matlab/rdmds ++ ++There is an MITgcm_contrib repository for code that is not in the main trunk yet: ++MITgcm_contrib/MPMice/beaufort presents a scenario for a quick coupler. ++ ++}}} ++Extra nodes{{{ ++cd install/verification/ ++./testreport -of ../tools/build_options/linux_amd64_gfortran ++ ++( results for baseline lab_sea verification ++ experiment are in verification/lab_sea/run ) ++ ++cd lab_sea/run ++there is routines in lab_sea/matlab ++ ++ma ++addpath('../matlab') ++eta=readbin('Eta.0000000001.data',[20 16],1); ++pcolor(eta') ++colorbar ++ ++addpath('../../../utils/matlab') ++eta=rdmds('Eta.0000000001'); ++}}} Index: /issm/oecreview/Archive/11700-11718/ISSM-11711-11712.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11711-11712.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11711-11712.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11711) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11712) +@@ -35,6 +35,8 @@ + #endif + + SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); ++ _assert_(uf); ++ _assert_(uf->vector); + VecGetSize(uf->vector,&uf->M); + #else + _error_("not supported yet!"); Index: /issm/oecreview/Archive/11700-11718/ISSM-11712-11713.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11712-11713.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11712-11713.diff (revision 11991) @@ -0,0 +1,197 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11712) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11713) +@@ -149,6 +149,7 @@ + void Vector::Assemble(void){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecAssemblyBegin(this->vector); + VecAssemblyEnd(this->vector); + #else +@@ -162,6 +163,7 @@ + + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecSetValues(this->vector,ssize,list,values,ISSMToPetscInsertMode(mode)); + #else + _error_("not implemented yet!"); +@@ -172,8 +174,8 @@ + /*FUNCTION Vector::SetValue{{{1*/ + void Vector::SetValue(int dof, double value, InsMode mode){ + +- + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecSetValues(this->vector,1,&dof,&value,ISSMToPetscInsertMode(mode)); + #else + _error_("not implemented yet!"); +@@ -184,20 +186,19 @@ + /*FUNCTION Vector::GetValue{{{1*/ + void Vector::GetValue(double* pvalue,int dof){ + +- + #ifdef _HAVE_PETSC_ +- VecGetValues(this->vector,1,&dof,pvalue); ++ _assert_(this->vector); ++ VecGetValues(this->vector,1,&dof,pvalue); + #else + _error_("not implemented yet!"); + #endif +- + } + /*}}}*/ +- + /*FUNCTION Vector::GetSize{{{1*/ + void Vector::GetSize(int* pM){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecGetSize(this->vector,pM); + #else + _error_("not implemented yet!"); +@@ -209,6 +210,7 @@ + void Vector::GetLocalSize(int* pM){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecGetLocalSize(this->vector,pM); + #else + _error_("not implemented yet!"); +@@ -223,6 +225,7 @@ + output=new Vector(); + #ifdef _HAVE_PETSC_ + Vec vec_output=NULL; ++ _assert_(this->vector); + VecDuplicate(this->vector,&vec_output); + output->vector=vec_output; + VecGetSize(output->vector,&output->M); +@@ -237,6 +240,7 @@ + void Vector::Set(double value){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecSet(this->vector,value); + #else + _error_("not implemented yet!"); +@@ -248,6 +252,7 @@ + void Vector::AXPY(Vector* X, double a){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecAXPY(this->vector,a,X->vector); + #else + _error_("not implemented yet!"); +@@ -258,6 +263,7 @@ + void Vector::AYPX(Vector* X, double a){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecAYPX(this->vector,a,X->vector); + #else + _error_("not implemented yet!"); +@@ -296,7 +302,8 @@ + + double norm=0; + #ifdef _HAVE_PETSC_ +- VecNorm(this->vector,ISSMToPetscNormMode(norm_type),&norm); ++ _assert_(this->vector); ++ VecNorm(this->vector,ISSMToPetscNormMode(norm_type),&norm); + #else + _error_("not implemented yet!"); + #endif +@@ -307,18 +314,20 @@ + void Vector::Scale(double scale_factor){ + + #ifdef _HAVE_PETSC_ +- VecScale(this->vector,scale_factor); ++ _assert_(this->vector); ++ VecScale(this->vector,scale_factor); + #else + _error_("not implemented yet!"); + #endif + } + /*}}}*/ +-/*FUNCTION Vector::Scale{{{1*/ ++/*FUNCTION Vector::Dot{{{1*/ + double Vector::Dot(Vector* vector){ + + double dot; + #ifdef _HAVE_PETSC_ +- VecDot(this->vector,vector->vector,&dot); ++ _assert_(this->vector); ++ VecDot(this->vector,vector->vector,&dot); + #else + _error_("not implemented yet!"); + #endif +@@ -329,6 +338,7 @@ + void Vector::PointwiseDivide(Vector* x,Vector* y){ + + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + VecPointwiseDivide(this->vector,x->vector,y->vector); + #else + _error_("not implemented yet!"); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11712) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11713) +@@ -182,6 +182,7 @@ + /*FUNCTION Matrix::Assemble{{{1*/ + void Matrix::Assemble(void){ + #ifdef _HAVE_PETSC_ ++ _assert_(this->matrix); + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); + #if _PETSC_MAJOR_ == 2 +@@ -198,7 +199,8 @@ + + double norm=0; + #ifdef _HAVE_PETSC_ +- MatNorm(this->matrix,ISSMToPetscNormMode(norm_type),&norm); ++ _assert_(this->matrix); ++ MatNorm(this->matrix,ISSMToPetscNormMode(norm_type),&norm); + #else + _error_("not implemented yet!"); + #endif +@@ -209,7 +211,8 @@ + void Matrix::GetSize(int* pM,int* pN){ + + #ifdef _HAVE_PETSC_ +- MatGetSize(this->matrix,pM,pN); ++ _assert_(this->matrix); ++ MatGetSize(this->matrix,pM,pN); + #else + _error_("not implemented yet!"); + #endif +@@ -219,7 +222,8 @@ + void Matrix::GetLocalSize(int* pM,int* pN){ + + #ifdef _HAVE_PETSC_ +- MatGetLocalSize(this->matrix,pM,pN); ++ _assert_(this->matrix); ++ MatGetLocalSize(this->matrix,pM,pN); + #else + _error_("not implemented yet!"); + #endif +@@ -229,7 +233,9 @@ + void Matrix::MatMult(Vector* X,Vector* AX){ + + #ifdef _HAVE_PETSC_ +- MatMultPatch(this->matrix,X->vector,AX->vector); ++ _assert_(this->matrix); ++ _assert_(X->vector); ++ MatMultPatch(this->matrix,X->vector,AX->vector); + #else + _error_("not implemented yet!"); + #endif +@@ -243,6 +249,7 @@ + output=new Matrix(); + + #ifdef _HAVE_PETSC ++ _assert_(this->matrix); + MatDuplicate(this->matrix,MAT_COPY_VALUES,&output->matrix); + #else + _error_("not implemented yet!"); Index: /issm/oecreview/Archive/11700-11718/ISSM-11713-11714.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11713-11714.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11713-11714.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11713) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11714) +@@ -32,7 +32,7 @@ + + /*If uf is NULL in input, f-set is nil, model is fully constrained, therefore converged from + * the get go: */ +- if(!uf){ ++ if(uf->M==0){ + *pconverged=true; + return; + } Index: /issm/oecreview/Archive/11700-11718/ISSM-11714-11715.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11714-11715.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11714-11715.diff (revision 11991) @@ -0,0 +1,20 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11714) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11715) +@@ -35,9 +35,12 @@ + #endif + + SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); +- _assert_(uf); +- _assert_(uf->vector); +- VecGetSize(uf->vector,&uf->M); ++ if(uf->vector == NULL){ ++ uf->M; ++ } ++ else{ ++ VecGetSize(uf->vector,&uf->M); ++ } + #else + _error_("not supported yet!"); + #endif Index: /issm/oecreview/Archive/11700-11718/ISSM-11715-11716.diff =================================================================== --- /issm/oecreview/Archive/11700-11718/ISSM-11715-11716.diff (revision 11991) +++ /issm/oecreview/Archive/11700-11718/ISSM-11715-11716.diff (revision 11991) @@ -0,0 +1,127 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11715) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11716) +@@ -285,7 +285,7 @@ + + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ +- outmatrix=NULL; ++ outmatrix=new Matrix(0,0); + } + else{ + +@@ -433,7 +433,7 @@ + + if(mxIsEmpty(dataref)){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ +- vector=NULL; ++ vector=new Vector(0); + } + else if (mxIsClass(dataref,"double") ){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp (revision 11715) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/WriteMatlabData.cpp (revision 11716) +@@ -113,7 +113,6 @@ + mxArray* dataref=NULL; + + if(vector){ +- + /*call toolkit routine: */ + dataref=vector->ToMatlabVector(); + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11715) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11716) +@@ -15,18 +15,21 @@ + + void Solverx(Vector** puf, Matrix* Kff, Vector* pf, Vector* uf0,Vector* df, Parameters* parameters){ + +- /*output: */ +- Vector* uf=NULL; +- uf=new Vector(); +- + /*Intermediary: */ + int analysis_type; + ++ /*output: */ ++ Vector *uf=new Vector(); ++ ++ /*In debugging mode, check that stiffness matrix and load vectors are not NULL (they can be empty)*/ ++ _assert_(Kff); ++ _assert_(pf); ++ + #ifdef _HAVE_PETSC_ + Vec uf0_vector = NULL; + Vec df_vector = NULL; +- if(uf0) uf0_vector=uf0->vector; +- if(df) df_vector = df->vector; ++ if(uf0) uf0_vector = uf0->vector; ++ if(df) df_vector = df->vector; + + /*In serial mode, the Petsc Options database has not been initialized properly: */ + #ifdef _SERIAL_ +@@ -36,7 +39,7 @@ + + SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); + if(uf->vector == NULL){ +- uf->M; ++ uf->M = 0; + } + else{ + VecGetSize(uf->vector,&uf->M); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToMatlabVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToMatlabVector.cpp (revision 11715) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToMatlabVector.cpp (revision 11716) +@@ -26,25 +26,28 @@ + + int PetscVectorToMatlabVector(mxArray** pdataref,Vec vector){ + ++ int i; ++ int rows; ++ int *idxm = NULL; ++ double *values = NULL; + +- int i; +- int rows; +- int* idxm=NULL; +- double* values=NULL; +- + /*output: */ + mxArray* dataref=NULL; + + /*Get size of vector: */ +- VecGetSize(vector,&rows); ++ if(vector){ ++ VecGetSize(vector,&rows); ++ if(rows){ ++ idxm=(int*)xmalloc(rows*sizeof(int)); ++ values=(double*)xmalloc(rows*sizeof(double)); ++ for(i=0;iFetchDataToInput(elements,BathymetryEnum); + iomodel->FetchDataToInput(elements,MaskElementonfloatingiceEnum); + iomodel->FetchDataToInput(elements,MaskElementonwaterEnum); +- iomodel->FetchDataToInput(elements,SurfaceforcingsPrecipitationEnum); + iomodel->FetchDataToInput(elements,SurfaceforcingsMassBalanceEnum); + iomodel->FetchDataToInput(elements,BasalforcingsMeltingRateEnum); + iomodel->FetchDataToInput(elements,BasalforcingsMeltingRateCorrectionEnum); Index: /issm/oecreview/Archive/11718-11730/ISSM-11719-11720.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11719-11720.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11719-11720.diff (revision 11991) @@ -0,0 +1,34 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11719) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Elements/Tria.cpp (revision 11720) +@@ -1872,7 +1872,7 @@ + } + this->inputs->AddInput(transientinput); + } +- else _error_("nodal vector is either numberofnodes (%i), or numberofnodes+1 long. Field provided is %i long",numberofvertices,M); ++ else _error_("nodal vector is either numberofnodes or numberofnodes+1 long. Field provided (%s) is %i long",EnumToStringx(vector_enum),M); + } + else if(vector_type==2){ //element vector + /*Are we in transient or static? */ +@@ -3667,7 +3667,7 @@ + // adjointy_input->GetInputValue(&mu, gauss); + // vx_input->GetInputValue(&vx,gauss); + // vy_input->GetInputValue(&vy,gauss); +- // grade_g[iv] = -2*drag*alpha_complement*(lambda*vx+mu*vy)/((double)connectivity[iv]); ++ // grade_g[iv] = -2*1.e+7*drag*alpha_complement*(lambda*vx+mu*vy)/((double)connectivity[iv]); + //} + /*End Analytical gradient*/ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 11719) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/objects.h (revision 11720) +@@ -29,6 +29,7 @@ + #include "./Gauss/GaussPenta.h" + + /*Loads: */ ++#include "./Loads/Load.h" + #include "./Loads/Friction.h" + #include "./Loads/Icefront.h" + #include "./Loads/Numericalflux.h" Index: /issm/oecreview/Archive/11718-11730/ISSM-11720-11721.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11720-11721.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11720-11721.diff (revision 11991) @@ -0,0 +1,35 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp (revision 11720) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp (revision 11721) +@@ -51,7 +51,16 @@ + + /*Initialize Petsc: */ + PetscInitializeNoArguments(); ++ #else ++ #ifdef _HAVE_MPI_ ++ int mp_init = 0; ++ MPI_Initialized(&mp_init); ++ if(!mp_init){ ++ MPI_Init(NULL,NULL); ++ } ++ #else ++ /*Do nothing*/ ++ #endif + #endif +- + return 1; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleEnd.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleEnd.cpp (revision 11720) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Matlab/ModuleEnd.cpp (revision 11721) +@@ -17,6 +17,8 @@ + PetscBeganMPI = PETSC_FALSE; + ierr=PetscFinalize();CHKERRQ(ierr); + } ++ #else ++ /*Do nothing*/ + #endif + + return 1; Index: /issm/oecreview/Archive/11718-11730/ISSM-11721-11722.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11721-11722.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11721-11722.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11721) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11722) +@@ -180,3 +180,6 @@ + + #android-ant + ANDROID_ANT_DIR="$ISSM_TIER/externalpackages/android-sdk/install-ant" ++ ++#gsl ++GSL_DIR="$ISSM_TIER/externalpackages/gsl/install" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11721) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11722) +@@ -244,3 +244,6 @@ + + #ANDROID_ANT + export PATH="$PATH:$ANDROID_ANT_DIR/" ++ ++#GSL ++export PATH="$PATH:$GSL_DIR/bin" Index: /issm/oecreview/Archive/11718-11730/ISSM-11722-11723.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11722-11723.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11722-11723.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 11722) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/mex/Makefile.am (revision 11723) +@@ -104,7 +104,7 @@ + endif + #}}} + #Flags and libraries {{{1 +-LDADD = $(TRIANGLELIB) ../c/libISSM.a $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(MEXLIB) ++LDADD = $(TRIANGLELIB) ../c/libISSM.a $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(SHAPELIBLIB) $(MEXLIB) $(GSLLIB) + + AM_LDFLAGS = $(MEXLINK) + Index: /issm/oecreview/Archive/11718-11730/ISSM-11723-11724.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11723-11724.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11723-11724.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 11723) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/issm.cpp (revision 11724) +@@ -40,7 +40,7 @@ + + MODULEBOOT(); + +- #if !defined(_PARALLEL_) || (defined(_PARALLEL_) && !defined(_HAVE_PETSC_)) ++ #ifndef _PARALLEL_ + _error_(" parallel executable was compiled without support of parallel libraries!"); + #endif + Index: /issm/oecreview/Archive/11718-11730/ISSM-11724-11725.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11724-11725.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11724-11725.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11724) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11725) +@@ -23,6 +23,7 @@ + double nKUoldF; + double nF; + double solver_residue,res; ++ int M; + + /*convergence options*/ + double eps_res; +@@ -32,7 +33,8 @@ + + /*If uf is NULL in input, f-set is nil, model is fully constrained, therefore converged from + * the get go: */ +- if(uf->M==0){ ++ uf->GetSize(&M); ++ if(M==0){ + *pconverged=true; + return; + } Index: /issm/oecreview/Archive/11718-11730/ISSM-11725-11726.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11725-11726.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11725-11726.diff (revision 11991) @@ -0,0 +1,138 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11725) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11726) +@@ -26,26 +26,30 @@ + _assert_(pf); + + #ifdef _HAVE_PETSC_ +- Vec uf0_vector = NULL; +- Vec df_vector = NULL; +- if(uf0) uf0_vector = uf0->vector; +- if(df) df_vector = df->vector; ++ Vec uf0_vector = NULL; ++ Vec df_vector = NULL; ++ if(uf0) uf0_vector = uf0->vector; ++ if(df) df_vector = df->vector; + +- /*In serial mode, the Petsc Options database has not been initialized properly: */ +- #ifdef _SERIAL_ +- parameters->FindParam(&analysis_type,AnalysisTypeEnum); +- PetscOptionsFromAnalysis(parameters,analysis_type); +- #endif ++ /*In serial mode, the Petsc Options database has not been initialized properly: */ ++ #ifdef _SERIAL_ ++ parameters->FindParam(&analysis_type,AnalysisTypeEnum); ++ PetscOptionsFromAnalysis(parameters,analysis_type); ++ #endif + +- SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); +- if(uf->vector == NULL){ +- uf->M = 0; +- } +- else{ +- VecGetSize(uf->vector,&uf->M); +- } ++ SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); ++ if(uf->vector == NULL){ ++ uf->M = 0; ++ } ++ else{ ++ VecGetSize(uf->vector,&uf->M); ++ } + #else +- _error_("not supported yet!"); ++ #ifdef _HAVE_GSL_ ++ SolverxGsl(&uf->vector,Kff->matrix,pf->vector); ++ #else ++ _error_("not supported yet!"); ++ #endif + #endif + + /*Assign output pointers: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h (revision 11725) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.h (revision 11726) +@@ -21,5 +21,9 @@ + void DofTypesToIndexSet(IS* pisv, IS* pisp, Vec df,int typeenum); + #endif + ++#ifdef _HAVE_GSL_ ++void SolverxGsl(SeqVec** puf,SeqMat* Kff, SeqVec* pf); ++#endif ++ + #endif /* _SOLVERX_H */ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp (revision 11726) +@@ -0,0 +1,67 @@ ++/*!\file SolverxGsl ++ * \brief Gsl implementation of solver ++ */ ++ ++#include "./Solverx.h" ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++#include "../../io/io.h" ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++ ++void SolverxGsl(SeqVec** puf,SeqMat* Kff, SeqVec* pf){ ++ ++ /*intermediary: */ ++ SeqMat* KffCopy=NULL; ++ ++ /*Output: */ ++ SeqVec* uf = NULL; ++ ++ /*We are going to do an in place LU decomp, so we need to save the matrix with its original structure: */ ++ KffCopy=Kff->Duplicate(); ++ ++ /*GSL Matrices and vectors: */ ++ gsl_matrix_view m; ++ gsl_vector_view b; ++ gsl_vector* x=NULL; ++ gsl_permutation* p=NULL; ++ ++ /*Intermediary: */ ++ int M,N,N2,s; ++ ++ Kff->GetSize(&M,&N); ++ pf->GetSize(&N2); ++ ++ if(N!=N2)_error_("Right hand side vector of size %i, when matrix is of size %i-%i !",N2,M,N); ++ if(M!=N)_error_("Stiffness matrix should be square!"); ++ ++ /*Initialize gsl matrices and vectors: */ ++ m = gsl_matrix_view_array (KffCopy->matrix, M, N); ++ b = gsl_vector_view_array (pf->vector, N); ++ x = gsl_vector_alloc (N); ++ ++ /*Run LU and solve: */ ++ p = gsl_permutation_alloc (N); ++ gsl_linalg_LU_decomp (&m.matrix, p, &s); ++ gsl_linalg_LU_solve (&m.matrix, p, &b.vector, x); ++ ++ //printf ("x = \n"); ++ //gsl_vector_fprintf (stdout, x, "%g"); ++ ++ /*Get uf initialized with the results: */ ++ uf=new SeqVec(gsl_vector_ptr(x,0),M); ++ ++ /*Free resources:*/ ++ gsl_permutation_free (p); ++ gsl_vector_free (x); ++ delete KffCopy; ++ ++ /*Assign output pointers:*/ ++ *puf=uf; ++} Index: /issm/oecreview/Archive/11718-11730/ISSM-11726-11727.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11726-11727.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11726-11727.diff (revision 11991) @@ -0,0 +1,38 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ispetsc.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ispetsc.m (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/utils/OS/ispetsc.m (revision 11727) +@@ -0,0 +1,33 @@ ++function flag=ispetsc() ++%ISPETSC - figure out if PETSC package was compiled with ISSM ++% ++% Usage: ++% flag=ispetsc(); ++ ++ ++configfile=[issmtier() '/bin/config.h']; %should find it in the install target ++if ~exist(configfile,'file'), ++ error(['File ' configfile ' not found. ISSM has not been configured yet!']); ++end ++ ++%go through the file, and recover the line we want ++flag=2; ++fid=fopen(configfile,'r'); ++if(fid==-1), error(['could not open file: ' configfile]); end ++ ++while(true), ++ tline=fgets(fid); ++ if ~ischar(tline), break, end ++ if strncmp(tline,'/* #undef _HAVE_PETSC_ */',25), ++ flag=0; ++ break; ++ end ++ if strncmp(tline,'#define _HAVE_PETSC_',20), ++ flag=1; ++ break; ++ end ++end ++fclose(fid); ++if flag==2, ++ error('could not determine whether PETSC was or was not compiled'); ++end Index: /issm/oecreview/Archive/11718-11730/ISSM-11727-11728.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11727-11728.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11727-11728.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/petscversion.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/petscversion.m (revision 11727) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/petscversion.m (revision 11728) +@@ -4,6 +4,8 @@ + % Usage: + % PETSC_VERSION=petscversion(); + ++%default ++PETSC_VERSION=3; + + configfile=[issmtier() '/config.h']; + if ~exist(configfile,'file'), Index: /issm/oecreview/Archive/11718-11730/ISSM-11728-11729.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11728-11729.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11728-11729.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/solveparallel.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/solveparallel.m (revision 11728) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/solveparallel.m (revision 11729) +@@ -11,6 +11,12 @@ + md=loadresultsfromcluster(md); + else + ++ %In parallel mode, we need to make sure we have PETSC support, otherwise, we run with only one cpu: ++ if ~ispetsc, ++ disp('PETSC support not included, running on 1 cpu only!'); ++ cluster.np=1; ++ end ++ + %First, build a runtime name that is unique, that we will use to create + %directories, name jobs, etc ... + c=clock; md.private.runtimename=sprintf('%s-%02i-%02i-%04i-%02i-%02i-%02i-%i',md.miscellaneous.name,c(2),c(3),c(1),c(4),c(5),floor(c(6)),feature('GetPid')); Index: /issm/oecreview/Archive/11718-11730/ISSM-11729-11730.diff =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-11729-11730.diff (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-11729-11730.diff (revision 11991) @@ -0,0 +1,28 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11729) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/shared/Alloc/alloc.cpp (revision 11730) +@@ -90,8 +90,10 @@ + #else + /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ + * correctly: */ +- MatFree(&(*pv)->matrix); ++ #ifdef _HAVE_PETSC_ ++ MatFree(&(*pv)->matrix); + #endif ++ #endif + *pv=NULL; + } + } +@@ -107,8 +109,10 @@ + #else + /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ + * correctly: */ +- VecFree(&(*pv)->vector); ++ #ifdef _HAVE_PETSC_ ++ VecFree(&(*pv)->vector); + #endif ++ #endif + *pv=NULL; + } + } Index: /issm/oecreview/Archive/11718-11730/ISSM-DocReview-11718-11730.tex =================================================================== --- /issm/oecreview/Archive/11718-11730/ISSM-DocReview-11718-11730.tex (revision 11991) +++ /issm/oecreview/Archive/11718-11730/ISSM-DocReview-11718-11730.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11718-11730/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11718-11730/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11718-11730/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11718-11730 Index: /issm/oecreview/Archive/11718-11730/Makefile =================================================================== --- /issm/oecreview/Archive/11718-11730/Makefile (revision 11991) +++ /issm/oecreview/Archive/11718-11730/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11718-11730 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11718-11730/log.tex =================================================================== --- /issm/oecreview/Archive/11718-11730/log.tex (revision 11991) +++ /issm/oecreview/Archive/11718-11730/log.tex (revision 11991) @@ -0,0 +1,24 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11718-11719.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/android-sdk/install.sh \\ Export determination: 6. \\Rationale: Modified the install.sh script of Android-SDK +M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp Precipitation not needed for prognostic \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11719-11720.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp \\ Export determination: 6. \\Rationale: Precipitation not needed for prognostic +M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/objects.h Better error message if input does not have the right length \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11720-11721.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Elements/Tria.cpp M /issm/trunk-jpl/src/c/objects/objects.h \\ Export determination: 6. \\Rationale: Better error message if input does not have the right length +M /issm/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp M /issm/trunk-jpl/src/c/shared/Matlab/ModuleEnd.cpp Live without Petsc \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11721-11722.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Matlab/ModuleBoot.cpp M /issm/trunk-jpl/src/c/shared/Matlab/ModuleEnd.cpp \\ Export determination: 6. \\Rationale: Live without Petsc +M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh Add GSL support \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11722-11723.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh \\ Export determination: 6. \\Rationale: Add GSL support +M /issm/trunk-jpl/src/mex/Makefile.am Add GSL support \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11723-11724.diff: \\ Function name: \\M /issm/trunk-jpl/src/mex/Makefile.am \\ Export determination: 6. \\Rationale: Add GSL support +M /issm/trunk-jpl/src/c/solutions/issm.cpp Broader definition of when issm should run in parallel. \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11724-11725.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/solutions/issm.cpp \\ Export determination: 6. \\Rationale: Broader definition of when issm should run in parallel. +M /issm/trunk-jpl/src/c/solutions/convergence.cpp Shield some potentially dangerous API dependency \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11725-11726.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/solutions/convergence.cpp \\ Export determination: 6. \\Rationale: Shield some potentially dangerous API dependency +M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.h A /issm/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp Added GSL solver \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11726-11727.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.h A /issm/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp \\ Export determination: 6. \\Rationale: Added GSL solver +A /issm/trunk-jpl/src/m/utils/OS/ispetsc.m Detect petsc compilation in config.h \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11727-11728.diff: \\ Function name: \\A /issm/trunk-jpl/src/m/utils/OS/ispetsc.m \\ Export determination: 6. \\Rationale: Detect petsc compilation in config.h +M /issm/trunk-jpl/src/m/model/petscversion.m Added a default petsc version \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11728-11729.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/petscversion.m \\ Export determination: 6. \\Rationale: Added a default petsc version +M /issm/trunk-jpl/src/m/model/solveparallel.m Detect presence of petsc for solving in parallel. Otherwise, run with 1 cpu only \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11729-11730.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/solveparallel.m \\ Export determination: 6. \\Rationale: Detect presence of petsc for solving in parallel. Otherwise, run with 1 cpu only +M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp Avoid potential API issue when Petsc is absent \\\\ Index: /issm/oecreview/Archive/11718-11730/r1.tex =================================================================== --- /issm/oecreview/Archive/11718-11730/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11718-11730/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11718 Index: /issm/oecreview/Archive/11718-11730/r2.tex =================================================================== --- /issm/oecreview/Archive/11718-11730/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11718-11730/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11730 Index: /issm/oecreview/Archive/11730-11748/Date.tex =================================================================== --- /issm/oecreview/Archive/11730-11748/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11730-11748/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11730-11748/ISSM-11730-11731.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11730-11731.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11730-11731.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11730) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour.sh (revision 11731) +@@ -12,7 +12,6 @@ + --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ + --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ + --with-fortran-lib="/usr/local/lib/libgfortran.a" \ +- --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ + --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ +@@ -25,3 +24,4 @@ + --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ ++ #--with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ Index: /issm/oecreview/Archive/11730-11748/ISSM-11731-11732.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11731-11732.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11731-11732.diff (revision 11991) @@ -0,0 +1,39 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 11732) +@@ -0,0 +1,28 @@ ++#!/bin/sh ++ ++#petsc 3.2 ++#mpich 1.4 ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ ++ --with-fortran-lib="/usr/local/lib/libgfortran.a" \ ++ --with-math-lib="/usr/lib/libm.dylib" \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ ++ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ ++ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ ++ --with-numthreads=8 \ ++ --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install ++# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++# --with-petsc-arch=$ISSM_ARCH \ ++# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ ++# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ ++# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11730-11748/ISSM-11732-11733.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11732-11733.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11732-11733.diff (revision 11991) @@ -0,0 +1,699 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp (revision 11732) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp (revision 11733) +@@ -79,8 +79,13 @@ + if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); + + /*allocate and memcpy*/ +- vector=(double*)xmalloc(rows*sizeof(double)); +- memcpy(vector,mxvector_ptr,rows*sizeof(double)); ++ if(rows){ ++ vector=(double*)xmalloc(rows*sizeof(double)); ++ memcpy(vector,mxvector_ptr,rows*sizeof(double)); ++ } ++ else{ ++ vector=NULL; ++ } + } + + /*Assign output pointer: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 11733) +@@ -0,0 +1,62 @@ ++/*!\file: SeqMat.h ++ * \brief wrapper to SeqMat objects, which are just wrappers to a simple double* buffer. ++ */ ++ ++#ifndef _SEQMAT_H_ ++#define _SEQMAT_H_ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../toolkitsenums.h" ++ ++#ifdef _SERIAL_ ++#include "mex.h" ++#endif ++ ++/*}}}*/ ++class SeqVec; ++ ++class SeqMat{ ++ ++ public: ++ ++ int M,N; ++ double* matrix; ++ ++ /*SeqMat constructors, destructors {{{1*/ ++ SeqMat(); ++ SeqMat(int M,int N); ++ SeqMat(int M,int N,double sparsity); ++ SeqMat(double* serial_mat,int M,int N,double sparsity); ++ SeqMat(int M,int N,int connectivity,int numberofdofspernode); ++ ~SeqMat(); ++ /*}}}*/ ++ /*SeqMat specific routines {{{1*/ ++ void Echo(void); ++ #ifdef _SERIAL_ ++ mxArray* ToMatlabMatrix(void); ++ #endif ++ void Assemble(void); ++ double Norm(NormMode norm_type); ++ void GetSize(int* pM,int* pN); ++ void GetLocalSize(int* pM,int* pN); ++ void MatMult(SeqVec* X,SeqVec* AX); ++ SeqMat* Duplicate(void); ++ double* ToSerial(void); ++ void SetValues(int m,int* idxm,int n,int* idxn,double* values,InsMode mode); ++ /*}}}*/ ++ ++}; ++ ++/*API :*/ ++#ifdef _SERIAL_ ++SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); ++#endif ++ ++#endif //#ifndef _SEQMAT_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp (revision 11733) +@@ -0,0 +1,269 @@ ++/*!\file SeqVec.cpp ++ * \brief: implementation of the SeqVec object ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../toolkits.h" ++#include "../../shared/shared.h" ++ ++/*}}}*/ ++ ++/*SeqVec constructors and destructor*/ ++/*FUNCTION SeqVec::SeqVec(){{{1*/ ++SeqVec::SeqVec(){ ++ ++ this->M=0; ++ this->vector=NULL; ++} ++/*}}}*/ ++/*FUNCTION SeqVec::SeqVec(int M,bool fromlocalsize){{{1*/ ++SeqVec::SeqVec(int pM,bool fromlocalsize){ ++ ++ this->M=pM; ++ if(this->M) this->vector=(double*)xcalloc(pM,sizeof(double)); ++ else this->vector=NULL; ++} ++/*}}}*/ ++/*FUNCTION SeqVec::SeqVec(double* serial_vec,int M){{{1*/ ++SeqVec::SeqVec(double* buffer,int pM){ ++ ++ int i,j; ++ ++ this->M=pM; ++ this->vector=(double*)xcalloc(pM,sizeof(double)); ++ memcpy(this->vector,buffer,pM*sizeof(double)); ++} ++/*}}}*/ ++ /*FUNCTION SeqVec::~SeqVec(){{{1*/ ++SeqVec::~SeqVec(){ ++ xfree((void**)&this->vector); ++ M=0; ++} ++/*}}}*/ ++ ++/*SeqVec specific routines: */ ++/*FUNCTION SeqVec::Echo{{{1*/ ++void SeqVec::Echo(void){ ++ ++ int i; ++ printf("SeqVec size %i\n",this->M); ++ for(i=0;iM*sizeof(double)); ++ memcpy(buffer,vector,M*sizeof(double)); ++ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(dataref,this->M); ++ mxSetN(dataref,1); ++ mxSetPr(dataref,buffer); ++ ++ ++ /*do not erase buffer!: */ ++ return dataref; ++ ++} ++/*}}}*/ ++/*FUNCTION MatlabVectorToSeqVec{{{1*/ ++SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ ++ ++ SeqVec* output=NULL; ++ ++ output=new SeqVec(); ++ MatlabVectorToDoubleVector(&output->vector,&output->M,dataref); ++ return output; ++ ++} ++/*}}}*/ ++#endif ++/*FUNCTION SeqVec::Assemble{{{1*/ ++void SeqVec::Assemble(void){ ++ ++ /*do nothing*/ ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::SetValues{{{1*/ ++void SeqVec::SetValues(int ssize, int* list, double* values, InsMode mode){ ++ ++ int i; ++ switch(mode){ ++ case ADD_VAL: ++ for(i=0;ivector[list[i]]+=values[i]; ++ break; ++ case INS_VAL: ++ for(i=0;ivector[list[i]]=values[i]; ++ break; ++ default: ++ _error_("unknown insert mode!"); ++ break; ++ } ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::SetValue{{{1*/ ++void SeqVec::SetValue(int dof, double value, InsMode mode){ ++ ++ switch(mode){ ++ case ADD_VAL: ++ this->vector[dof]+=value; ++ break; ++ case INS_VAL: ++ this->vector[dof]=value; ++ break; ++ default: ++ _error_("unknown insert mode!"); ++ break; ++ } ++} ++/*}}}*/ ++/*FUNCTION SeqVec::GetValue{{{1*/ ++void SeqVec::GetValue(double* pvalue,int dof){ ++ ++ *pvalue=this->vector[dof]; ++ ++} ++/*}}}*/ ++ ++/*FUNCTION SeqVec::GetSize{{{1*/ ++void SeqVec::GetSize(int* pM){ ++ ++ *pM=this->M; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::GetLocalSize{{{1*/ ++void SeqVec::GetLocalSize(int* pM){ ++ ++ *pM=this->M; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::Duplicate{{{1*/ ++SeqVec* SeqVec::Duplicate(void){ ++ ++ return new SeqVec(this->vector,this->M); ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::Set{{{1*/ ++void SeqVec::Set(double value){ ++ ++ int i; ++ for(i=0;iM;i++)this->vector[i]=value; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::AXPY{{{1*/ ++void SeqVec::AXPY(SeqVec* X, double a){ ++ ++ int i; ++ ++ /*y=a*x+y where this->vector is y*/ ++ for(i=0;iM;i++)this->vector[i]=a*X->vector[i]+this->vector[i]; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::AYPX{{{1*/ ++void SeqVec::AYPX(SeqVec* X, double a){ ++ ++ int i; ++ ++ /*y=x+a*y where this->vector is y*/ ++ for(i=0;iM;i++)this->vector[i]=X->vector[i]+a*this->vector[i]; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::ToMPISerial{{{1*/ ++double* SeqVec::ToMPISerial(void){ ++ ++ double* buffer=NULL; ++ ++ if(this->M){ ++ buffer=(double*)xmalloc(this->M*sizeof(double)); ++ memcpy(buffer,this->vector,this->M*sizeof(double)); ++ } ++ return buffer; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::Copy{{{1*/ ++void SeqVec::Copy(SeqVec* to){ ++ ++ int i; ++ ++ to->M=this->M; ++ for(i=0;iM;i++)to->vector[i]=this->vector[i]; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::Norm{{{1*/ ++double SeqVec::Norm(NormMode mode){ ++ ++ double norm; ++ int i; ++ ++ switch(mode){ ++ case NORM_INF: ++ norm=0; for(i=0;iM;i++)norm=fmax(norm,fabs(this->vector[i])); ++ return norm; ++ break; ++ case NORM_TWO: ++ norm=0; ++ for(i=0;iM;i++)norm+=pow(this->vector[i],2); ++ return sqrt(norm); ++ break; ++ default: ++ _error_("unknown norm !"); ++ break; ++ } ++} ++/*}}}*/ ++/*FUNCTION SeqVec::Scale{{{1*/ ++void SeqVec::Scale(double scale_factor){ ++ ++ int i; ++ for(i=0;iM;i++)this->vector[i]=scale_factor*this->vector[i]; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::Dot{{{1*/ ++double SeqVec::Dot(SeqVec* input){ ++ ++ int i; ++ ++ double dot=0; ++ for(i=0;iM;i++)dot+=this->vector[i]*input->vector[i]; ++ return dot; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqVec::PointwiseDivide{{{1*/ ++void SeqVec::PointwiseDivide(SeqVec* x,SeqVec* y){ ++ ++ int i; ++ /*pointwise w=x/y where this->vector is w: */ ++ for(i=0;iM;i++)this->vector[i]=x->vector[i]/y->vector[i]; ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/issmtoolkit.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/issmtoolkit.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/issmtoolkit.h (revision 11733) +@@ -0,0 +1,11 @@ ++/* \file issmtoolkit.h ++ * \brief all includes for MPI layer ++ */ ++ ++#ifndef _ISSM_TOOLKIT_H_ ++#define _ISSM_TOOLKIT_H_ ++ ++#include "./SeqMat.h" ++#include "./SeqVec.h" ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp (revision 11733) +@@ -0,0 +1,234 @@ ++/*!\file SeqMat.cpp ++ * \brief: implementation of the SeqMat object ++ */ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../toolkits.h" ++#include "../../shared/shared.h" ++ ++/*}}}*/ ++ ++/*SeqMat constructors and destructor*/ ++/*FUNCTION SeqMat::SeqMat(){{{1*/ ++SeqMat::SeqMat(){ ++ ++ this->M=0; ++ this->N=0; ++ this->matrix=NULL; ++} ++/*}}}*/ ++/*FUNCTION SeqMat::SeqMat(int M,int N){{{1*/ ++SeqMat::SeqMat(int pM,int pN){ ++ ++ this->M=pM; ++ this->N=pN; ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++} ++/*}}}*/ ++/*FUNCTION SeqMat::SeqMat(int M,int N, double sparsity){{{1*/ ++SeqMat::SeqMat(int pM,int pN, double sparsity){ ++ ++ this->M=pM; ++ this->N=pN; ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++} ++/*}}}*/ ++/*FUNCTION SeqMat(double* serial_mat,int M,int N,double sparsity){{{1*/ ++SeqMat::SeqMat(double* serial_mat,int pM,int pN,double sparsity){ ++ ++ int i,j; ++ ++ this->M=pM; ++ this->N=pN; ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ memcpy(this->matrix,serial_mat,pM*pN*sizeof(double)); ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::SeqMat(int M,int N, int connectivity, int numberofdofspernode){{{1*/ ++SeqMat::SeqMat(int pM,int pN, int connectivity,int numberofdofspernode){ ++ ++ this->M=pM; ++ this->N=pN; ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++} ++/*}}}*/ ++/*FUNCTION SeqMat::~SeqMat(){{{1*/ ++SeqMat::~SeqMat(){ ++ ++ xfree((void**)&this->matrix); ++ M=0; ++ N=0; ++} ++/*}}}*/ ++ ++/*SeqMat specific routines: */ ++/*FUNCTION SeqMat::Echo{{{1*/ ++void SeqMat::Echo(void){ ++ ++ int i,j; ++ printf("SeqMat size %i-%i\n",this->M,this->N); ++ for(i=0;imatrix[N*i+j]); ++ } ++ printf("\n"); ++ } ++} ++/*}}}*/ ++ ++#ifdef _SERIAL_ ++/*FUNCTION SeqMat::ToMatlabMatrix{{{1*/ ++mxArray* SeqMat::ToMatlabMatrix(void){ ++ ++ double* buffer=NULL; ++ ++ mxArray* dataref=NULL; ++ ++ /*copy vector into a new buffer: */ ++ buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); ++ memcpy(buffer,this->matrix,M*N*sizeof(double)); ++ ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(dataref,this->M); ++ mxSetN(dataref,this->N); ++ mxSetPr(dataref,buffer); ++ ++ ++ /*do not erase buffer!: */ ++ return dataref; ++ ++} ++/*}}}*/ ++/*FUNCTION MatlabMatrixToSeqMat{{{1*/ ++SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ ++ ++ SeqMat* output=NULL; ++ ++ output=new SeqMat(); ++ MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); ++ return output; ++ ++} ++/*}}}*/ ++#endif ++/*FUNCTION SeqMat::Assemble{{{1*/ ++void SeqMat::Assemble(void){ ++ ++ /*do nothing*/ ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::Norm{{{1*/ ++double SeqMat::Norm(NormMode mode){ ++ ++ double norm; ++ double absolute; ++ int i,j; ++ ++ switch(mode){ ++ case NORM_INF: ++ norm=0; ++ for(i=0;iM;i++){ ++ absolute=0; ++ for(j=0;jN;j++){ ++ absolute+=fabs(this->matrix[N*i+j]); ++ } ++ norm=max(norm,absolute); ++ } ++ return norm; ++ break; ++ default: ++ _error_("unknown norm !"); ++ break; ++ } ++} ++/*}}}*/ ++/*FUNCTION SeqMat::GetSize{{{1*/ ++void SeqMat::GetSize(int* pM,int* pN){ ++ ++ *pM=this->M; ++ *pN=this->N; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::GetLocalSize{{{1*/ ++void SeqMat::GetLocalSize(int* pM,int* pN){ ++ ++ *pM=this->M; ++ *pN=this->N; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::MatMult{{{1*/ ++void SeqMat::MatMult(SeqVec* X,SeqVec* AX){ ++ ++ int i,j; ++ int XM,AXM; ++ double dummy; ++ ++ X->GetSize(&XM); ++ AX->GetSize(&AXM); ++ ++ if(M!=AXM)_error_("A and AX should have the same number of rows!"); ++ if(N!=XM)_error_("A and X should have the same number of columns!"); ++ ++ for(i=0;imatrix[N*i+j]*X->vector[j]; ++ } ++ AX->vector[i]=dummy; ++ } ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::Duplicate{{{1*/ ++SeqMat* SeqMat::Duplicate(void){ ++ ++ double dummy=0; ++ ++ return new SeqMat(this->matrix,this->M,this->N,dummy); ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::ToSerial{{{1*/ ++double* SeqMat::ToSerial(void){ ++ ++ double* buffer=NULL; ++ ++ if(this->M*this->N){ ++ buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); ++ memcpy(buffer,this->matrix,this->M*this->N*sizeof(double)); ++ } ++ return buffer; ++ ++} ++/*}}}*/ ++/*FUNCTION SeqMat::SetValues{{{1*/ ++void SeqMat::SetValues(int m,int* idxm,int n,int* idxn,double* values,InsMode mode){ ++ ++ int i,j; ++ switch(mode){ ++ case ADD_VAL: ++ for(i=0;imatrix[N*idxm[i]+idxn[j]]+=values[n*i+j]; ++ break; ++ case INS_VAL: ++ for(i=0;imatrix[N*idxm[i]+idxn[j]]=values[n*i+j]; ++ break; ++ default: ++ _error_("unknown insert mode!"); ++ break; ++ } ++ ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 11733) +@@ -0,0 +1,67 @@ ++/*!\file: SeqVec.h ++ * \brief wrapper to our SeqVec object, which is just a wrapper to a double* ++ */ ++ ++#ifndef _SEQVEC_H_ ++#define _SEQVEC_H_ ++ ++/*Headers:*/ ++/*{{{1*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../toolkitsenums.h" ++ ++#ifdef _SERIAL_ ++#include "mex.h" ++#endif ++ ++/*}}}*/ ++ ++class SeqVec{ ++ ++ public: ++ ++ double* vector; ++ int M; ++ ++ /*SeqVec constructors, destructors {{{1*/ ++ SeqVec(); ++ SeqVec(int M,bool fromlocalsize=false); ++ SeqVec(double* buffer, int M); ++ ~SeqVec(); ++ /*}}}*/ ++ /*SeqVec specific routines {{{1*/ ++ void Echo(void); ++ #ifdef _SERIAL_ ++ mxArray* ToMatlabVector(void); ++ #endif ++ void Assemble(void); ++ void SetValues(int ssize, int* list, double* values, InsMode mode); ++ void SetValue(int dof, double value, InsMode mode); ++ void GetValue(double* pvalue, int dof); ++ void GetSize(int* pM); ++ void GetLocalSize(int* pM); ++ SeqVec* Duplicate(void); ++ void Set(double value); ++ void AXPY(SeqVec* X, double a); ++ void AYPX(SeqVec* X, double a); ++ double* ToMPISerial(void); ++ void Copy(SeqVec* to); ++ double Norm(NormMode norm_type); ++ void Scale(double scale_factor); ++ void PointwiseDivide(SeqVec* x,SeqVec* y); ++ double Dot(SeqVec* vector); ++ /*}}}*/ ++}; ++ ++ ++/*API :*/ ++#ifdef _SERIAL_ ++SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); ++#endif ++ ++#endif //#ifndef _SEQVEC_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 11732) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/toolkits.h (revision 11733) +@@ -21,5 +21,6 @@ + #include "./matlab/matlabincludes.h" + #include "./double/double.h" + #include "./toolkitsenums.h" ++#include "./issm/issmtoolkit.h" + + #endif Index: /issm/oecreview/Archive/11730-11748/ISSM-11733-11734.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11733-11734.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11733-11734.diff (revision 11991) @@ -0,0 +1,712 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp (revision 11733) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp (revision 11734) +@@ -259,47 +259,43 @@ + /*In debugging mode, check consistency (no NaN, and values not too big)*/ + this->CheckConsistency(); + +- #ifdef _HAVE_PETSC_ +- if(this->dofsymmetrical){ +- /*only use row dofs to add values into global matrices: */ +- +- if(this->row_fsize){ +- /*first, retrieve values that are in the f-set from the g-set values matrix: */ +- localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); +- for(i=0;irow_fsize;i++){ +- for(j=0;jrow_fsize;j++){ +- *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); +- } +- } +- /*add local values into global matrix, using the fglobaldoflist: */ +- MatSetValues(Kff->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); ++ if(this->dofsymmetrical){ ++ /*only use row dofs to add values into global matrices: */ + +- /*Free ressources:*/ +- xfree((void**)&localvalues); ++ if(this->row_fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values matrix: */ ++ localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); ++ for(i=0;irow_fsize;i++){ ++ for(j=0;jrow_fsize;j++){ ++ *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); ++ } + } ++ /*add local values into global matrix, using the fglobaldoflist: */ ++ Kff->SetValues(this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,localvalues,ADD_VAL); + ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); ++ } + +- if((this->row_ssize!=0) && (this->row_fsize!=0)){ +- /*first, retrieve values that are in the f and s-set from the g-set values matrix: */ +- localvalues=(double*)xmalloc(this->row_fsize*this->row_ssize*sizeof(double)); +- for(i=0;irow_fsize;i++){ +- for(j=0;jrow_ssize;j++){ +- *(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]); +- } +- } +- /*add local values into global matrix, using the fglobaldoflist: */ +- MatSetValues(Kfs->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,(const double*)localvalues,ADD_VALUES); + +- /*Free ressources:*/ +- xfree((void**)&localvalues); ++ if((this->row_ssize!=0) && (this->row_fsize!=0)){ ++ /*first, retrieve values that are in the f and s-set from the g-set values matrix: */ ++ localvalues=(double*)xmalloc(this->row_fsize*this->row_ssize*sizeof(double)); ++ for(i=0;irow_fsize;i++){ ++ for(j=0;jrow_ssize;j++){ ++ *(localvalues+this->row_ssize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_slocaldoflist[j]); ++ } + } ++ /*add local values into global matrix, using the fglobaldoflist: */ ++ Kfs->SetValues(this->row_fsize,this->row_fglobaldoflist,this->row_ssize,this->row_sglobaldoflist,localvalues,ADD_VAL); ++ ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- else{ +- _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); +- } +- #else +- _error_("not supported yet!"); +- #endif ++ } ++ else{ ++ _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); ++ } + + } + /*}}}*/ +@@ -315,33 +311,29 @@ + /*In debugging mode, check consistency (no NaN, and values not too big)*/ + this->CheckConsistency(); + +- #ifdef _HAVE_PETSC_ +- if(this->dofsymmetrical){ +- /*only use row dofs to add values into global matrices: */ ++ if(this->dofsymmetrical){ ++ /*only use row dofs to add values into global matrices: */ + +- if(this->row_fsize){ +- /*first, retrieve values that are in the f-set from the g-set values matrix: */ +- localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); +- for(i=0;irow_fsize;i++){ +- for(j=0;jrow_fsize;j++){ +- *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); +- } ++ if(this->row_fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values matrix: */ ++ localvalues=(double*)xmalloc(this->row_fsize*this->row_fsize*sizeof(double)); ++ for(i=0;irow_fsize;i++){ ++ for(j=0;jrow_fsize;j++){ ++ *(localvalues+this->row_fsize*i+j)=*(this->values+this->ncols*this->row_flocaldoflist[i]+this->row_flocaldoflist[j]); + } +- /*add local values into global matrix, using the fglobaldoflist: */ +- MatSetValues(Jff->matrix,this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,(const double*)localvalues,ADD_VALUES); +- +- /*Free ressources:*/ +- xfree((void**)&localvalues); + } ++ /*add local values into global matrix, using the fglobaldoflist: */ ++ Jff->SetValues(this->row_fsize,this->row_fglobaldoflist,this->row_fsize,this->row_fglobaldoflist,localvalues,ADD_VAL); + ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); + } +- else{ +- _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); +- } +- #else +- _error_("not supported yet!"); +- #endif + ++ } ++ else{ ++ _error_(" non dofsymmetrical matrix AddToGlobal routine not support yet!"); ++ } ++ + } + /*}}}*/ + /*FUNCTION ElementMatrix::CheckConsistency{{{1*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11733) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11734) +@@ -24,7 +24,6 @@ + /*FUNCTION Vector::Vector(){{{1*/ + Vector::Vector(){ + +- this->M=0; + #ifdef _HAVE_PETSC_ + this->vector=NULL; + #else +@@ -41,8 +40,7 @@ + #ifdef _HAVE_PETSC_ + this->vector=NewVec(pM,fromlocalsize); + #else +- this->M=pM; +- this->vector=(double*)xcalloc(pM,sizeof(double)); ++ this->vector=new SeqVec(pM,fromlocalsize); + #endif + #ifdef _HAVE_ADOLC_ + this->avector=(adouble*)xmalloc(pM*sizeof(adouble)); +@@ -50,14 +48,14 @@ + } + /*}}}*/ + /*FUNCTION Vector::Vector(double* serial_vec,int M){{{1*/ +-Vector::Vector(double* serial_vec,int pM){ ++Vector::Vector(double* serial_vec,int M){ + + int i,j; + + #ifdef _HAVE_PETSC_ + int* idxm=NULL; + +- this->vector=NewVec(pM); ++ this->vector=NewVec(M); + + idxm=(int*)xmalloc(M*sizeof(int)); + for(i=0;iM=pM; +- this->vector=(double*)xcalloc(pM,sizeof(double)); ++ this->vector=new SeqVec(serial_vec,M); + #endif + #ifdef _HAVE_ADOLC_ +- this->avector=(adouble*)xmalloc(pM*sizeof(adouble)); ++ this->avector=(adouble*)xmalloc(M*sizeof(adouble)); + #endif + } + /*}}}*/ +@@ -81,9 +78,6 @@ + /*FUNCTION Vector::Vector(Vec petsc_vec){{{1*/ + Vector::Vector(Vec petsc_vec){ + +- /*Get Vector size*/ +- VecGetSize(petsc_vec,&this->M); +- + /*copy vector*/ + VecDuplicate(petsc_vec,&this->vector); + VecCopy(petsc_vec,this->vector); +@@ -97,7 +91,7 @@ + #ifdef _HAVE_PETSC_ + VecFree(&this->vector); + #else +- xfree((void**)&this->vector); ++ delete this->vector; + #endif + #ifdef _HAVE_ADOLC_ + xfree((void**)&this->avector); +@@ -114,18 +108,11 @@ + #ifdef _HAVE_PETSC_ + VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); + #else +- printf("Vector size: %i\n",M); +- for(i=0;ivector->Echo(); + #endif + + #ifdef _HAVE_ADOLC_ +- /*Not sure about that one. Should we use the overloaded operator >>?*/ +- printf("ADOLC Vector equivalent:" ); +- for(i=0;ivector); + #else +- _error_("not implemented yet!"); ++ dataref=this->vector->ToMatlabVector(); + #endif + return dataref; + + } + /*}}}*/ ++/*FUNCTION MatlabVectorToVector{{{1*/ ++Vector* MatlabVectorToVector(const mxArray* mxvector){ ++ ++ int dummy; ++ Vector* vector=NULL; ++ ++ /*allocate vector object: */ ++ vector=new Vector(); ++ ++ #ifdef _HAVE_PETSC_ ++ MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); ++ #else ++ vector->vector=MatlabVectorToSeqVec(mxvector); ++ #endif ++ ++ return vector; ++} ++/*}}}*/ + #endif + /*FUNCTION Vector::Assemble{{{1*/ + void Vector::Assemble(void){ +@@ -153,7 +158,7 @@ + VecAssemblyBegin(this->vector); + VecAssemblyEnd(this->vector); + #else +- /*do nothing*/ ++ this->vector->Assemble(); + #endif + + } +@@ -166,7 +171,7 @@ + _assert_(this->vector); + VecSetValues(this->vector,ssize,list,values,ISSMToPetscInsertMode(mode)); + #else +- _error_("not implemented yet!"); ++ this->vector->SetValues(ssize,list,values,mode); + #endif + + } +@@ -178,7 +183,7 @@ + _assert_(this->vector); + VecSetValues(this->vector,1,&dof,&value,ISSMToPetscInsertMode(mode)); + #else +- _error_("not implemented yet!"); ++ this->vector->SetValue(dof,value,mode); + #endif + + } +@@ -190,7 +195,7 @@ + _assert_(this->vector); + VecGetValues(this->vector,1,&dof,pvalue); + #else +- _error_("not implemented yet!"); ++ this->vector->GetValue(pvalue,dof); + #endif + } + /*}}}*/ +@@ -201,7 +206,7 @@ + _assert_(this->vector); + VecGetSize(this->vector,pM); + #else +- _error_("not implemented yet!"); ++ this->vector->GetSize(pM); + #endif + + } +@@ -213,7 +218,7 @@ + _assert_(this->vector); + VecGetLocalSize(this->vector,pM); + #else +- _error_("not implemented yet!"); ++ this->vector->GetLocalSize(pM); + #endif + + } +@@ -228,9 +233,8 @@ + _assert_(this->vector); + VecDuplicate(this->vector,&vec_output); + output->vector=vec_output; +- VecGetSize(output->vector,&output->M); + #else +- _error_("not implemented yet!"); ++ output->vector=this->vector->Duplicate(); + #endif + return output; + +@@ -243,7 +247,7 @@ + _assert_(this->vector); + VecSet(this->vector,value); + #else +- _error_("not implemented yet!"); ++ this->vector->Set(value); + #endif + + } +@@ -255,7 +259,7 @@ + _assert_(this->vector); + VecAXPY(this->vector,a,X->vector); + #else +- _error_("not implemented yet!"); ++ this->vector->AXPY(X->vector,a); + #endif + } + /*}}}*/ +@@ -266,7 +270,7 @@ + _assert_(this->vector); + VecAYPX(this->vector,a,X->vector); + #else +- _error_("not implemented yet!"); ++ this->vector->AYPX(X->vector,a); + #endif + + } +@@ -279,7 +283,7 @@ + #ifdef _HAVE_PETSC_ + VecToMPISerial(&vec_serial, this->vector); + #else +- _error_("not implemented yet!"); ++ vec_serial=this->vector->ToMPISerial(); + #endif + + return vec_serial; +@@ -292,7 +296,7 @@ + #ifdef _HAVE_PETSC_ + VecCopy(this->vector,to->vector); + #else +- _error_("not implemented yet!"); ++ this->vector->Copy(to->vector); + #endif + + } +@@ -305,7 +309,7 @@ + _assert_(this->vector); + VecNorm(this->vector,ISSMToPetscNormMode(norm_type),&norm); + #else +- _error_("not implemented yet!"); ++ norm=this->vector->Norm(norm_type); + #endif + return norm; + } +@@ -317,7 +321,7 @@ + _assert_(this->vector); + VecScale(this->vector,scale_factor); + #else +- _error_("not implemented yet!"); ++ this->vector->Scale(scale_factor); + #endif + } + /*}}}*/ +@@ -329,7 +333,7 @@ + _assert_(this->vector); + VecDot(this->vector,vector->vector,&dot); + #else +- _error_("not implemented yet!"); ++ dot=this->vector->Dot(vector->vector); + #endif + return dot; + } +@@ -341,7 +345,7 @@ + _assert_(this->vector); + VecPointwiseDivide(this->vector,x->vector,y->vector); + #else +- _error_("not implemented yet!"); ++ this->vector->PointwiseDivide(x->vector,y->vector); + #endif + } + /*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11733) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11734) +@@ -47,7 +47,7 @@ + #ifdef _HAVE_PETSC_ + this->matrix=NewMat(pM,pN); + #else +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=new SeqMat(pM,pN); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); +@@ -63,7 +63,7 @@ + #ifdef _HAVE_PETSC_ + this->matrix=NewMat(pM,pN,sparsity); + #else +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=new SeqMat(pM,pN,sparsity); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); +@@ -96,7 +96,7 @@ + xfree((void**)&idxm); + xfree((void**)&idxn); + #else +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=new SeqMat(serial_mat,pM,pN,sparsity); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); +@@ -112,7 +112,7 @@ + #ifdef _HAVE_PETSC_ + this->matrix=NewMat(pM,pN,connectivity,numberofdofspernode); + #else +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=new SeqMat(pM,pN,connectivity,numberofdofspernode); + #endif + #ifdef _HAVE_ADOLC_ + this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); +@@ -125,7 +125,7 @@ + #ifdef _HAVE_PETSC_ + MatFree(&this->matrix); + #else +- xfree((void**)&this->matrix); ++ delete this->matrix; + #endif + #ifdef _HAVE_ADOLC_ + xfree((void**)&this->amatrix); +@@ -142,13 +142,7 @@ + #ifdef _HAVE_PETSC_ + MatView(this->matrix,PETSC_VIEWER_STDOUT_WORLD); + #else +- printf("Matrix size: %i-%i\n",M,N); +- for(i=0;imatrix->Echo(); + #endif + + #ifdef _HAVE_ADOLC_ +@@ -172,12 +166,30 @@ + #ifdef _HAVE_PETSC_ + PetscMatrixToMatlabMatrix(&dataref,this->matrix); + #else +- _error_("not implemented yet!"); ++ dataref=this->matrix->ToMatlabMatrix(); + #endif + return dataref; + + } + /*}}}*/ ++/*FUNCTION MatlabMatrixToMatrix{{{1*/ ++Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ ++ ++ int dummy; ++ Matrix* matrix=NULL; ++ ++ /*allocate matrix object: */ ++ matrix=new Matrix(); ++ ++ #ifdef _HAVE_PETSC_ ++ MatlabMatrixToPetscMatrix(&matrix->matrix,&matrix->M,&matrix->N,mxmatrix); ++ #else ++ matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); ++ #endif ++ ++ return matrix; ++} ++/*}}}*/ + #endif + /*FUNCTION Matrix::Assemble{{{1*/ + void Matrix::Assemble(void){ +@@ -189,7 +201,7 @@ + MatCompress(this->matrix); + #endif + #else +- /*do nothing:*/ ++ this->matrix->Assemble(); + #endif + + } +@@ -202,7 +214,7 @@ + _assert_(this->matrix); + MatNorm(this->matrix,ISSMToPetscNormMode(norm_type),&norm); + #else +- _error_("not implemented yet!"); ++ norm=this->matrix->Norm(norm_type); + #endif + return norm; + } +@@ -214,7 +226,7 @@ + _assert_(this->matrix); + MatGetSize(this->matrix,pM,pN); + #else +- _error_("not implemented yet!"); ++ this->matrix->GetSize(pM,pN); + #endif + } + /*}}}*/ +@@ -225,7 +237,7 @@ + _assert_(this->matrix); + MatGetLocalSize(this->matrix,pM,pN); + #else +- _error_("not implemented yet!"); ++ this->matrix->GetLocalSize(pM,pN); + #endif + } + /*}}}*/ +@@ -237,7 +249,7 @@ + _assert_(X->vector); + MatMultPatch(this->matrix,X->vector,AX->vector); + #else +- _error_("not implemented yet!"); ++ this->matrix->MatMult(X->vector,AX->vector); + #endif + } + /*}}}*/ +@@ -248,11 +260,11 @@ + + output=new Matrix(); + +- #ifdef _HAVE_PETSC ++ #ifdef _HAVE_PETSC_ + _assert_(this->matrix); + MatDuplicate(this->matrix,MAT_COPY_VALUES,&output->matrix); + #else +- _error_("not implemented yet!"); ++ output->matrix=this->matrix->Duplicate(); + #endif + } + /*}}}*/ +@@ -261,11 +273,21 @@ + + double* output=NULL; + +- #ifdef _HAVE_PETSC ++ #ifdef _HAVE_PETSC_ + MatToSerial(&output,this->matrix); + #else +- _error_("not implemented yet!"); ++ output=this->matrix->ToSerial(); + #endif + return output; + } + /*}}}*/ ++/*FUNCTION Matrix::SetValues{{{1*/ ++void Matrix::SetValues(int m,int* idxm,int n,int* idxn,double* values,InsMode mode){ ++ ++ #ifdef _HAVE_PETSC_ ++ MatSetValues(this->matrix,m,idxm,n,idxn,values,ISSMToPetscInsertMode(mode)); ++ #else ++ this->matrix->SetValues(m,idxm,n,idxn,values,mode); ++ #endif ++} ++/*}}}*/ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11733) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11734) +@@ -30,12 +30,10 @@ + + public: + +- int M; +- + #ifdef _HAVE_PETSC_ + Vec vector; + #else +- double* vector; ++ SeqVec* vector; + #endif + #ifdef _HAVE_ADOLC_ + adouble* avector; +@@ -73,4 +71,10 @@ + double Dot(Vector* vector); + /*}}}*/ + }; ++ ++/*API: */ ++#ifdef _SERIAL_ ++Vector* MatlabVectorToVector(const mxArray* mxvector); ++#endif ++ + #endif //#ifndef _VECTOR_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11733) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11734) +@@ -36,7 +36,7 @@ + #ifdef _HAVE_PETSC_ + Mat matrix; + #else +- double* matrix; ++ SeqMat* matrix; + #endif + #ifdef _HAVE_ADOLC_ + adouble* amatrix; +@@ -62,7 +62,13 @@ + void MatMult(Vector* X,Vector* AX); + Matrix* Duplicate(void); + double* ToSerial(void); ++ void SetValues(int m,int* idxm,int n,int* idxn,double* values,InsMode mode); + /*}}}*/ + + }; ++/*API: */ ++#ifdef _SERIAL_ ++Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); ++#endif ++ + #endif //#ifndef _MATRIX_H_ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp (revision 11733) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp (revision 11734) +@@ -165,22 +165,18 @@ + int i; + double* localvalues=NULL; + +- #ifdef _HAVE_PETSC_ +- if(this->fsize){ +- /*first, retrieve values that are in the f-set from the g-set values vector: */ +- localvalues=(double*)xmalloc(this->fsize*sizeof(double)); +- for(i=0;ifsize;i++){ +- localvalues[i]=this->values[this->flocaldoflist[i]]; +- } +- /*add local values into global vector, using the fglobaldoflist: */ +- VecSetValues(pf->vector,this->fsize,this->fglobaldoflist,(const double*)localvalues,ADD_VALUES); +- +- /*Free ressources:*/ +- xfree((void**)&localvalues); ++ if(this->fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values vector: */ ++ localvalues=(double*)xmalloc(this->fsize*sizeof(double)); ++ for(i=0;ifsize;i++){ ++ localvalues[i]=this->values[this->flocaldoflist[i]]; + } +- #else +- _error_("not supported yet!"); +- #endif ++ /*add local values into global vector, using the fglobaldoflist: */ ++ pf->SetValues(this->fsize,this->fglobaldoflist,localvalues,ADD_VAL); ++ ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); ++ } + + } + /*}}}*/ +@@ -190,23 +186,19 @@ + int i; + double* localvalues=NULL; + +- #ifdef _HAVE_PETSC_ +- if(this->fsize){ +- /*first, retrieve values that are in the f-set from the g-set values vector: */ +- localvalues=(double*)xmalloc(this->fsize*sizeof(double)); +- for(i=0;ifsize;i++){ +- localvalues[i]=this->values[this->flocaldoflist[i]]; +- } +- /*add local values into global vector, using the fglobaldoflist: */ +- VecSetValues(pf->vector,this->fsize,this->fglobaldoflist,(const double*)localvalues,INSERT_VALUES); +- +- /*Free ressources:*/ +- xfree((void**)&localvalues); ++ if(this->fsize){ ++ /*first, retrieve values that are in the f-set from the g-set values vector: */ ++ localvalues=(double*)xmalloc(this->fsize*sizeof(double)); ++ for(i=0;ifsize;i++){ ++ localvalues[i]=this->values[this->flocaldoflist[i]]; + } +- #else +- _error_("not supported yet!"); +- #endif ++ /*add local values into global vector, using the fglobaldoflist: */ ++ pf->SetValues(this->fsize,this->fglobaldoflist,localvalues,INS_VAL); + ++ /*Free ressources:*/ ++ xfree((void**)&localvalues); ++ } ++ + } + /*}}}*/ + /*FUNCTION ElementVector::Echo{{{1*/ Index: /issm/oecreview/Archive/11730-11748/ISSM-11734-11735.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11734-11735.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11734-11735.diff (revision 11991) @@ -0,0 +1,79 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11734) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11735) +@@ -1,4 +1,4 @@ +-INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ ++INCLUDES = @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @MPIINCL@ @MATLABINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @HYPREINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ + EXEEXT=$(ISSMEXT) + + #Library declaration {{{1 +@@ -213,6 +213,11 @@ + ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ + ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ + ./toolkits/metis/metisincludes.h\ ++ ./toolkits/issm/issmtoolkit.h\ ++ ./toolkits/issm/SeqVec.h\ ++ ./toolkits/issm/SeqVec.cpp\ ++ ./toolkits/issm/SeqMat.h\ ++ ./toolkits/issm/SeqMat.cpp\ + ./toolkits/metis/patches/metispatches.h\ + ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ + ./toolkits/triangle/triangleincludes.h\ +@@ -236,6 +241,8 @@ + ./modules/ModelProcessorx/CreateSingleNodeToElementConnectivity.cpp\ + ./modules/ModelProcessorx/CreateNumberNodeToElementConnectivity.cpp\ + ./modules/ModelProcessorx/CreateElementsVerticesAndMaterials.cpp\ ++ ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ ++ ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ + ./modules/NodesDofx/NodesDofx.h\ + ./modules/NodesDofx/NodesDofx.cpp\ + ./modules/NodalValuex/NodalValuex.h\ +@@ -693,8 +700,6 @@ + ./shared/Matlab/CheckNumMatlabArguments.cpp\ + ./toolkits/matlab/matlabincludes.h\ + ./toolkits/matlab/MatlabNArrayToNArray.cpp\ +- ./toolkits/matlab/MatlabMatrixToMatrix.cpp\ +- ./toolkits/matlab/MatlabVectorToVector.cpp\ + ./toolkits/double/MatlabVectorToDoubleVector.cpp\ + ./toolkits/double/double.h\ + ./toolkits/double/MatlabMatrixToDoubleMatrix.cpp\ +@@ -735,12 +740,14 @@ + ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\ + ./toolkits/petsc/petscincludes.h\ + ./shared/Numerics/PetscOptionsFromAnalysis.cpp\ +- ./modules/ParsePetscOptionsx/ParsePetscOptionsx.h\ +- ./modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp\ + ./modules/Solverx/SolverxPetsc.cpp\ + ./modules/Solverx/DofTypesToIndexSet.cpp + + #}}} ++#Gsl sources {{{1 ++gsl_sources= ./modules/Solverx/SolverxGsl.cpp ++ ++#}}} + #Serialsources {{{1 + serial_sources= ./objects/Options/Option.cpp\ + ./objects/Options/Option.h\ +@@ -845,6 +852,12 @@ + issm_psources += $(petsc_psources) + endif + ++if GSL ++issm_sources += $(gsl_sources) ++issm_psources += $(gsl_psources) ++endif ++ ++ + if TRANSIENT + issm_sources += $(transient_sources) + issm_psources += $(transient_psources) +@@ -946,7 +959,7 @@ + LDADD = ./libpISSM.a ./libOverload.a + + #External packages +-LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) ++LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) + + issm_SOURCES = solutions/issm.cpp + issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) Index: /issm/oecreview/Archive/11730-11748/ISSM-11735-11736.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11735-11736.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11735-11736.diff (revision 11991) @@ -0,0 +1,77 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11735) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/m4/issm_options.m4 (revision 11736) +@@ -374,6 +374,29 @@ + AM_CONDITIONAL([ADIC2], [test x$HAVE_ADIC2 = xyes]) + AC_MSG_RESULT($HAVE_ADIC2) + dnl }}} ++ dnl gsl{{{1 ++ AC_ARG_WITH([gsl-dir], ++ AS_HELP_STRING([--with-gsl-dir = DIR], [gsl root directory.]), ++ [GSL_ROOT=$withval],[GSL_ROOT=""]) ++ AC_MSG_CHECKING(for Gsl) ++ ++ if test -d "$GSL_ROOT"; then ++ ++ dnl defaults ++ HAVE_GSL=yes ++ GSLINCL="-I$GSL_ROOT/include" ++ GSLLIB="-L$GSL_ROOT/lib/ -lgsl -lgslcblas -lm" ++ ++ AC_DEFINE([_HAVE_GSL_],[1],[with gsl in ISSM src]) ++ AC_SUBST([GSLINCL]) ++ AC_SUBST([GSLLIB]) ++ ++ else ++ HAVE_GSL=no ++ fi ++ AM_CONDITIONAL([GSL], [test x$HAVE_GSL = xyes]) ++ AC_MSG_RESULT($HAVE_GSL) ++ dnl }}} + dnl rose{{{1 + AC_ARG_WITH([rose-dir], + AS_HELP_STRING([--with-rose-dir = DIR], [rose root directory.]), +@@ -478,21 +501,14 @@ + AS_HELP_STRING([--with-mpi-include = DIR], + [mpi include directory, necessary for parallel build]), + [MPI_INCLUDE=$withval],[MPI_INCLUDE=""]) +- +- dnl check that --with-mpi-include and --with-mpi-lib have been provided ++ + if test -z "$MPILIB" ; then +- if test "$PARALLEL_VALUE" = "yes" ; then +- AC_MSG_ERROR([empty --with-mpi-lib options! MPI is needed to run ISSM in parallel!]) +- fi ++ HAVE_MPI=no + else + if test -z "$MPI_INCLUDE" ; then +- if test "$PARALLEL_VALUE" = "yes" ; then +- AC_MSG_ERROR([empty --with-mpi-include directory! MPI is needed to run ISSM in parallel!]) +- fi ++ HAVE_MPI=no + else +- HAVE_MPI=yes + MPIINCL=-I"$MPI_INCLUDE/" +- + AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src]) + AC_DEFINE([HAVE_MPI],[1],[with Mpi in ISSM src]) + AC_SUBST([MPIINCL]) +@@ -1142,6 +1158,17 @@ + AM_CONDITIONAL([THREED], [test x$HAVE_THREED = xyes]) + AC_MSG_RESULT($HAVE_THREED) + dnl }}} ++ dnl checks{{{1 ++ AC_MSG_CHECKING(checking consistency between all libraries) ++ ++ dnl check that if petsc is requested in parallel, mpi should be specified ++ if test "$HAVE_PETSC" = "yes" ; then ++ if test "$HAVE_MPI" = "NO"; then ++ AC_MSG_ERROR([petsc requires mpi!]); ++ fi ++ fi ++ AC_MSG_RESULT(done) ++ dnl }}} + + dnl other options + dnl optimization{{{1 Index: /issm/oecreview/Archive/11730-11748/ISSM-11736-11737.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11736-11737.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11736-11737.diff (revision 11991) @@ -0,0 +1,189 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco.patch (revision 11736) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco.patch (revision 11737) +@@ -240,7 +240,7 @@ + *** 2,18 **** + DEST= ${DEST_DIR}/chaco + CC = gcc +- IFLAG = -Imain ++ IFLAG = -Imain + ! #IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include + ! #CFLAGS = -O2 + ! #OFLAGS = -O2 +@@ -258,7 +258,7 @@ + --- 2,9 ---- + DEST= ${DEST_DIR}/chaco + CC = gcc +- IFLAG = -Imain ++ IFLAG = -Imain -I/usr/include/sys + ! CFLAGS = -O2 + ! OFLAGS = -O2 + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11736) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11737) +@@ -1,18 +1,4 @@ + #!/bin/bash +- +-#Erase symlink + rm -rf install + +-#Select or create a new simlink +-ln -s /usr/local/pkgs/matlab-7.6/ install +-#ln -s /usr/local/matlab704/ install +-#ln -s /usr/local/matlab711/ install +-#ln -s /usr/local/matlab712/ install +-#ln -s /usr/local/pkgs/matlab-7.6/ install +- +-# Macintosh (OSX) simlink +-#ln -s /Applications/MATLAB_R2008a/ install +-#ln -s /Applications/MATLAB_R2009a.app/ install +-#ln -s /Applications/MATLAB_R2010a.app/ install +-#ln -s /Applications/MATLAB_R2011b.app/ install +-#ln -s /Applications/MATLAB*.app/ install ++ln -s /Applications/MATLAB_R2010a.app/ install +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/install.sh (revision 11736) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/mitgcm/install.sh (revision 11737) +@@ -14,6 +14,7 @@ + cvs login + + #Download code from server ++cvs login + cvs co -P MITgcm + + #move +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adolc/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adolc/install.sh (revision 11736) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/adolc/install.sh (revision 11737) +@@ -1,5 +1,7 @@ + #!/bin/bash + ++#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. ++ + #Some cleanup + rm -rf install ADOL-C-2.2.0 src + +@@ -15,11 +17,14 @@ + + #Compile ADOL-C + cd src ++ + ./configure \ + --prefix=$ISSM_TIER/externalpackages/adolc/install \ + --enable-sparse \ + --enable-docexa \ +- --enable-addexa ++ --enable-addexa \ ++ --disable-shave ++ + if [ -z $1 ]; then + make + else +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh (revision 11737) +@@ -0,0 +1,31 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install petsc-2.3.2-p3 src ++mkdir install src ++ ++#Untar and move petsc to install directory ++tar -zxvf petsc-2.3.2-p3.tar.gz ++mv petsc-2.3.2-p3/* src/ ++rm -rf petsc-2.3.2-p3 ++ ++#configure ++cd src ++./config/configure.py \ ++ --prefix="$ISSM_TIER/externalpackages/petsc/install" \ ++ --PETSC_DIR="$ISSM_TIER/externalpackages/petsc/src" \ ++ --PETSC_ARCH=macosx-gnu \ ++ --with-mpi-dir="$ISSM_TIER/externalpackages/mpich2/install" \ ++ --with-debugging=0 \ ++ --with-shared-libraries=0 \ ++ --download-mumps=yes \ ++ --download-scalapack=yes \ ++ --download-blacs=yes \ ++ --download-blas=yes \ ++ --download-plapack=yes \ ++ --download-parmetis=yes \ ++ --download-f-blas-lapack=yes ++ ++#Compile petsc and install it ++make ++make install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11736) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11737) +@@ -19,7 +19,7 @@ + int analysis_type; + + /*output: */ +- Vector *uf=new Vector(); ++ Vector *uf=NULL; + + /*In debugging mode, check that stiffness matrix and load vectors are not NULL (they can be empty)*/ + _assert_(Kff); +@@ -28,6 +28,7 @@ + #ifdef _HAVE_PETSC_ + Vec uf0_vector = NULL; + Vec df_vector = NULL; ++ Vec uf_vector = NULL; + if(uf0) uf0_vector = uf0->vector; + if(df) df_vector = df->vector; + +@@ -37,13 +38,10 @@ + PetscOptionsFromAnalysis(parameters,analysis_type); + #endif + +- SolverxPetsc(&uf->vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); +- if(uf->vector == NULL){ +- uf->M = 0; +- } +- else{ +- VecGetSize(uf->vector,&uf->M); +- } ++ SolverxPetsc(&uf_vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); ++ ++ /*Create vector out of petsc vector: */ ++ uf=new Vector(uf_vector); + #else + #ifdef _HAVE_GSL_ + SolverxGsl(&uf->vector,Kff->matrix,pf->vector); +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11736) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11737) +@@ -78,9 +78,14 @@ + /*FUNCTION Vector::Vector(Vec petsc_vec){{{1*/ + Vector::Vector(Vec petsc_vec){ + +- /*copy vector*/ +- VecDuplicate(petsc_vec,&this->vector); +- VecCopy(petsc_vec,this->vector); ++ if(petsc_vec==NULL){ ++ this->vector=NULL; ++ } ++ else{ ++ /*copy vector*/ ++ VecDuplicate(petsc_vec,&this->vector); ++ VecCopy(petsc_vec,this->vector); ++ } + + } + /*}}}*/ Index: /issm/oecreview/Archive/11730-11748/ISSM-11737-11738.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11737-11738.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11737-11738.diff (revision 11991) @@ -0,0 +1,24 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11737) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11738) +@@ -1,4 +1,18 @@ + #!/bin/bash ++ ++#Erase symlink + rm -rf install + +-ln -s /Applications/MATLAB_R2010a.app/ install ++#Select or create a new simlink ++ln -s /usr/local/pkgs/matlab-7.6/ install ++#ln -s /usr/local/matlab704/ install ++#ln -s /usr/local/matlab711/ install ++#ln -s /usr/local/matlab712/ install ++#ln -s /usr/local/pkgs/matlab-7.6/ install ++ ++# Macintosh (OSX) simlink ++#ln -s /Applications/MATLAB_R2008a/ install ++#ln -s /Applications/MATLAB_R2009a.app/ install ++#ln -s /Applications/MATLAB_R2010a.app/ install ++#ln -s /Applications/MATLAB_R2011b.app/ install ++#ln -s /Applications/MATLAB*.app/ install Index: /issm/oecreview/Archive/11730-11748/ISSM-11738-11739.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11738-11739.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11738-11739.diff (revision 11991) @@ -0,0 +1,61 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11738) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11739) +@@ -111,7 +111,10 @@ + int i; + + #ifdef _HAVE_PETSC_ +- VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); ++ if(!this->vector){ ++ printf("Vector size: 0\n"); ++ } ++ else VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); + #else + this->vector->Echo(); + #endif +@@ -208,8 +211,8 @@ + void Vector::GetSize(int* pM){ + + #ifdef _HAVE_PETSC_ +- _assert_(this->vector); +- VecGetSize(this->vector,pM); ++ if(!this->vector)*pM=0; ++ else VecGetSize(this->vector,pM); + #else + this->vector->GetSize(pM); + #endif +@@ -220,8 +223,8 @@ + void Vector::GetLocalSize(int* pM){ + + #ifdef _HAVE_PETSC_ +- _assert_(this->vector); +- VecGetLocalSize(this->vector,pM); ++ if(!this->vector)*pM=0; ++ else VecGetLocalSize(this->vector,pM); + #else + this->vector->GetLocalSize(pM); + #endif +@@ -235,9 +238,10 @@ + output=new Vector(); + #ifdef _HAVE_PETSC_ + Vec vec_output=NULL; +- _assert_(this->vector); +- VecDuplicate(this->vector,&vec_output); +- output->vector=vec_output; ++ if(!this->vector){ ++ VecDuplicate(this->vector,&vec_output); ++ output->vector=vec_output; ++ } + #else + output->vector=this->vector->Duplicate(); + #endif +@@ -299,7 +303,7 @@ + void Vector::Copy(Vector* to){ + + #ifdef _HAVE_PETSC_ +- VecCopy(this->vector,to->vector); ++ if(this->vector) VecCopy(this->vector,to->vector); + #else + this->vector->Copy(to->vector); + #endif Index: /issm/oecreview/Archive/11730-11748/ISSM-11739-11740.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11739-11740.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11739-11740.diff (revision 11991) @@ -0,0 +1,15 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m (revision 11739) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m (revision 11740) +@@ -124,6 +124,10 @@ + + %Ok, now deal with the other fields from the 2d mesh: + ++%lat lon ++md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node'); ++md.mesh.lon=project3d(md,'vector',md.mesh.lon,'type','node'); ++ + %drag coefficient is limited to nodes that are on the bedrock. + md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1); + Index: /issm/oecreview/Archive/11730-11748/ISSM-11740-11741.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11740-11741.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11740-11741.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco.patch (revision 11740) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/chaco/chaco.patch (revision 11741) +@@ -240,7 +240,7 @@ + *** 2,18 **** + DEST= ${DEST_DIR}/chaco + CC = gcc +- IFLAG = -Imain ++ IFLAG = -Imain + ! #IFLAG = -Imain -I/usr/local/pkgs/matlab-7.6/extern/include + ! #CFLAGS = -O2 + ! #OFLAGS = -O2 +@@ -258,7 +258,7 @@ + --- 2,9 ---- + DEST= ${DEST_DIR}/chaco + CC = gcc +- IFLAG = -Imain -I/usr/include/sys ++ IFLAG = -Imain + ! CFLAGS = -O2 + ! OFLAGS = -O2 + Index: /issm/oecreview/Archive/11730-11748/ISSM-11741-11742.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11741-11742.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11741-11742.diff (revision 11991) @@ -0,0 +1,16 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m (revision 11741) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/extrude.m (revision 11742) +@@ -124,9 +124,9 @@ + + %Ok, now deal with the other fields from the 2d mesh: + +-%lat lon ++%lat long + md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node'); +-md.mesh.lon=project3d(md,'vector',md.mesh.lon,'type','node'); ++md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node'); + + %drag coefficient is limited to nodes that are on the bedrock. + md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1); Index: /issm/oecreview/Archive/11730-11748/ISSM-11742-11743.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11742-11743.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11742-11743.diff (revision 11991) @@ -0,0 +1,336 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToPetscVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToPetscVector.cpp (revision 11742) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToPetscVector.cpp (revision 11743) +@@ -93,7 +93,6 @@ + VecAssemblyBegin(vector); + VecAssemblyEnd(vector); + +- + /*Assign output pointer: */ + *pvector=vector; + *pvector_rows=rows; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp (revision 11742) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp (revision 11743) +@@ -115,8 +115,8 @@ + + /*Assign output pointer: */ + *pmatrix=matrix; +- *pmatrix_rows=rows; +- *pmatrix_cols=cols; ++ if(pmatrix_rows) *pmatrix_rows=rows; ++ if(pmatrix_cols) *pmatrix_cols=cols; + + return 1; + } +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11742) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11743) +@@ -50,22 +50,16 @@ + /*FUNCTION Vector::Vector(double* serial_vec,int M){{{1*/ + Vector::Vector(double* serial_vec,int M){ + +- int i,j; +- + #ifdef _HAVE_PETSC_ +- int* idxm=NULL; ++ int* idxm=(int*)xmalloc(M*sizeof(int)); ++ for(int i=0;ivector=NewVec(M); +- +- idxm=(int*)xmalloc(M*sizeof(int)); +- for(i=0;ivector,M,idxm,serial_vec,INSERT_VALUES); +- + VecAssemblyBegin(this->vector); + VecAssemblyEnd(this->vector); + + xfree((void**)&idxm); +- + #else + this->vector=new SeqVec(serial_vec,M); + #endif +@@ -111,10 +105,8 @@ + int i; + + #ifdef _HAVE_PETSC_ +- if(!this->vector){ +- printf("Vector size: 0\n"); +- } +- else VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); ++ _assert_(this->vector); ++ VecView(this->vector,PETSC_VIEWER_STDOUT_WORLD); + #else + this->vector->Echo(); + #endif +@@ -211,7 +203,7 @@ + void Vector::GetSize(int* pM){ + + #ifdef _HAVE_PETSC_ +- if(!this->vector)*pM=0; ++ _assert_(this->vector); + else VecGetSize(this->vector,pM); + #else + this->vector->GetSize(pM); +@@ -219,12 +211,24 @@ + + } + /*}}}*/ ++/*FUNCTION Vector::IsEmpty{{{1*/ ++bool Vector::IsEmpty(void){ ++ ++ int M; ++ this->GetSize(&M); ++ ++ if(M==0) ++ return true; ++ else ++ return false; ++} ++/*}}}*/ + /*FUNCTION Vector::GetLocalSize{{{1*/ + void Vector::GetLocalSize(int* pM){ + + #ifdef _HAVE_PETSC_ +- if(!this->vector)*pM=0; +- else VecGetLocalSize(this->vector,pM); ++ _assert_(this->vector); ++ VecGetLocalSize(this->vector,pM); + #else + this->vector->GetLocalSize(pM); + #endif +@@ -235,14 +239,13 @@ + Vector* Vector::Duplicate(void){ + + Vector* output=NULL; +- output=new Vector(); + #ifdef _HAVE_PETSC_ ++ _assert_(this->vector); + Vec vec_output=NULL; +- if(!this->vector){ +- VecDuplicate(this->vector,&vec_output); +- output->vector=vec_output; +- } ++ VecDuplicate(this->vector,&vec_output); ++ output=new Vector(vec_output); + #else ++ output=new Vector(); + output->vector=this->vector->Duplicate(); + #endif + return output; +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11742) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.cpp (revision 11743) +@@ -25,9 +25,6 @@ + /*FUNCTION Matrix::Matrix(){{{1*/ + Matrix::Matrix(){ + +- this->M=0; +- this->N=0; +- + #ifdef _HAVE_PETSC_ + this->matrix=NULL; + #else +@@ -39,83 +36,67 @@ + } + /*}}}*/ + /*FUNCTION Matrix::Matrix(int M,int N){{{1*/ +-Matrix::Matrix(int pM,int pN){ ++Matrix::Matrix(int M,int N){ + +- this->M=pM; +- this->N=pN; +- + #ifdef _HAVE_PETSC_ +- this->matrix=NewMat(pM,pN); ++ this->matrix=NewMat(M,N); + #else +- this->matrix=new SeqMat(pM,pN); ++ this->matrix=new SeqMat(M,N); + #endif + #ifdef _HAVE_ADOLC_ +- this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ this->amatrix=(adouble*)xmalloc(M*N*sizeof(adouble)); + #endif + } + /*}}}*/ + /*FUNCTION Matrix::Matrix(int M,int N,double sparsity){{{1*/ +-Matrix::Matrix(int pM,int pN,double sparsity){ ++Matrix::Matrix(int M,int N,double sparsity){ + +- this->M=pM; +- this->N=pN; +- + #ifdef _HAVE_PETSC_ +- this->matrix=NewMat(pM,pN,sparsity); ++ this->matrix=NewMat(M,N,sparsity); + #else +- this->matrix=new SeqMat(pM,pN,sparsity); ++ this->matrix=new SeqMat(M,N,sparsity); + #endif + #ifdef _HAVE_ADOLC_ +- this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ this->amatrix=(adouble*)xmalloc(M*N*sizeof(adouble)); + #endif + } + /*}}}*/ + /*FUNCTION Matrix::Matrix(double* serial_mat, int M,int N,double sparsity){{{1*/ +-Matrix::Matrix(double* serial_mat, int pM,int pN,double sparsity){ ++Matrix::Matrix(double* serial_mat, int M,int N,double sparsity){ + +- this->M=pM; +- this->N=pN; +- + #ifdef _HAVE_PETSC_ + int i; +- int* idxm=NULL; +- int* idxn=NULL; + +- this->matrix=NewMat(pM,pN,sparsity); +- +- idxm=(int*)xmalloc(M*sizeof(int)); +- idxn=(int*)xmalloc(N*sizeof(int)); ++ int* idxm=(int*)xmalloc(M*sizeof(int)); ++ int* idxn=(int*)xmalloc(N*sizeof(int)); + for(i=0;imatrix=NewMat(M,N,sparsity); + MatSetValues(this->matrix,M,idxm,N,idxn,serial_mat,INSERT_VALUES); +- + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); + + xfree((void**)&idxm); + xfree((void**)&idxn); + #else +- this->matrix=new SeqMat(serial_mat,pM,pN,sparsity); ++ this->matrix=new SeqMat(serial_mat,M,N,sparsity); + #endif + #ifdef _HAVE_ADOLC_ +- this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ this->amatrix=(adouble*)xmalloc(M*N*sizeof(adouble)); + #endif + } + /*}}}*/ + /*FUNCTION Matrix::Matrix(int M,int N,int connectivity,int numberofdofspernode){{{1*/ +-Matrix::Matrix(int pM,int pN,int connectivity,int numberofdofspernode){ ++Matrix::Matrix(int M,int N,int connectivity,int numberofdofspernode){ + +- this->M=pM; +- this->N=pN; +- + #ifdef _HAVE_PETSC_ +- this->matrix=NewMat(pM,pN,connectivity,numberofdofspernode); ++ this->matrix=NewMat(M,N,connectivity,numberofdofspernode); + #else +- this->matrix=new SeqMat(pM,pN,connectivity,numberofdofspernode); ++ this->matrix=new SeqMat(M,N,connectivity,numberofdofspernode); + #endif + #ifdef _HAVE_ADOLC_ +- this->amatrix=(adouble*)xmalloc(pM*pN*sizeof(adouble)); ++ this->amatrix=(adouble*)xmalloc(M*N*sizeof(adouble)); + #endif + } + /*}}}*/ +@@ -182,7 +163,7 @@ + matrix=new Matrix(); + + #ifdef _HAVE_PETSC_ +- MatlabMatrixToPetscMatrix(&matrix->matrix,&matrix->M,&matrix->N,mxmatrix); ++ MatlabMatrixToPetscMatrix(&matrix->matrix,NULL,NULL,mxmatrix); + #else + matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); + #endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11742) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11743) +@@ -1,5 +1,5 @@ + /*!\file: Vector.h +- * \brief wrapper to vector objects. The goal is to control which API (PETSC,Scalpack, Plapack?) ++ * \brief wrapper to vector objects. The goal is to control which API (PETSc,Scalpack, Plapack?) + * implements our underlying vector format. + */ + +@@ -31,12 +31,12 @@ + public: + + #ifdef _HAVE_PETSC_ +- Vec vector; ++ Vec vector; + #else +- SeqVec* vector; ++ SeqVec* vector; + #endif + #ifdef _HAVE_ADOLC_ +- adouble* avector; ++ adouble* avector; + #endif + + /*Vector constructors, destructors {{{1*/ +@@ -53,22 +53,23 @@ + #ifdef _SERIAL_ + mxArray* ToMatlabVector(void); + #endif +- void Assemble(void); +- void SetValues(int ssize, int* list, double* values, InsMode mode); +- void SetValue(int dof, double value, InsMode mode); +- void GetValue(double* pvalue, int dof); +- void GetSize(int* pM); +- void GetLocalSize(int* pM); +- Vector* Duplicate(void); +- void Set(double value); +- void AXPY(Vector* X, double a); +- void AYPX(Vector* X, double a); +- double* ToMPISerial(void); +- void Copy(Vector* to); +- double Norm(NormMode norm_type); +- void Scale(double scale_factor); +- void PointwiseDivide(Vector* x,Vector* y); +- double Dot(Vector* vector); ++ void AXPY(Vector *X, double a); ++ void AYPX(Vector *X, double a); ++ void Assemble(void); ++ void Copy(Vector *to); ++ double Dot(Vector *vector); ++ Vector *Duplicate(void); ++ void GetValue(double *pvalue, int dof); ++ void GetSize(int *pM); ++ void GetLocalSize(int *pM); ++ bool IsEmpty(void); ++ double Norm(NormMode norm_type); ++ void PointwiseDivide(Vector *x,Vector*y); ++ void Scale(double scale_factor); ++ void Set(double value); ++ void SetValues(int ssize, int *list, double*values, InsMode mode); ++ void SetValue(int dof, double value, InsMode mode); ++ double *ToMPISerial(void); + /*}}}*/ + }; + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11742) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Matrix.h (revision 11743) +@@ -1,5 +1,5 @@ + /*!\file: Matrix.h +- * \brief wrapper to matrix objects. The goal is to control which API (PETSC,Scalpack, Plapack?) ++ * \brief wrapper to matrix objects. The goal is to control which API (PETSc,Scalpack, Plapack?) + * implements our underlying matrix format. + */ + +@@ -31,8 +31,6 @@ + + public: + +- int M,N; +- + #ifdef _HAVE_PETSC_ + Mat matrix; + #else Index: /issm/oecreview/Archive/11730-11748/ISSM-11743-11744.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11743-11744.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11743-11744.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11743) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/solutions/convergence.cpp (revision 11744) +@@ -23,7 +23,6 @@ + double nKUoldF; + double nF; + double solver_residue,res; +- int M; + + /*convergence options*/ + double eps_res; +@@ -33,8 +32,7 @@ + + /*If uf is NULL in input, f-set is nil, model is fully constrained, therefore converged from + * the get go: */ +- uf->GetSize(&M); +- if(M==0){ ++ if(uf->IsEmpty()){ + *pconverged=true; + return; + } Index: /issm/oecreview/Archive/11730-11748/ISSM-11744-11745.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11744-11745.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11744-11745.diff (revision 11991) @@ -0,0 +1,13 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11744) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11745) +@@ -204,7 +204,7 @@ + + #ifdef _HAVE_PETSC_ + _assert_(this->vector); +- else VecGetSize(this->vector,pM); ++ VecGetSize(this->vector,pM); + #else + this->vector->GetSize(pM); + #endif Index: /issm/oecreview/Archive/11730-11748/ISSM-11745-11746.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11745-11746.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11745-11746.diff (revision 11991) @@ -0,0 +1,7 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/execution +___________________________________________________________________ +Added: svn:ignore + + test* + + Index: /issm/oecreview/Archive/11730-11748/ISSM-11746-11747.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11746-11747.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11746-11747.diff (revision 11991) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh (revision 11747) +@@ -0,0 +1,28 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf src install gsl-1.15 ++mkdir src install ++ ++#Untar ++tar -zxvf gsl-1.15.tar.gz ++ ++#Move gsl into src directory ++mv gsl-1.15/* src ++rm -rf gsl-1.15 ++ ++#Configure gsl ++cd src ++ ++export CFLAGS=" -arch x86_64" ++ ++./configure \ ++ --prefix="$ISSM_TIER/externalpackages/gsl/install" ++ ++#Compile gsl ++if [ -z $1 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/install-macosx64.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/gsl-1.15.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/gsl-1.15.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/README +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/README (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl/README (revision 11747) +@@ -0,0 +1 @@ ++GNU Scientfic Library, obtained from: http://www.gnu.org/software/gsl/ Index: /issm/oecreview/Archive/11730-11748/ISSM-11747-11748.diff =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-11747-11748.diff (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-11747-11748.diff (revision 11991) @@ -0,0 +1,47 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh (revision 11748) +@@ -0,0 +1,26 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf install src make-3.82 ++mkdir install src ++ ++#Untar ++tar -zxvf make-3.82.tar.gz ++ ++#Move make into install directory ++mv make-3.82/* src ++rm -rf make-3.82 ++ ++#Apply patches ++cd src ++ ++#Configure and compile: ++./configure --prefix=$ISSM_TIER/externalpackages/gmake/install ++ ++if [ -z $1 ]; then ++ make ++ make install ++else ++ make -j $1; ++ make -j $1 install; ++fi + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/make-3.82.tar.gz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gmake/make-3.82.tar.gz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + Index: /issm/oecreview/Archive/11730-11748/ISSM-DocReview-11730-11748.tex =================================================================== --- /issm/oecreview/Archive/11730-11748/ISSM-DocReview-11730-11748.tex (revision 11991) +++ /issm/oecreview/Archive/11730-11748/ISSM-DocReview-11730-11748.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11730-11748/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11730-11748/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11730-11748/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11730-11748 Index: /issm/oecreview/Archive/11730-11748/Makefile =================================================================== --- /issm/oecreview/Archive/11730-11748/Makefile (revision 11991) +++ /issm/oecreview/Archive/11730-11748/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11730-11748 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11730-11748/log.tex =================================================================== --- /issm/oecreview/Archive/11730-11748/log.tex (revision 11991) +++ /issm/oecreview/Archive/11730-11748/log.tex (revision 11991) @@ -0,0 +1,36 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11730-11731.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/shared/Alloc/alloc.cpp \\ Export determination: 6. \\Rationale: Avoid potential API issue when Petsc is absent +M /issm/trunk-jpl/configs/config-macosx64-larour.sh No dakota for now \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11731-11732.diff: \\ Function name: \\M /issm/trunk-jpl/configs/config-macosx64-larour.sh \\ Export determination: 6. \\Rationale: No dakota for now +A /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh No dakota, no petsc, to test gsl API \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11732-11733.diff: \\ Function name: \\A /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh \\ Export determination: 6. \\Rationale: No dakota, no petsc, to test gsl API +M /issm/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp A /issm/trunk-jpl/src/c/toolkits/issm A /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp A /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.h A /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp A /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.h A /issm/trunk-jpl/src/c/toolkits/issm/issmtoolkit.h M /issm/trunk-jpl/src/c/toolkits/toolkits.h Adding issm toolkit \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11733-11734.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp A /issm/trunk-jpl/src/c/toolkits/issm A /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp A /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.h A /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp A /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.h A /issm/trunk-jpl/src/c/toolkits/issm/issmtoolkit.h M /issm/trunk-jpl/src/c/toolkits/toolkits.h \\ Export determination: 6. \\Rationale: Adding issm toolkit +M /issm/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h Hook up new issm toolkit \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11734-11735.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/ElementMatrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/ElementVector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h \\ Export determination: 6. \\Rationale: Hook up new issm toolkit +M /issm/trunk-jpl/src/c/Makefile.am Adding gsl support, issm toolkit. \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11735-11736.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/Makefile.am \\ Export determination: 6. \\Rationale: Adding gsl support, issm toolkit. +M /issm/trunk-jpl/m4/issm\_options.m4 Added gsl support + relaxed constraints on presence of PETSC to compile. Also added a fold where we should put all the checks post-m4 configuration. \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11736-11737.diff: \\ Function name: \\M /issm/trunk-jpl/m4/issm\_options.m4 \\ Export determination: 6. \\Rationale: Added gsl support + relaxed constraints on presence of PETSC to compile. Also added a fold where we should put all the checks post-m4 configuration. +M /issm/trunk-jpl/externalpackages/adolc/install.sh M /issm/trunk-jpl/externalpackages/chaco/chaco.patch M /issm/trunk-jpl/externalpackages/matlab/install.sh M /issm/trunk-jpl/externalpackages/mitgcm/install.sh A /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp Vector object does not have an M size. \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11737-11738.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/adolc/install.sh M /issm/trunk-jpl/externalpackages/chaco/chaco.patch M /issm/trunk-jpl/externalpackages/matlab/install.sh M /issm/trunk-jpl/externalpackages/mitgcm/install.sh A /issm/trunk-jpl/externalpackages/petsc/install-2.3.2-macosx64.sh M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: Vector object does not have an M size. +M /issm/trunk-jpl/externalpackages/matlab/install.sh reverting \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11738-11739.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/matlab/install.sh \\ Export determination: 6. \\Rationale: reverting +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp Some legitimate demands if the vector is a NULL pointer \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11739-11740.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: Some legitimate demands if the vector is a NULL pointer +M /issm/trunk-jpl/src/m/model/extrude.m Added lat/lon extrusion \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11740-11741.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/extrude.m \\ Export determination: 6. \\Rationale: Added lat/lon extrusion +M /issm/trunk-jpl/externalpackages/chaco/chaco.patch reverted chaco installation back to normal (cannot compile on larsen/astrid) \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11741-11742.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/chaco/chaco.patch \\ Export determination: 6. \\Rationale: reverted chaco installation back to normal (cannot compile on larsen/astrid) +M /issm/trunk-jpl/src/m/model/extrude.m minor \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11742-11743.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/extrude.m \\ Export determination: 6. \\Rationale: minor +M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToPetscVector.cpp no NULL pointer allowed for Vector or Matrix \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11743-11744.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Matrix.h M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/patches/MatlabVectorToPetscVector.cpp \\ Export determination: 6. \\Rationale: no NULL pointer allowed for Vector or Matrix +M /issm/trunk-jpl/src/c/solutions/convergence.cpp no NULL pointer allowed for Vector or Matrix \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11744-11745.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/solutions/convergence.cpp \\ Export determination: 6. \\Rationale: no NULL pointer allowed for Vector or Matrix +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp fixed issue with GetSize \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11745-11746.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: fixed issue with GetSize +M /issm/trunk-jpl/execution Ignore test decks* \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11746-11747.diff: \\ Function name: \\M /issm/trunk-jpl/execution \\ Export determination: 6. \\Rationale: Ignore test decks* +A /issm/trunk-jpl/externalpackages/gsl A /issm/trunk-jpl/externalpackages/gsl/README A /issm/trunk-jpl/externalpackages/gsl/gsl-1.15.tar.gz A /issm/trunk-jpl/externalpackages/gsl/install-macosx64.sh gsl package \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-11747-11748.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gsl A /issm/trunk-jpl/externalpackages/gsl/README A /issm/trunk-jpl/externalpackages/gsl/gsl-1.15.tar.gz A /issm/trunk-jpl/externalpackages/gsl/install-macosx64.sh \\ Export determination: 6. \\Rationale: gsl package +A /issm/trunk-jpl/externalpackages/gmake A /issm/trunk-jpl/externalpackages/gmake/install.sh A /issm/trunk-jpl/externalpackages/gmake/make-3.82.tar.gz GNU make \\\\ Index: /issm/oecreview/Archive/11730-11748/r1.tex =================================================================== --- /issm/oecreview/Archive/11730-11748/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11730-11748/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11730 Index: /issm/oecreview/Archive/11730-11748/r2.tex =================================================================== --- /issm/oecreview/Archive/11730-11748/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11730-11748/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11748 Index: /issm/oecreview/Archive/11748-11766/Date.tex =================================================================== --- /issm/oecreview/Archive/11748-11766/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11748-11766/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11748-11766/ISSM-11748-11749.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11748-11749.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11748-11749.diff (revision 11991) @@ -0,0 +1,38 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/modelE/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/modelE/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/modelE/install.sh (revision 11749) +@@ -0,0 +1,17 @@ ++#!/bin/bash ++#modelE downloaded from the gis repository of the GISS (Goddard Institute for Space Studies) ++#at http://www.giss.nasa.gov/tools/modelE/ ++ ++#Some cleanup ++rm -rf src install modelE_AR5_branch ++mkdir src ++ ++#Untar ++tar -zxvf modelE_AR5_branch.2012.03.13_10.12.21.tgz ++ ++#Move modelE into install directory ++mv modelE_AR5_branch/* src ++rm -rf modelE_AR5_branch ++ ++#Apply patches ++cd src + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/modelE/install.sh +___________________________________________________________________ +Added: svn:executable + + * + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/modelE/modelE_AR5_branch.2012.03.13_10.12.21.tgz +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/modelE/modelE_AR5_branch.2012.03.13_10.12.21.tgz +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + Index: /issm/oecreview/Archive/11748-11766/ISSM-11749-11750.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11749-11750.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11749-11750.diff (revision 11991) @@ -0,0 +1,18 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/packagemaker/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/packagemaker/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/packagemaker/install.sh (revision 11750) +@@ -0,0 +1,7 @@ ++#!/bin/bash ++ ++#Erase symlink ++rm -rf install ++ ++#Select or create a new simlink ++ln -s /Developer/Applications/Utilities/PackageMaker.app/Contents/MacOS/ install + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/packagemaker/install.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11748-11766/ISSM-11750-11751.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11750-11751.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11750-11751.diff (revision 11991) @@ -0,0 +1,19 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/petsc +___________________________________________________________________ +Modified: svn:ignore + - install +src + + + install +install-3.1 +src + + + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/packagemaker +___________________________________________________________________ +Added: svn:ignore + + install + + Index: /issm/oecreview/Archive/11748-11766/ISSM-11751-11752.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11751-11752.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11751-11752.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11751) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment_variables.sh (revision 11752) +@@ -183,3 +183,6 @@ + + #gsl + GSL_DIR="$ISSM_TIER/externalpackages/gsl/install" ++ ++#gnu make ++GMAKE_DIR="$ISSM_TIER/externalpackages/gmake/install" +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11751) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/etc/environment.sh (revision 11752) +@@ -247,3 +247,6 @@ + + #GSL + export PATH="$PATH:$GSL_DIR/bin" ++ ++#GMAKE ++export PATH="$GMAKE_DIR/bin:$PATH" Index: /issm/oecreview/Archive/11748-11766/ISSM-11752-11753.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11752-11753.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11752-11753.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/geos5/install.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/geos5/install.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/geos5/install.sh (revision 11753) +@@ -0,0 +1,6 @@ ++#!/bin/bash ++ ++#Some cleanup ++rm -rf GEOSagcm ++#svn download ++svn --username eric.larour@jpl.nasa.gov checkout http://geos5.org/svn/branches/Fortuna-2_5_p1 GEOSagcm + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/geos5/install.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11748-11766/ISSM-11753-11754.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11753-11754.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11753-11754.diff (revision 11991) @@ -0,0 +1,285 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/proguard.cfg +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/proguard.cfg (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/proguard.cfg (revision 11754) +@@ -0,0 +1,40 @@ ++-optimizationpasses 5 ++-dontusemixedcaseclassnames ++-dontskipnonpubliclibraryclasses ++-dontpreverify ++-verbose ++-optimizations !code/simplification/arithmetic,!field/*,!class/merging/* ++ ++-keep public class * extends android.app.Activity ++-keep public class * extends android.app.Application ++-keep public class * extends android.app.Service ++-keep public class * extends android.content.BroadcastReceiver ++-keep public class * extends android.content.ContentProvider ++-keep public class * extends android.app.backup.BackupAgentHelper ++-keep public class * extends android.preference.Preference ++-keep public class com.android.vending.licensing.ILicensingService ++ ++-keepclasseswithmembernames class * { ++ native ; ++} ++ ++-keepclasseswithmembers class * { ++ public (android.content.Context, android.util.AttributeSet); ++} ++ ++-keepclasseswithmembers class * { ++ public (android.content.Context, android.util.AttributeSet, int); ++} ++ ++-keepclassmembers class * extends android.app.Activity { ++ public void *(android.view.View); ++} ++ ++-keepclassmembers enum * { ++ public static **[] values(); ++ public static ** valueOf(java.lang.String); ++} ++ ++-keep class * implements android.os.Parcelable { ++ public static final android.os.Parcelable$Creator *; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/project.properties +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/project.properties (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/project.properties (revision 11754) +@@ -0,0 +1,11 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must be checked in Version Control Systems. ++# ++# To customize properties used by the Ant build system use, ++# "ant.properties", and override values to adapt the script to your ++# project structure. ++ ++# Project target. ++target=android-15 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/local.properties +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/local.properties (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/local.properties (revision 11754) +@@ -0,0 +1,10 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must *NOT* be checked in Version Control Systems, ++# as it contains information specific to your local configuration. ++ ++# location of the SDK. This is only used by Ant ++# For customization when using a Version Control System, please read the ++# header note. ++sdk.dir=/Users/gperez/issm/trunk-jpl/externalpackages/android-sdk/install-sdk +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/AndroidManifest.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/AndroidManifest.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/AndroidManifest.xml (revision 11754) +@@ -0,0 +1,15 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld/HelloWorldActivity.java +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld/HelloWorldActivity.java (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld/HelloWorldActivity.java (revision 11754) +@@ -0,0 +1,15 @@ ++package com.example.helloworld; ++ ++import android.app.Activity; ++import android.os.Bundle; ++ ++public class HelloWorldActivity extends Activity ++{ ++ /** Called when the activity is first created. */ ++ @Override ++ public void onCreate(Bundle savedInstanceState) ++ { ++ super.onCreate(savedInstanceState); ++ setContentView(R.layout.main); ++ } ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/values/strings.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/values/strings.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/values/strings.xml (revision 11754) +@@ -0,0 +1,4 @@ ++ ++ ++ HelloWorldActivity ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/layout/main.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/layout/main.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/res/layout/main.xml (revision 11754) +@@ -0,0 +1,13 @@ ++ ++ ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/ant.properties +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/ant.properties (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/ant.properties (revision 11754) +@@ -0,0 +1,17 @@ ++# This file is used to override default values used by the Ant build system. ++# ++# This file must be checked in Version Control Systems, as it is ++# integral to the build system of your project. ++ ++# This file is only used by the Ant script. ++ ++# You can use this to override default values such as ++# 'source.dir' for the location of your java source folder and ++# 'out.dir' for the location of your output folder. ++ ++# You can also use it define how the release builds are signed by declaring ++# the following properties: ++# 'key.store' for the location of your keystore and ++# 'key.alias' for the name of the key to use. ++# The password will be asked during the build when you use the 'release' target. ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/build.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/build.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/build.xml (revision 11754) +@@ -0,0 +1,85 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ Index: /issm/oecreview/Archive/11748-11766/ISSM-11754-11755.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11754-11755.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11754-11755.diff (revision 11991) @@ -0,0 +1,22 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11754) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11755) +@@ -73,7 +73,7 @@ + Vector::Vector(Vec petsc_vec){ + + if(petsc_vec==NULL){ +- this->vector=NULL; ++ this->vector=NewVec(0); + } + else{ + /*copy vector*/ +@@ -215,6 +215,8 @@ + bool Vector::IsEmpty(void){ + + int M; ++ ++ _assert_(this->vector); + this->GetSize(&M); + + if(M==0) Index: /issm/oecreview/Archive/11748-11766/ISSM-11755-11756.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11755-11756.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11755-11756.diff (revision 11991) @@ -0,0 +1,14 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/slope.m +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/slope.m (revision 11755) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/m/model/slope.m (revision 11756) +@@ -26,7 +26,7 @@ + s=sqrt(sx.^2+sy.^2); + + if md.mesh.dimension==3, +- sx=project3d(md,sx,'element'); +- sy=project3d(md,sy,'element'); ++ sx=project3d(md,'vector',sx,'type','element'); ++ sy=project3d(md,'vector',sy,'type','element'); + s=sqrt(sx.^2+sy.^2); + end Index: /issm/oecreview/Archive/11748-11766/ISSM-11756-11757.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11756-11757.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11756-11757.diff (revision 11991) @@ -0,0 +1,8 @@ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/gsl +___________________________________________________________________ +Added: svn:ignore + + install +src + + Index: /issm/oecreview/Archive/11748-11766/ISSM-11757-11758.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11757-11758.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11757-11758.diff (revision 11991) @@ -0,0 +1,33 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11757) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp (revision 11758) +@@ -282,16 +282,10 @@ + int dummy=0; + + if (mxIsClass(dataref,"double") ){ ++ ++ /*Convert matlab matrix to matrix: */ ++ outmatrix=MatlabMatrixToMatrix(dataref); + +- /*Check dataref is not pointing to NaN: */ +- if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ +- outmatrix=new Matrix(0,0); +- } +- else{ +- +- /*Convert matlab matrix to petsc matrix: */ +- outmatrix=MatlabMatrixToMatrix(dataref); +- } + } + else{ + /*This is an error: we don't have the correct input!: */ +@@ -427,7 +421,7 @@ + /*}}}*/ + /*FUNCTION FetchMatlabData(Vector** pvector,const mxArray* dataref){{{1*/ + void FetchMatlabData(Vector** pvector,const mxArray* dataref){ +- ++ + Vector* vector=NULL; + int dummy; + Index: /issm/oecreview/Archive/11748-11766/ISSM-11758-11759.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11758-11759.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11758-11759.diff (revision 11991) @@ -0,0 +1,41 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11758) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11759) +@@ -84,6 +84,22 @@ + } + /*}}}*/ + #endif ++#ifdef _HAVE_GSL_ ++/*FUNCTION SeqVec*tor::SeqVec*tor(SeqVec* seq_vec){{{1*/ ++Vector::Vector(SeqVec* seq_vec){ ++ ++ if(seq_vec==NULL){ ++ this->vector=NULL; ++ } ++ else{ ++ /*copy vector*/ ++ this->vector=seq_vec->Duplicate(); ++ } ++ ++} ++/*}}}*/ ++#endif ++ + /*FUNCTION Vector::~Vector(){{{1*/ + Vector::~Vector(){ + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11758) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.h (revision 11759) +@@ -46,6 +46,9 @@ + #ifdef _HAVE_PETSC_ + Vector(Vec petsc_vec); + #endif ++ #ifdef _HAVE_GSL_ ++ Vector(SeqVec* seq_vec); ++ #endif + ~Vector(); + /*}}}*/ + /*Vector specific routines {{{1*/ Index: /issm/oecreview/Archive/11748-11766/ISSM-11759-11760.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11759-11760.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11759-11760.diff (revision 11991) @@ -0,0 +1,66 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11759) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/Solverx.cpp (revision 11760) +@@ -42,11 +42,23 @@ + + /*Create vector out of petsc vector: */ + uf=new Vector(uf_vector); ++ ++ /*Free ressources: */ ++ VecFree(&uf_vector); + #else + #ifdef _HAVE_GSL_ +- SolverxGsl(&uf->vector,Kff->matrix,pf->vector); ++ SeqVec* uf_vector=NULL; ++ ++ SolverxGsl(&uf_vector,Kff->matrix,pf->vector); ++ ++ /*Create vector out of SeqVec vector: */ ++ uf=new Vector(uf_vector); ++ ++ /*Free ressources: */ ++ delete uf_vector; ++ + #else +- _error_("not supported yet!"); ++ _error_("GSL support not compiled in!"); + #endif + #endif + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp (revision 11759) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp (revision 11760) +@@ -23,15 +23,17 @@ + /*Output: */ + SeqVec* uf = NULL; + +- /*We are going to do an in place LU decomp, so we need to save the matrix with its original structure: */ +- KffCopy=Kff->Duplicate(); +- ++ + /*GSL Matrices and vectors: */ + gsl_matrix_view m; + gsl_vector_view b; + gsl_vector* x=NULL; + gsl_permutation* p=NULL; + ++ /*We are going to do an in place LU decomp, so we need to save the matrix with its original structure: */ ++ KffCopy=Kff->Duplicate(); ++ ++ + /*Intermediary: */ + int M,N,N2,s; + +@@ -60,8 +62,10 @@ + /*Free resources:*/ + gsl_permutation_free (p); + gsl_vector_free (x); ++ + delete KffCopy; + ++ + /*Assign output pointers:*/ + *puf=uf; + } Index: /issm/oecreview/Archive/11748-11766/ISSM-11760-11761.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11760-11761.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11760-11761.diff (revision 11991) @@ -0,0 +1,109 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp (revision 11760) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp (revision 11761) +@@ -51,19 +51,21 @@ + + nz=(int)((double)nnz/(double)rows); + +- vector=(double*)xcalloc(rows,sizeof(double)); ++ if(rows){ ++ vector=(double*)xcalloc(rows,sizeof(double)); + +- /*Now, get ir,jc and pr: */ +- pr=mxGetPr(mxvector); +- ir=mxGetIr(mxvector); +- jc=mxGetJc(mxvector); ++ /*Now, get ir,jc and pr: */ ++ pr=mxGetPr(mxvector); ++ ir=mxGetIr(mxvector); ++ jc=mxGetJc(mxvector); + +- /*Now, start inserting data into sparse vector: */ +- count=0; +- for(i=0;iM=pM; ++ this->vector=NULL; + if(this->M) this->vector=(double*)xcalloc(pM,sizeof(double)); +- else this->vector=NULL; + } + /*}}}*/ + /*FUNCTION SeqVec::SeqVec(double* serial_vec,int M){{{1*/ +@@ -39,8 +39,11 @@ + int i,j; + + this->M=pM; +- this->vector=(double*)xcalloc(pM,sizeof(double)); +- memcpy(this->vector,buffer,pM*sizeof(double)); ++ this->vector=NULL; ++ if(this->M){ ++ this->vector=(double*)xcalloc(pM,sizeof(double)); ++ memcpy(this->vector,buffer,pM*sizeof(double)); ++ } + } + /*}}}*/ + /*FUNCTION SeqVec::~SeqVec(){{{1*/ +@@ -71,13 +74,16 @@ + mxArray* dataref=NULL; + + /*copy vector into a new buffer: */ +- buffer=(double*)xmalloc(this->M*sizeof(double)); +- memcpy(buffer,vector,M*sizeof(double)); ++ if(this->M){ ++ buffer=(double*)xmalloc(this->M*sizeof(double)); ++ memcpy(buffer,vector,M*sizeof(double)); + +- dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(dataref,this->M); +- mxSetN(dataref,1); +- mxSetPr(dataref,buffer); ++ dataref = mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(dataref,this->M); ++ mxSetN(dataref,1); ++ mxSetPr(dataref,buffer); ++ } ++ else dataref = mxCreateDoubleMatrix(0,0,mxREAL); + + + /*do not erase buffer!: */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp (revision 11761) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp (revision 11762) +@@ -31,7 +31,8 @@ + + this->M=pM; + this->N=pN; +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=NULL; ++ if(M*N) this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + } + /*}}}*/ + /*FUNCTION SeqMat::SeqMat(int M,int N, double sparsity){{{1*/ +@@ -39,7 +40,8 @@ + + this->M=pM; + this->N=pN; +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=NULL; ++ if(M*N) this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + } + /*}}}*/ + /*FUNCTION SeqMat(double* serial_mat,int M,int N,double sparsity){{{1*/ +@@ -49,8 +51,11 @@ + + this->M=pM; + this->N=pN; +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); +- memcpy(this->matrix,serial_mat,pM*pN*sizeof(double)); ++ this->matrix=NULL; ++ if(M*N){ ++ this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ memcpy(this->matrix,serial_mat,pM*pN*sizeof(double)); ++ } + + } + /*}}}*/ +@@ -59,7 +64,8 @@ + + this->M=pM; + this->N=pN; +- this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); ++ this->matrix=NULL; ++ if(M*N)this->matrix=(double*)xcalloc(pM*pN,sizeof(double)); + } + /*}}}*/ + /*FUNCTION SeqMat::~SeqMat(){{{1*/ +@@ -90,24 +96,36 @@ + /*FUNCTION SeqMat::ToMatlabMatrix{{{1*/ + mxArray* SeqMat::ToMatlabMatrix(void){ + ++ /*Intermediary: */ + double* buffer=NULL; ++ mxArray* pfield=NULL; + ++ /*output: */ + mxArray* dataref=NULL; + + /*copy vector into a new buffer: */ +- buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); +- memcpy(buffer,this->matrix,M*N*sizeof(double)); ++ if(this->M*this->N){ ++ buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); ++ memcpy(buffer,this->matrix,M*N*sizeof(double)); + +- dataref = mxCreateDoubleMatrix(0,0,mxREAL); +- mxSetM(dataref,this->M); +- mxSetN(dataref,this->N); +- mxSetPr(dataref,buffer); ++ pfield=mxCreateDoubleMatrix(0,0,mxREAL); ++ mxSetM(pfield,this->N); ++ mxSetN(pfield,this->M); ++ mxSetPr(pfield,buffer); ++ ++ //transpose the matrix, written directly to matlab! from C to matlab. ++ mexCallMATLAB(1,&dataref, 1, &pfield, "transpose"); ++ } ++ else dataref=mxCreateDoubleMatrix(0,0,mxREAL); + +- + /*do not erase buffer!: */ + return dataref; + + } ++ ++ ++ ++ + /*}}}*/ + /*FUNCTION MatlabMatrixToSeqMat{{{1*/ + SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ Index: /issm/oecreview/Archive/11748-11766/ISSM-11762-11763.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11762-11763.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11762-11763.diff (revision 11991) @@ -0,0 +1,95 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp (revision 11762) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp (revision 11763) +@@ -1,36 +0,0 @@ +-/* \file MatlabVectorToVector.cpp +- * \brief: convert a sparse or dense matlab vector to a vector: +- */ +- +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-#ifdef _SERIAL_ +- +-/*Matlab includes: */ +-#include "mex.h" +-#include "../../objects/objects.h" +- +-Vector* MatlabVectorToVector(const mxArray* mxvector){ +- +- Vector* vector=NULL; +- +- #ifdef _HAVE_PETSC_ +- /*allocate vector object: */ +- vector=new Vector(); +- +- /*Call Matlab to Petsc API: */ +- MatlabVectorToPetscVector(&vector->vector,&vector->M,mxvector); +- +- #else +- _error_("not supported yet!"); +- #endif +- +- return vector; +-} +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp (revision 11762) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp (revision 11763) +@@ -1,36 +0,0 @@ +-/* \file MatlabMatrixToMatrix.cpp +- * \brief: convert a sparse or dense matlab matrix to a matrix: +- */ +- +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-#ifdef _SERIAL_ +- +-/*Matlab includes: */ +-#include "mex.h" +-#include "../../objects/objects.h" +- +-Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ +- +- Matrix* matrix=NULL; +- +- #ifdef _HAVE_PETSC_ +- /*allocate matrix object: */ +- matrix=new Matrix(); +- +- /*Call Matlab to Petsc API: */ +- MatlabMatrixToPetscMatrix(&matrix->matrix,&matrix->M,&matrix->N,mxmatrix); +- +- #else +- _error_("not supported yet!"); +- #endif +- +- return matrix; +-} +-#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h (revision 11762) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h (revision 11763) +@@ -13,8 +13,6 @@ + int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +-Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); +-Vector* MatlabVectorToVector(const mxArray* mxvector); + #endif + + #endif Index: /issm/oecreview/Archive/11748-11766/ISSM-11763-11764.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11763-11764.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11763-11764.diff (revision 11991) @@ -0,0 +1,102 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch (revision 11763) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch (revision 11764) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = gcc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = cc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O2 -m32 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch (revision 11763) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch (revision 11764) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = icc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = cc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O2 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch (revision 11763) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch (revision 11764) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = gcc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = icc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O3 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch (revision 11763) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch (revision 11764) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = gcc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = cc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O2 -m64 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch (revision 11763) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch (revision 11764) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = gcc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = icc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O2 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch (revision 11763) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch (revision 11764) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = gcc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = cc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O2 Index: /issm/oecreview/Archive/11748-11766/ISSM-11764-11765.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11764-11765.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11764-11765.diff (revision 11991) @@ -0,0 +1,17 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 11764) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 11765) +@@ -1,10 +1,8 @@ +-3,5c3 ++3c3 + < CC = gcc +-< OBJ_EXT=o +-< LIB_EXT=a + --- + > CC = cc +-8c6 ++8c8 + < OPTFLAGS = -DLINUX -fPIC + --- + > OPTFLAGS = -O2 Index: /issm/oecreview/Archive/11748-11766/ISSM-11765-11766.diff =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-11765-11766.diff (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-11765-11766.diff (revision 11991) @@ -0,0 +1,55 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 11765) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch (revision 11766) +@@ -1,8 +1,10 @@ +-3c3 +-< CC = gcc ++3c3,5 ++< CC = cc + --- +-> CC = cc +-8c8 +-< OPTFLAGS = -DLINUX -fPIC ++> CC = gcc ++> OBJ_EXT=o ++> LIB_EXT=a ++6c8 ++< OPTFLAGS = -O2 + --- +-> OPTFLAGS = -O2 ++> OPTFLAGS = -DLINUX -fPIC +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/metis-4.0.patch +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/metis-4.0.patch (revision 11765) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/metis/metis-4.0.patch (revision 11766) +@@ -235,29 +235,3 @@ + + clean: + (cd Lib ; make clean ) +-diff -crB install/Makefile.in install2/Makefile.in +-*** install/Makefile.in 1998-10-02 14:28:35.000000000 -0700 +---- install2/Makefile.in 2011-06-08 15:19:00.536540378 -0700 +-*************** +-*** 1,9 **** +- +- # Which compiler to use +-! CC = cc +- +- # What optimization level to use +-! OPTFLAGS = -O2 +- +- # What options to be used by the compiler +- COPTIONS = +---- 1,11 ---- +- +- # Which compiler to use +-! CC = gcc +-! OBJ_EXT=o +-! LIB_EXT=a +- +- # What optimization level to use +-! OPTFLAGS = -DLINUX -fPIC +- +- # What options to be used by the compiler +- COPTIONS = Index: /issm/oecreview/Archive/11748-11766/ISSM-DocReview-11748-11766.tex =================================================================== --- /issm/oecreview/Archive/11748-11766/ISSM-DocReview-11748-11766.tex (revision 11991) +++ /issm/oecreview/Archive/11748-11766/ISSM-DocReview-11748-11766.tex (revision 11991) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature.eps} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/11748-11766/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/11748-11766/LogNumber.tex (revision 11991) +++ /issm/oecreview/Archive/11748-11766/LogNumber.tex (revision 11991) @@ -0,0 +1,1 @@ +11748-11766 Index: /issm/oecreview/Archive/11748-11766/Makefile =================================================================== --- /issm/oecreview/Archive/11748-11766/Makefile (revision 11991) +++ /issm/oecreview/Archive/11748-11766/Makefile (revision 11991) @@ -0,0 +1,11 @@ +name=ISSM-DocReview-11748-11766 + + +all: + latex $(name).tex + dvips $(name).dvi + ps2pdf $(name).ps $(name).pdf + rm -rf *.dvi *.log *.aux *.ps + +clean: + rm -rf *.dvi *.log *.aux Index: /issm/oecreview/Archive/11748-11766/log.tex =================================================================== --- /issm/oecreview/Archive/11748-11766/log.tex (revision 11991) +++ /issm/oecreview/Archive/11748-11766/log.tex (revision 11991) @@ -0,0 +1,36 @@ +\noindent \textbf{Change \#1} with diff file ISSM-11748-11749.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/gmake A /issm/trunk-jpl/externalpackages/gmake/install.sh A /issm/trunk-jpl/externalpackages/gmake/make-3.82.tar.gz \\ Export determination: 6. \\Rationale: GNU make +A /issm/trunk-jpl/externalpackages/modelE A /issm/trunk-jpl/externalpackages/modelE/install.sh A /issm/trunk-jpl/externalpackages/modelE/modelE\_AR5\_branch.2012.03.13\_10.12.21.tgz modelE from GISS \\\\ +\noindent \textbf{Change \#2} with diff file ISSM-11749-11750.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/modelE A /issm/trunk-jpl/externalpackages/modelE/install.sh A /issm/trunk-jpl/externalpackages/modelE/modelE\_AR5\_branch.2012.03.13\_10.12.21.tgz \\ Export determination: 6. \\Rationale: modelE from GISS +A /issm/trunk-jpl/externalpackages/packagemaker A /issm/trunk-jpl/externalpackages/packagemaker/install.sh packagemaker soft link \\\\ +\noindent \textbf{Change \#3} with diff file ISSM-11750-11751.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/packagemaker A /issm/trunk-jpl/externalpackages/packagemaker/install.sh \\ Export determination: 6. \\Rationale: packagemaker soft link +M /issm/trunk-jpl/externalpackages/packagemaker M /issm/trunk-jpl/externalpackages/petsc Some ignoring of files in svn \\\\ +\noindent \textbf{Change \#4} with diff file ISSM-11751-11752.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/packagemaker M /issm/trunk-jpl/externalpackages/petsc \\ Export determination: 6. \\Rationale: Some ignoring of files in svn +M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh GNU make environment variables \\\\ +\noindent \textbf{Change \#5} with diff file ISSM-11752-11753.diff: \\ Function name: \\M /issm/trunk-jpl/etc/environment.sh M /issm/trunk-jpl/etc/environment\_variables.sh \\ Export determination: 6. \\Rationale: GNU make environment variables +A /issm/trunk-jpl/externalpackages/geos5 A /issm/trunk-jpl/externalpackages/geos5/install.sh geos-5 \\\\ +\noindent \textbf{Change \#6} with diff file ISSM-11753-11754.diff: \\ Function name: \\A /issm/trunk-jpl/externalpackages/geos5 A /issm/trunk-jpl/externalpackages/geos5/install.sh \\ Export determination: 6. \\Rationale: geos-5 +A /issm/trunk-jpl/src/android/HelloWorldProject A /issm/trunk-jpl/src/android/HelloWorldProject/AndroidManifest.xml A /issm/trunk-jpl/src/android/HelloWorldProject/ant.properties A /issm/trunk-jpl/src/android/HelloWorldProject/bin A /issm/trunk-jpl/src/android/HelloWorldProject/build.xml A /issm/trunk-jpl/src/android/HelloWorldProject/libs A /issm/trunk-jpl/src/android/HelloWorldProject/local.properties A /issm/trunk-jpl/src/android/HelloWorldProject/proguard.cfg A /issm/trunk-jpl/src/android/HelloWorldProject/project.properties A /issm/trunk-jpl/src/android/HelloWorldProject/res A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi/ic\_launcher.png A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi/ic\_launcher.png A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi/ic\_launcher.png A /issm/trunk-jpl/src/android/HelloWorldProject/res/layout A /issm/trunk-jpl/src/android/HelloWorldProject/res/layout/main.xml A /issm/trunk-jpl/src/android/HelloWorldProject/res/values A /issm/trunk-jpl/src/android/HelloWorldProject/res/values/strings.xml A /issm/trunk-jpl/src/android/HelloWorldProject/src A /issm/trunk-jpl/src/android/HelloWorldProject/src/com A /issm/trunk-jpl/src/android/HelloWorldProject/src/com/example A /issm/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld A /issm/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld/HelloWorldActivity.java Added the simple HelloWorldProject to the Android directory. Makefile to replace ANT script to follow. \\\\ +\noindent \textbf{Change \#7} with diff file ISSM-11754-11755.diff: \\ Function name: \\A /issm/trunk-jpl/src/android/HelloWorldProject A /issm/trunk-jpl/src/android/HelloWorldProject/AndroidManifest.xml A /issm/trunk-jpl/src/android/HelloWorldProject/ant.properties A /issm/trunk-jpl/src/android/HelloWorldProject/bin A /issm/trunk-jpl/src/android/HelloWorldProject/build.xml A /issm/trunk-jpl/src/android/HelloWorldProject/libs A /issm/trunk-jpl/src/android/HelloWorldProject/local.properties A /issm/trunk-jpl/src/android/HelloWorldProject/proguard.cfg A /issm/trunk-jpl/src/android/HelloWorldProject/project.properties A /issm/trunk-jpl/src/android/HelloWorldProject/res A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi/ic\_launcher.png A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi/ic\_launcher.png A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi A /issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi/ic\_launcher.png A /issm/trunk-jpl/src/android/HelloWorldProject/res/layout A /issm/trunk-jpl/src/android/HelloWorldProject/res/layout/main.xml A /issm/trunk-jpl/src/android/HelloWorldProject/res/values A /issm/trunk-jpl/src/android/HelloWorldProject/res/values/strings.xml A /issm/trunk-jpl/src/android/HelloWorldProject/src A /issm/trunk-jpl/src/android/HelloWorldProject/src/com A /issm/trunk-jpl/src/android/HelloWorldProject/src/com/example A /issm/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld A /issm/trunk-jpl/src/android/HelloWorldProject/src/com/example/helloworld/HelloWorldActivity.java \\ Export determination: 6. \\Rationale: Added the simple HelloWorldProject to the Android directory. Makefile to replace ANT script to follow. +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp vector cannot be NULL \\\\ +\noindent \textbf{Change \#8} with diff file ISSM-11755-11756.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp \\ Export determination: 6. \\Rationale: vector cannot be NULL +M /issm/trunk-jpl/src/m/model/slope.m fixed slope routine (very old way of calling project3d) \\\\ +\noindent \textbf{Change \#9} with diff file ISSM-11756-11757.diff: \\ Function name: \\M /issm/trunk-jpl/src/m/model/slope.m \\ Export determination: 6. \\Rationale: fixed slope routine (very old way of calling project3d) +M /issm/trunk-jpl/externalpackages/gsl Ignore install and src files \\\\ +\noindent \textbf{Change \#10} with diff file ISSM-11757-11758.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/gsl \\ Export determination: 6. \\Rationale: Ignore install and src files +M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp Took out segfault, remnant of data references from Cielo \\\\ +\noindent \textbf{Change \#11} with diff file ISSM-11758-11759.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/io/Matlab/FetchMatlabData.cpp \\ Export determination: 6. \\Rationale: Took out segfault, remnant of data references from Cielo +M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h Fixed segfaults + bugs \\\\ +\noindent \textbf{Change \#12} with diff file ISSM-11759-11760.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/objects/Numerics/Vector.cpp M /issm/trunk-jpl/src/c/objects/Numerics/Vector.h \\ Export determination: 6. \\Rationale: Fixed segfaults + bugs +M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp More robuts Solverx \\\\ +\noindent \textbf{Change \#13} with diff file ISSM-11760-11761.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/modules/Solverx/Solverx.cpp M /issm/trunk-jpl/src/c/modules/Solverx/SolverxGsl.cpp \\ Export determination: 6. \\Rationale: More robuts Solverx +M /issm/trunk-jpl/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp M /issm/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp More checks on empty matrices and vectors \\\\ +\noindent \textbf{Change \#14} with diff file ISSM-11761-11762.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/toolkits/double/MatlabMatrixToDoubleMatrix.cpp M /issm/trunk-jpl/src/c/toolkits/double/MatlabVectorToDoubleVector.cpp \\ Export determination: 6. \\Rationale: More checks on empty matrices and vectors +M /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp M /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp More checks on empty matrices and vectors \\\\ +\noindent \textbf{Change \#15} with diff file ISSM-11762-11763.diff: \\ Function name: \\M /issm/trunk-jpl/src/c/toolkits/issm/SeqMat.cpp M /issm/trunk-jpl/src/c/toolkits/issm/SeqVec.cpp \\ Export determination: 6. \\Rationale: More checks on empty matrices and vectors +D /issm/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp D /issm/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp M /issm/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h removed unused functions \\\\ +\noindent \textbf{Change \#16} with diff file ISSM-11763-11764.diff: \\ Function name: \\D /issm/trunk-jpl/src/c/toolkits/matlab/MatlabMatrixToMatrix.cpp D /issm/trunk-jpl/src/c/toolkits/matlab/MatlabVectorToVector.cpp M /issm/trunk-jpl/src/c/toolkits/matlab/matlabincludes.h \\ Export determination: 6. \\Rationale: removed unused functions +M /issm/trunk-jpl/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch Fixed patches to get the right library extensions \\\\ +\noindent \textbf{Change \#17} with diff file ISSM-11764-11765.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/metis/configs/4.0/altix64/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/cosmos/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/greenplanet/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/macosx32/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/macosx64/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/configs/4.0/pleiades/Makefile.in.patch \\ Export determination: 6. \\Rationale: Fixed patches to get the right library extensions +M /issm/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch fPIC \\\\ +\noindent \textbf{Change \#18} with diff file ISSM-11765-11766.diff: \\ Function name: \\M /issm/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch \\ Export determination: 6. \\Rationale: fPIC +M /issm/trunk-jpl/externalpackages/metis/configs/4.0/linux64/Makefile.in.patch M /issm/trunk-jpl/externalpackages/metis/metis-4.0.patch Fixed linux 64 patch \\\\ Index: /issm/oecreview/Archive/11748-11766/r1.tex =================================================================== --- /issm/oecreview/Archive/11748-11766/r1.tex (revision 11991) +++ /issm/oecreview/Archive/11748-11766/r1.tex (revision 11991) @@ -0,0 +1,1 @@ +11748 Index: /issm/oecreview/Archive/11748-11766/r2.tex =================================================================== --- /issm/oecreview/Archive/11748-11766/r2.tex (revision 11991) +++ /issm/oecreview/Archive/11748-11766/r2.tex (revision 11991) @@ -0,0 +1,1 @@ +11766 Index: /issm/oecreview/Archive/11767-11785/Date.tex =================================================================== --- /issm/oecreview/Archive/11767-11785/Date.tex (revision 11991) +++ /issm/oecreview/Archive/11767-11785/Date.tex (revision 11991) @@ -0,0 +1,1 @@ +Apr-16-2012 Index: /issm/oecreview/Archive/11767-11785/ISSM-11767-11768.diff =================================================================== --- /issm/oecreview/Archive/11767-11785/ISSM-11767-11768.diff (revision 11991) +++ /issm/oecreview/Archive/11767-11785/ISSM-11767-11768.diff (revision 11991) @@ -0,0 +1,38 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh (revision 11768) +@@ -0,0 +1,27 @@ ++#!/bin/sh ++ ++./configure \ ++ --prefix=$ISSM_TIER \ ++ --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_TIER/externalpackages/mpich2/install/lib/ -lmpich" \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ ++ --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ ++ --with-graphics-lib=/usr/lib64/libX11.so \ ++ --with-scotch-dir="$ISSM_TIER/externalpackages/scotch/install" \ ++ --with-chaco-dir="$ISSM_TIER/externalpackages/chaco/install" \ ++ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ ++ --with-numthreads=18 \ ++ --enable-debugging \ ++ --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install ++ ++ ++# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ ++# --with-petsc-arch=$ISSM_ARCH \ ++# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ ++# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ \ ++# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/configs/config-linux64-murdo-nopetsc.sh +___________________________________________________________________ +Added: svn:executable + + * + Index: /issm/oecreview/Archive/11767-11785/ISSM-11768-11769.diff =================================================================== --- /issm/oecreview/Archive/11767-11785/ISSM-11768-11769.diff (revision 11991) +++ /issm/oecreview/Archive/11767-11785/ISSM-11768-11769.diff (revision 11991) @@ -0,0 +1,21 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11768) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/objects/Numerics/Vector.cpp (revision 11769) +@@ -85,7 +85,7 @@ + /*}}}*/ + #endif + #ifdef _HAVE_GSL_ +-/*FUNCTION SeqVec*tor::SeqVec*tor(SeqVec* seq_vec){{{1*/ ++/*FUNCTION Vector::Vector(SeqVec* seq_vec){{{1*/ + Vector::Vector(SeqVec* seq_vec){ + + if(seq_vec==NULL){ +@@ -95,7 +95,6 @@ + /*copy vector*/ + this->vector=seq_vec->Duplicate(); + } +- + } + /*}}}*/ + #endif Index: /issm/oecreview/Archive/11767-11785/ISSM-11770-11771.diff =================================================================== --- /issm/oecreview/Archive/11767-11785/ISSM-11770-11771.diff (revision 11991) +++ /issm/oecreview/Archive/11767-11785/ISSM-11770-11771.diff (revision 11991) @@ -0,0 +1,678 @@ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/Android.mk +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/Android.mk (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/Android.mk (revision 11771) +@@ -0,0 +1,41 @@ ++# Copyright (C) 2009 The Android Open Source Project ++# ++# Licensed under the Apache License, Version 2.0 (the "License"); ++# you may not use this file except in compliance with the License. ++# You may obtain a copy of the License at ++# ++# http://www.apache.org/licenses/LICENSE-2.0 ++# ++# Unless required by applicable law or agreed to in writing, software ++# distributed under the License is distributed on an "AS IS" BASIS, ++# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++# See the License for the specific language governing permissions and ++# limitations under the License. ++# ++ ++# the purpose of this sample is to demonstrate how one can ++# generate two distinct shared libraries and have them both ++# uploaded in ++# ++ ++LOCAL_PATH:= $(call my-dir) ++ ++# first lib, which will be built statically ++# ++include $(CLEAR_VARS) ++ ++LOCAL_MODULE := libtwolib-first ++LOCAL_SRC_FILES := first.c ++ ++include $(BUILD_STATIC_LIBRARY) ++ ++# second lib, which will depend on and include the first one ++# ++include $(CLEAR_VARS) ++ ++LOCAL_MODULE := libtwolib-second ++LOCAL_SRC_FILES := second.c ++ ++LOCAL_STATIC_LIBRARIES := libtwolib-first ++ ++include $(BUILD_SHARED_LIBRARY) +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/first.c +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/first.c (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/first.c (revision 11771) +@@ -0,0 +1,22 @@ ++/* ++ * Copyright (C) 2009 The Android Open Source Project ++ * ++ * Licensed under the Apache License, Version 2.0 (the "License"); ++ * you may not use this file except in compliance with the License. ++ * You may obtain a copy of the License at ++ * ++ * http://www.apache.org/licenses/LICENSE-2.0 ++ * ++ * Unless required by applicable law or agreed to in writing, software ++ * distributed under the License is distributed on an "AS IS" BASIS, ++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++ * See the License for the specific language governing permissions and ++ * limitations under the License. ++ * ++ */ ++#include "first.h" ++ ++int first(int x, int y) ++{ ++ return x + y; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/second.c +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/second.c (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/second.c (revision 11771) +@@ -0,0 +1,27 @@ ++/* ++ * Copyright (C) 2009 The Android Open Source Project ++ * ++ * Licensed under the Apache License, Version 2.0 (the "License"); ++ * you may not use this file except in compliance with the License. ++ * You may obtain a copy of the License at ++ * ++ * http://www.apache.org/licenses/LICENSE-2.0 ++ * ++ * Unless required by applicable law or agreed to in writing, software ++ * distributed under the License is distributed on an "AS IS" BASIS, ++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++ * See the License for the specific language governing permissions and ++ * limitations under the License. ++ * ++ */ ++#include "first.h" ++#include ++ ++jint ++Java_com_example_twolibs_TwoLibs_add( JNIEnv* env, ++ jobject this, ++ jint x, ++ jint y ) ++{ ++ return first(x, y); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/first.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/first.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/jni/first.h (revision 11771) +@@ -0,0 +1,22 @@ ++/* ++ * Copyright (C) 2009 The Android Open Source Project ++ * ++ * Licensed under the Apache License, Version 2.0 (the "License"); ++ * you may not use this file except in compliance with the License. ++ * You may obtain a copy of the License at ++ * ++ * http://www.apache.org/licenses/LICENSE-2.0 ++ * ++ * Unless required by applicable law or agreed to in writing, software ++ * distributed under the License is distributed on an "AS IS" BASIS, ++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++ * See the License for the specific language governing permissions and ++ * limitations under the License. ++ * ++ */ ++#ifndef FIRST_H ++#define FIRST_H ++ ++extern int first(int x, int y); ++ ++#endif /* FIRST_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/proguard.cfg +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/proguard.cfg (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/proguard.cfg (revision 11771) +@@ -0,0 +1,40 @@ ++-optimizationpasses 5 ++-dontusemixedcaseclassnames ++-dontskipnonpubliclibraryclasses ++-dontpreverify ++-verbose ++-optimizations !code/simplification/arithmetic,!field/*,!class/merging/* ++ ++-keep public class * extends android.app.Activity ++-keep public class * extends android.app.Application ++-keep public class * extends android.app.Service ++-keep public class * extends android.content.BroadcastReceiver ++-keep public class * extends android.content.ContentProvider ++-keep public class * extends android.app.backup.BackupAgentHelper ++-keep public class * extends android.preference.Preference ++-keep public class com.android.vending.licensing.ILicensingService ++ ++-keepclasseswithmembernames class * { ++ native ; ++} ++ ++-keepclasseswithmembers class * { ++ public (android.content.Context, android.util.AttributeSet); ++} ++ ++-keepclasseswithmembers class * { ++ public (android.content.Context, android.util.AttributeSet, int); ++} ++ ++-keepclassmembers class * extends android.app.Activity { ++ public void *(android.view.View); ++} ++ ++-keepclassmembers enum * { ++ public static **[] values(); ++ public static ** valueOf(java.lang.String); ++} ++ ++-keep class * implements android.os.Parcelable { ++ public static final android.os.Parcelable$Creator *; ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/project.properties +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/project.properties (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/project.properties (revision 11771) +@@ -0,0 +1,11 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must be checked in Version Control Systems. ++# ++# To customize properties used by the Ant build system use, ++# "ant.properties", and override values to adapt the script to your ++# project structure. ++ ++# Project target. ++target=android-15 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/default.properties +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/default.properties (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/default.properties (revision 11771) +@@ -0,0 +1,11 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must be checked in Version Control Systems. ++# ++# To customize properties used by the Ant build system use, ++# "build.properties", and override values to adapt the script to your ++# project structure. ++ ++# Project target. ++target=android-3 +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/AndroidManifest.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/AndroidManifest.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/AndroidManifest.xml (revision 11771) +@@ -0,0 +1,21 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/src/com/example/TwoLib/TwoLibTest.java +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/src/com/example/TwoLib/TwoLibTest.java (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/tests/src/com/example/TwoLib/TwoLibTest.java (revision 11771) +@@ -0,0 +1,21 @@ ++package com.example.TwoLib; ++ ++import android.test.ActivityInstrumentationTestCase; ++ ++/** ++ * This is a simple framework for a test of an Application. See ++ * {@link android.test.ApplicationTestCase ApplicationTestCase} for more information on ++ * how to write and extend Application tests. ++ *

++ * To run this test, you can type: ++ * adb shell am instrument -w \ ++ * -e class com.example.TwoLib.TwoLibTest \ ++ * com.example.TwoLib.tests/android.test.InstrumentationTestRunner ++ */ ++public class TwoLibTest extends ActivityInstrumentationTestCase { ++ ++ public TwoLibTest() { ++ super("com.example.TwoLib", TwoLib.class); ++ } ++ ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/AndroidManifest.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/AndroidManifest.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/AndroidManifest.xml (revision 11771) +@@ -0,0 +1,16 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/src/com/example/twolibs/TwoLibs.java +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/src/com/example/twolibs/TwoLibs.java (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/src/com/example/twolibs/TwoLibs.java (revision 11771) +@@ -0,0 +1,46 @@ ++/* ++ * Copyright (C) 2009 The Android Open Source Project ++ * ++ * Licensed under the Apache License, Version 2.0 (the "License"); ++ * you may not use this file except in compliance with the License. ++ * You may obtain a copy of the License at ++ * ++ * http://www.apache.org/licenses/LICENSE-2.0 ++ * ++ * Unless required by applicable law or agreed to in writing, software ++ * distributed under the License is distributed on an "AS IS" BASIS, ++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++ * See the License for the specific language governing permissions and ++ * limitations under the License. ++ */ ++package com.example.twolibs; ++ ++import android.app.Activity; ++import android.widget.TextView; ++import android.os.Bundle; ++ ++public class TwoLibs extends Activity ++{ ++ /** Called when the activity is first created. */ ++ @Override ++ public void onCreate(Bundle savedInstanceState) ++ { ++ super.onCreate(savedInstanceState); ++ ++ TextView tv = new TextView(this); ++ int x = 1000; ++ int y = 42; ++ ++ // here, we dynamically load the library at runtime ++ // before calling the native method. ++ // ++ System.loadLibrary("twolib-second"); ++ ++ int z = add(x, y); ++ ++ tv.setText( "The sum of " + x + " and " + y + " is " + z ); ++ setContentView(tv); ++ } ++ ++ public native int add(int x, int y); ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs.ap_.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs.ap_.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs.ap_.d (revision 11771) +@@ -0,0 +1,3 @@ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/bin/two-libs.ap_ \ ++ : /Users/gperez/issm/trunk-jpl/src/android/two-libs/res/values/strings.xml \ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/AndroidManifest.xml \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug-unaligned.apk +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug-unaligned.apk +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug-unaligned.apk.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug-unaligned.apk.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug-unaligned.apk.d (revision 11771) +@@ -0,0 +1,4 @@ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/bin/two-libs-debug-unaligned.apk : \ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/bin/two-libs.ap_ \ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/bin/classes.dex \ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/libs/armeabi/libtwolib-second.so \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes.dex +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes.dex +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/R$string.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/R$string.class +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/R$attr.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/R$attr.class +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/R.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/R.class +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/TwoLibs.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes/com/example/twolibs/TwoLibs.class +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/build.prop +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/build.prop (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/build.prop (revision 11771) +@@ -0,0 +1,10 @@ ++#Last build type ++#Wed, 21 Mar 2012 11:35:09 -0700 ++ ++build.last.target=debug ++ ++build.last.is.instrumented=false ++ ++build.last.is.packaging.debug=true ++ ++build.last.is.signing.debug=true +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes.dex.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes.dex.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/classes.dex.d (revision 11771) +@@ -0,0 +1 @@ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/bin/classes.dex : \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug.apk +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs-debug.apk +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs.ap_ +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream + +Property changes on: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/bin/two-libs.ap_ +___________________________________________________________________ +Added: svn:mime-type + + application/octet-stream + +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/gen/R.java.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/gen/R.java.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/gen/R.java.d (revision 11771) +@@ -0,0 +1,3 @@ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/gen/com/example/twolibs/R.java \ ++ : /Users/gperez/issm/trunk-jpl/src/android/two-libs/res/values/strings.xml \ ++/Users/gperez/issm/trunk-jpl/src/android/two-libs/AndroidManifest.xml \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/gen/com/example/twolibs/R.java +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/gen/com/example/twolibs/R.java (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/gen/com/example/twolibs/R.java (revision 11771) +@@ -0,0 +1,16 @@ ++/* AUTO-GENERATED FILE. DO NOT MODIFY. ++ * ++ * This class was automatically generated by the ++ * aapt tool from the resource data it found. It ++ * should not be modified by hand. ++ */ ++ ++package com.example.twolibs; ++ ++public final class R { ++ public static final class attr { ++ } ++ public static final class string { ++ public static final int app_name=0x7f020000; ++ } ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/res/values/strings.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/res/values/strings.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/res/values/strings.xml (revision 11771) +@@ -0,0 +1,4 @@ ++ ++ ++ TwoLib ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/obj/local/armeabi/objs/twolib-first/first.o.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/obj/local/armeabi/objs/twolib-first/first.o.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/obj/local/armeabi/objs/twolib-first/first.o.d (revision 11771) +@@ -0,0 +1,3 @@ ++obj/local/armeabi/objs/twolib-first/first.o: jni/first.c jni/first.h ++ ++jni/first.h: +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/obj/local/armeabi/objs/twolib-second/second.o.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/obj/local/armeabi/objs/twolib-second/second.o.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/obj/local/armeabi/objs/twolib-second/second.o.d (revision 11771) +@@ -0,0 +1,6 @@ ++obj/local/armeabi/objs/twolib-second/second.o: jni/second.c jni/first.h \ ++ /Users/gperez/issm/trunk-jpl/externalpackages/android-ndk/install/platforms/android-3/arch-arm/usr/include/jni.h ++ ++jni/first.h: ++ ++/Users/gperez/issm/trunk-jpl/externalpackages/android-ndk/install/platforms/android-3/arch-arm/usr/include/jni.h: +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/build.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/build.xml (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/two-libs/build.xml (revision 11771) +@@ -0,0 +1,85 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/local.properties +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/local.properties (revision 11770) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/local.properties (revision 11771) +@@ -1,10 +0,0 @@ +-# This file is automatically generated by Android Tools. +-# Do not modify this file -- YOUR CHANGES WILL BE ERASED! +-# +-# This file must *NOT* be checked in Version Control Systems, +-# as it contains information specific to your local configuration. +- +-# location of the SDK. This is only used by Ant +-# For customization when using a Version Control System, please read the +-# header note. +-sdk.dir=/Users/gperez/issm/trunk-jpl/externalpackages/android-sdk/install-sdk +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/gen/R.java.d +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/gen/R.java.d (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/gen/R.java.d (revision 11771) +@@ -0,0 +1,10 @@ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/gen/com/example/helloworld/R.java \ ++ : /Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-hdpi/ic_launcher.png \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-ldpi/ic_launcher.png \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/res/drawable-mdpi/ic_launcher.png \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/res/layout/main.xml \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/res/values/strings.xml \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/bin/res/drawable-hdpi/ic_launcher.png \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/bin/res/drawable-ldpi/ic_launcher.png \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/bin/res/drawable-mdpi/ic_launcher.png \ ++/Users/gperez/issm/trunk-jpl/src/android/HelloWorldProject/AndroidManifest.xml \ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/gen/com/example/helloworld/R.java +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/gen/com/example/helloworld/R.java (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/gen/com/example/helloworld/R.java (revision 11771) +@@ -0,0 +1,22 @@ ++/* AUTO-GENERATED FILE. DO NOT MODIFY. ++ * ++ * This class was automatically generated by the ++ * aapt tool from the resource data it found. It ++ * should not be modified by hand. ++ */ ++ ++package com.example.helloworld; ++ ++public final class R { ++ public static final class attr { ++ } ++ public static final class drawable { ++ public static final int ic_launcher=0x7f020000; ++ } ++ public static final class layout { ++ public static final int main=0x7f030000; ++ } ++ public static final class string { ++ public static final int app_name=0x7f040000; ++ } ++} +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/makefile +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/makefile (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/makefile (revision 11771) +@@ -0,0 +1,7 @@ ++.PHONY build : ++ # $(ANDROID_SDK_DIR)/tools/emulator -avd Android-4.0.3 ++ $(ANDROID_ANT_DIR)/bin/ant debug ++ # $(ANDROID_SDK_DIR)/platform-tools/adb install ./bin/HelloWorldProject-debug.apk ++ ++clean : ++ rm -rf bin +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/build.xml +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/build.xml (revision 11770) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/HelloWorldProject/build.xml (revision 11771) +@@ -1,5 +1,5 @@ + +- ++ + + unnamed array of char_type ++ * @endcode ++ * ++ * Where the _M_p points to the first character in the string, and ++ * you cast it to a pointer-to-_Rep and subtract 1 to get a ++ * pointer to the header. ++ * ++ * This approach has the enormous advantage that a string object ++ * requires only one allocation. All the ugliness is confined ++ * within a single pair of inline functions, which each compile to ++ * a single "add" instruction: _Rep::_M_refdata(), and ++ * __rc_string_base::_M_rep(); and the allocation function which gets a ++ * block of raw bytes and with room enough and constructs a _Rep ++ * object at the front. ++ * ++ * The reason you want _M_data pointing to the character array and ++ * not the _Rep is so that the debugger can see the string ++ * contents. (Probably we should add a non-inline member to get ++ * the _Rep for the debugger to use, so users can check the actual ++ * string length.) ++ * ++ * Note that the _Rep object is a POD so that you can have a ++ * static "empty string" _Rep object already "constructed" before ++ * static constructors have run. The reference-count encoding is ++ * chosen so that a 0 indicates one reference, so you never try to ++ * destroy the empty-string _Rep object. ++ * ++ * All but the last paragraph is considered pretty conventional ++ * for a C++ string implementation. ++ */ ++ template ++ class __rc_string_base ++ : protected __vstring_utility<_CharT, _Traits, _Alloc> ++ { ++ public: ++ typedef _Traits traits_type; ++ typedef typename _Traits::char_type value_type; ++ typedef _Alloc allocator_type; ++ ++ typedef __vstring_utility<_CharT, _Traits, _Alloc> _Util_Base; ++ typedef typename _Util_Base::_CharT_alloc_type _CharT_alloc_type; ++ typedef typename _CharT_alloc_type::size_type size_type; ++ ++ private: ++ // _Rep: string representation ++ // Invariants: ++ // 1. String really contains _M_length + 1 characters: due to 21.3.4 ++ // must be kept null-terminated. ++ // 2. _M_capacity >= _M_length ++ // Allocated memory is always (_M_capacity + 1) * sizeof(_CharT). ++ // 3. _M_refcount has three states: ++ // -1: leaked, one reference, no ref-copies allowed, non-const. ++ // 0: one reference, non-const. ++ // n>0: n + 1 references, operations require a lock, const. ++ // 4. All fields == 0 is an empty string, given the extra storage ++ // beyond-the-end for a null terminator; thus, the shared ++ // empty string representation needs no constructor. ++ struct _Rep ++ { ++ union ++ { ++ struct ++ { ++ size_type _M_length; ++ size_type _M_capacity; ++ _Atomic_word _M_refcount; ++ } _M_info; ++ ++ // Only for alignment purposes. ++ _CharT _M_align; ++ }; ++ ++ typedef typename _Alloc::template rebind<_Rep>::other _Rep_alloc_type; ++ ++ _CharT* ++ _M_refdata() throw() ++ { return reinterpret_cast<_CharT*>(this + 1); } ++ ++ _CharT* ++ _M_refcopy() throw() ++ { ++ __atomic_add_dispatch(&_M_info._M_refcount, 1); ++ return _M_refdata(); ++ } // XXX MT ++ ++ void ++ _M_set_length(size_type __n) ++ { ++ _M_info._M_refcount = 0; // One reference. ++ _M_info._M_length = __n; ++ // grrr. (per 21.3.4) ++ // You cannot leave those LWG people alone for a second. ++ traits_type::assign(_M_refdata()[__n], _CharT()); ++ } ++ ++ // Create & Destroy ++ static _Rep* ++ _S_create(size_type, size_type, const _Alloc&); ++ ++ void ++ _M_destroy(const _Alloc&) throw(); ++ ++ _CharT* ++ _M_clone(const _Alloc&, size_type __res = 0); ++ }; ++ ++ struct _Rep_empty ++ : public _Rep ++ { ++ _CharT _M_terminal; ++ }; ++ ++ static _Rep_empty _S_empty_rep; ++ ++ // The maximum number of individual char_type elements of an ++ // individual string is determined by _S_max_size. This is the ++ // value that will be returned by max_size(). (Whereas npos ++ // is the maximum number of bytes the allocator can allocate.) ++ // If one was to divvy up the theoretical largest size string, ++ // with a terminating character and m _CharT elements, it'd ++ // look like this: ++ // npos = sizeof(_Rep) + (m * sizeof(_CharT)) + sizeof(_CharT) ++ // + sizeof(_Rep) - 1 ++ // (NB: last two terms for rounding reasons, see _M_create below) ++ // Solving for m: ++ // m = ((npos - 2 * sizeof(_Rep) + 1) / sizeof(_CharT)) - 1 ++ // In addition, this implementation halves this amount. ++ enum { _S_max_size = (((static_cast(-1) - 2 * sizeof(_Rep) ++ + 1) / sizeof(_CharT)) - 1) / 2 }; ++ ++ // Data Member (private): ++ mutable typename _Util_Base::template _Alloc_hider<_Alloc> _M_dataplus; ++ ++ void ++ _M_data(_CharT* __p) ++ { _M_dataplus._M_p = __p; } ++ ++ _Rep* ++ _M_rep() const ++ { return &((reinterpret_cast<_Rep*>(_M_data()))[-1]); } ++ ++ _CharT* ++ _M_grab(const _Alloc& __alloc) const ++ { ++ return (!_M_is_leaked() && _M_get_allocator() == __alloc) ++ ? _M_rep()->_M_refcopy() : _M_rep()->_M_clone(__alloc); ++ } ++ ++ void ++ _M_dispose() ++ { ++ if (__exchange_and_add_dispatch(&_M_rep()->_M_info._M_refcount, ++ -1) <= 0) ++ _M_rep()->_M_destroy(_M_get_allocator()); ++ } // XXX MT ++ ++ bool ++ _M_is_leaked() const ++ { return _M_rep()->_M_info._M_refcount < 0; } ++ ++ void ++ _M_set_sharable() ++ { _M_rep()->_M_info._M_refcount = 0; } ++ ++ void ++ _M_leak_hard(); ++ ++ // _S_construct_aux is used to implement the 21.3.1 para 15 which ++ // requires special behaviour if _InIterator is an integral type ++ template ++ static _CharT* ++ _S_construct_aux(_InIterator __beg, _InIterator __end, ++ const _Alloc& __a, std::__false_type) ++ { ++ typedef typename iterator_traits<_InIterator>::iterator_category _Tag; ++ return _S_construct(__beg, __end, __a, _Tag()); ++ } ++ ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 438. Ambiguity in the "do the right thing" clause ++ template ++ static _CharT* ++ _S_construct_aux(_Integer __beg, _Integer __end, ++ const _Alloc& __a, std::__true_type) ++ { return _S_construct(static_cast(__beg), __end, __a); } ++ ++ template ++ static _CharT* ++ _S_construct(_InIterator __beg, _InIterator __end, const _Alloc& __a) ++ { ++ typedef typename std::__is_integer<_InIterator>::__type _Integral; ++ return _S_construct_aux(__beg, __end, __a, _Integral()); ++ } ++ ++ // For Input Iterators, used in istreambuf_iterators, etc. ++ template ++ static _CharT* ++ _S_construct(_InIterator __beg, _InIterator __end, const _Alloc& __a, ++ std::input_iterator_tag); ++ ++ // For forward_iterators up to random_access_iterators, used for ++ // string::iterator, _CharT*, etc. ++ template ++ static _CharT* ++ _S_construct(_FwdIterator __beg, _FwdIterator __end, const _Alloc& __a, ++ std::forward_iterator_tag); ++ ++ static _CharT* ++ _S_construct(size_type __req, _CharT __c, const _Alloc& __a); ++ ++ public: ++ size_type ++ _M_max_size() const ++ { return size_type(_S_max_size); } ++ ++ _CharT* ++ _M_data() const ++ { return _M_dataplus._M_p; } ++ ++ size_type ++ _M_length() const ++ { return _M_rep()->_M_info._M_length; } ++ ++ size_type ++ _M_capacity() const ++ { return _M_rep()->_M_info._M_capacity; } ++ ++ bool ++ _M_is_shared() const ++ { return _M_rep()->_M_info._M_refcount > 0; } ++ ++ void ++ _M_set_leaked() ++ { _M_rep()->_M_info._M_refcount = -1; } ++ ++ void ++ _M_leak() // for use in begin() & non-const op[] ++ { ++ if (!_M_is_leaked()) ++ _M_leak_hard(); ++ } ++ ++ void ++ _M_set_length(size_type __n) ++ { _M_rep()->_M_set_length(__n); } ++ ++ __rc_string_base() ++ : _M_dataplus(_S_empty_rep._M_refcopy()) { } ++ ++ __rc_string_base(const _Alloc& __a); ++ ++ __rc_string_base(const __rc_string_base& __rcs); ++ ++#ifdef __GXX_EXPERIMENTAL_CXX0X__ ++ __rc_string_base(__rc_string_base&& __rcs) ++ : _M_dataplus(__rcs._M_get_allocator(), __rcs._M_data()) ++ { __rcs._M_data(_S_empty_rep._M_refcopy()); } ++#endif ++ ++ __rc_string_base(size_type __n, _CharT __c, const _Alloc& __a); ++ ++ template ++ __rc_string_base(_InputIterator __beg, _InputIterator __end, ++ const _Alloc& __a); ++ ++ ~__rc_string_base() ++ { _M_dispose(); } ++ ++ allocator_type& ++ _M_get_allocator() ++ { return _M_dataplus; } ++ ++ const allocator_type& ++ _M_get_allocator() const ++ { return _M_dataplus; } ++ ++ void ++ _M_swap(__rc_string_base& __rcs); ++ ++ void ++ _M_assign(const __rc_string_base& __rcs); ++ ++ void ++ _M_reserve(size_type __res); ++ ++ void ++ _M_mutate(size_type __pos, size_type __len1, const _CharT* __s, ++ size_type __len2); ++ ++ void ++ _M_erase(size_type __pos, size_type __n); ++ ++ void ++ _M_clear() ++ { _M_erase(size_type(0), _M_length()); } ++ ++ bool ++ _M_compare(const __rc_string_base&) const ++ { return false; } ++ }; ++ ++ template ++ typename __rc_string_base<_CharT, _Traits, _Alloc>::_Rep_empty ++ __rc_string_base<_CharT, _Traits, _Alloc>::_S_empty_rep; ++ ++ template ++ typename __rc_string_base<_CharT, _Traits, _Alloc>::_Rep* ++ __rc_string_base<_CharT, _Traits, _Alloc>::_Rep:: ++ _S_create(size_type __capacity, size_type __old_capacity, ++ const _Alloc& __alloc) ++ { ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 83. String::npos vs. string::max_size() ++ if (__capacity > size_type(_S_max_size)) ++ std::__throw_length_error(__N("__rc_string_base::_Rep::_S_create")); ++ ++ // The standard places no restriction on allocating more memory ++ // than is strictly needed within this layer at the moment or as ++ // requested by an explicit application call to reserve(). ++ ++ // Many malloc implementations perform quite poorly when an ++ // application attempts to allocate memory in a stepwise fashion ++ // growing each allocation size by only 1 char. Additionally, ++ // it makes little sense to allocate less linear memory than the ++ // natural blocking size of the malloc implementation. ++ // Unfortunately, we would need a somewhat low-level calculation ++ // with tuned parameters to get this perfect for any particular ++ // malloc implementation. Fortunately, generalizations about ++ // common features seen among implementations seems to suffice. ++ ++ // __pagesize need not match the actual VM page size for good ++ // results in practice, thus we pick a common value on the low ++ // side. __malloc_header_size is an estimate of the amount of ++ // overhead per memory allocation (in practice seen N * sizeof ++ // (void*) where N is 0, 2 or 4). According to folklore, ++ // picking this value on the high side is better than ++ // low-balling it (especially when this algorithm is used with ++ // malloc implementations that allocate memory blocks rounded up ++ // to a size which is a power of 2). ++ const size_type __pagesize = 4096; ++ const size_type __malloc_header_size = 4 * sizeof(void*); ++ ++ // The below implements an exponential growth policy, necessary to ++ // meet amortized linear time requirements of the library: see ++ // http://gcc.gnu.org/ml/libstdc++/2001-07/msg00085.html. ++ if (__capacity > __old_capacity && __capacity < 2 * __old_capacity) ++ { ++ __capacity = 2 * __old_capacity; ++ // Never allocate a string bigger than _S_max_size. ++ if (__capacity > size_type(_S_max_size)) ++ __capacity = size_type(_S_max_size); ++ } ++ ++ // NB: Need an array of char_type[__capacity], plus a terminating ++ // null char_type() element, plus enough for the _Rep data structure, ++ // plus sizeof(_Rep) - 1 to upper round to a size multiple of ++ // sizeof(_Rep). ++ // Whew. Seemingly so needy, yet so elemental. ++ size_type __size = ((__capacity + 1) * sizeof(_CharT) ++ + 2 * sizeof(_Rep) - 1); ++ ++ const size_type __adj_size = __size + __malloc_header_size; ++ if (__adj_size > __pagesize && __capacity > __old_capacity) ++ { ++ const size_type __extra = __pagesize - __adj_size % __pagesize; ++ __capacity += __extra / sizeof(_CharT); ++ if (__capacity > size_type(_S_max_size)) ++ __capacity = size_type(_S_max_size); ++ __size = (__capacity + 1) * sizeof(_CharT) + 2 * sizeof(_Rep) - 1; ++ } ++ ++ // NB: Might throw, but no worries about a leak, mate: _Rep() ++ // does not throw. ++ _Rep* __place = _Rep_alloc_type(__alloc).allocate(__size / sizeof(_Rep)); ++ _Rep* __p = new (__place) _Rep; ++ __p->_M_info._M_capacity = __capacity; ++ return __p; ++ } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>::_Rep:: ++ _M_destroy(const _Alloc& __a) throw () ++ { ++ const size_type __size = ((_M_info._M_capacity + 1) * sizeof(_CharT) ++ + 2 * sizeof(_Rep) - 1); ++ _Rep_alloc_type(__a).deallocate(this, __size / sizeof(_Rep)); ++ } ++ ++ template ++ _CharT* ++ __rc_string_base<_CharT, _Traits, _Alloc>::_Rep:: ++ _M_clone(const _Alloc& __alloc, size_type __res) ++ { ++ // Requested capacity of the clone. ++ const size_type __requested_cap = _M_info._M_length + __res; ++ _Rep* __r = _Rep::_S_create(__requested_cap, _M_info._M_capacity, ++ __alloc); ++ ++ if (_M_info._M_length) ++ _S_copy(__r->_M_refdata(), _M_refdata(), _M_info._M_length); ++ ++ __r->_M_set_length(_M_info._M_length); ++ return __r->_M_refdata(); ++ } ++ ++ template ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ __rc_string_base(const _Alloc& __a) ++ : _M_dataplus(__a, _S_construct(size_type(), _CharT(), __a)) { } ++ ++ template ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ __rc_string_base(const __rc_string_base& __rcs) ++ : _M_dataplus(__rcs._M_get_allocator(), ++ __rcs._M_grab(__rcs._M_get_allocator())) { } ++ ++ template ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ __rc_string_base(size_type __n, _CharT __c, const _Alloc& __a) ++ : _M_dataplus(__a, _S_construct(__n, __c, __a)) { } ++ ++ template ++ template ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ __rc_string_base(_InputIterator __beg, _InputIterator __end, ++ const _Alloc& __a) ++ : _M_dataplus(__a, _S_construct(__beg, __end, __a)) { } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _M_leak_hard() ++ { ++ if (_M_is_shared()) ++ _M_erase(0, 0); ++ _M_set_leaked(); ++ } ++ ++ // NB: This is the special case for Input Iterators, used in ++ // istreambuf_iterators, etc. ++ // Input Iterators have a cost structure very different from ++ // pointers, calling for a different coding style. ++ template ++ template ++ _CharT* ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _S_construct(_InIterator __beg, _InIterator __end, const _Alloc& __a, ++ std::input_iterator_tag) ++ { ++ if (__beg == __end && __a == _Alloc()) ++ return _S_empty_rep._M_refcopy(); ++ ++ // Avoid reallocation for common case. ++ _CharT __buf[128]; ++ size_type __len = 0; ++ while (__beg != __end && __len < sizeof(__buf) / sizeof(_CharT)) ++ { ++ __buf[__len++] = *__beg; ++ ++__beg; ++ } ++ _Rep* __r = _Rep::_S_create(__len, size_type(0), __a); ++ _S_copy(__r->_M_refdata(), __buf, __len); ++ __try ++ { ++ while (__beg != __end) ++ { ++ if (__len == __r->_M_info._M_capacity) ++ { ++ // Allocate more space. ++ _Rep* __another = _Rep::_S_create(__len + 1, __len, __a); ++ _S_copy(__another->_M_refdata(), __r->_M_refdata(), __len); ++ __r->_M_destroy(__a); ++ __r = __another; ++ } ++ __r->_M_refdata()[__len++] = *__beg; ++ ++__beg; ++ } ++ } ++ __catch(...) ++ { ++ __r->_M_destroy(__a); ++ __throw_exception_again; ++ } ++ __r->_M_set_length(__len); ++ return __r->_M_refdata(); ++ } ++ ++ template ++ template ++ _CharT* ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _S_construct(_InIterator __beg, _InIterator __end, const _Alloc& __a, ++ std::forward_iterator_tag) ++ { ++ if (__beg == __end && __a == _Alloc()) ++ return _S_empty_rep._M_refcopy(); ++ ++ // NB: Not required, but considered best practice. ++ if (__builtin_expect(__is_null_pointer(__beg) && __beg != __end, 0)) ++ std::__throw_logic_error(__N("__rc_string_base::" ++ "_S_construct NULL not valid")); ++ ++ const size_type __dnew = static_cast(std::distance(__beg, ++ __end)); ++ // Check for out_of_range and length_error exceptions. ++ _Rep* __r = _Rep::_S_create(__dnew, size_type(0), __a); ++ __try ++ { _S_copy_chars(__r->_M_refdata(), __beg, __end); } ++ __catch(...) ++ { ++ __r->_M_destroy(__a); ++ __throw_exception_again; ++ } ++ __r->_M_set_length(__dnew); ++ return __r->_M_refdata(); ++ } ++ ++ template ++ _CharT* ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _S_construct(size_type __n, _CharT __c, const _Alloc& __a) ++ { ++ if (__n == 0 && __a == _Alloc()) ++ return _S_empty_rep._M_refcopy(); ++ ++ // Check for out_of_range and length_error exceptions. ++ _Rep* __r = _Rep::_S_create(__n, size_type(0), __a); ++ if (__n) ++ _S_assign(__r->_M_refdata(), __n, __c); ++ ++ __r->_M_set_length(__n); ++ return __r->_M_refdata(); ++ } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _M_swap(__rc_string_base& __rcs) ++ { ++ if (_M_is_leaked()) ++ _M_set_sharable(); ++ if (__rcs._M_is_leaked()) ++ __rcs._M_set_sharable(); ++ ++ _CharT* __tmp = _M_data(); ++ _M_data(__rcs._M_data()); ++ __rcs._M_data(__tmp); ++ ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 431. Swapping containers with unequal allocators. ++ std::__alloc_swap::_S_do_it(_M_get_allocator(), ++ __rcs._M_get_allocator()); ++ } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _M_assign(const __rc_string_base& __rcs) ++ { ++ if (_M_rep() != __rcs._M_rep()) ++ { ++ _CharT* __tmp = __rcs._M_grab(_M_get_allocator()); ++ _M_dispose(); ++ _M_data(__tmp); ++ } ++ } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _M_reserve(size_type __res) ++ { ++ // Make sure we don't shrink below the current size. ++ if (__res < _M_length()) ++ __res = _M_length(); ++ ++ if (__res != _M_capacity() || _M_is_shared()) ++ { ++ _CharT* __tmp = _M_rep()->_M_clone(_M_get_allocator(), ++ __res - _M_length()); ++ _M_dispose(); ++ _M_data(__tmp); ++ } ++ } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _M_mutate(size_type __pos, size_type __len1, const _CharT* __s, ++ size_type __len2) ++ { ++ const size_type __how_much = _M_length() - __pos - __len1; ++ ++ _Rep* __r = _Rep::_S_create(_M_length() + __len2 - __len1, ++ _M_capacity(), _M_get_allocator()); ++ ++ if (__pos) ++ _S_copy(__r->_M_refdata(), _M_data(), __pos); ++ if (__s && __len2) ++ _S_copy(__r->_M_refdata() + __pos, __s, __len2); ++ if (__how_much) ++ _S_copy(__r->_M_refdata() + __pos + __len2, ++ _M_data() + __pos + __len1, __how_much); ++ ++ _M_dispose(); ++ _M_data(__r->_M_refdata()); ++ } ++ ++ template ++ void ++ __rc_string_base<_CharT, _Traits, _Alloc>:: ++ _M_erase(size_type __pos, size_type __n) ++ { ++ const size_type __new_size = _M_length() - __n; ++ const size_type __how_much = _M_length() - __pos - __n; ++ ++ if (_M_is_shared()) ++ { ++ // Must reallocate. ++ _Rep* __r = _Rep::_S_create(__new_size, _M_capacity(), ++ _M_get_allocator()); ++ ++ if (__pos) ++ _S_copy(__r->_M_refdata(), _M_data(), __pos); ++ if (__how_much) ++ _S_copy(__r->_M_refdata() + __pos, ++ _M_data() + __pos + __n, __how_much); ++ ++ _M_dispose(); ++ _M_data(__r->_M_refdata()); ++ } ++ else if (__how_much && __n) ++ { ++ // Work in-place. ++ _S_move(_M_data() + __pos, ++ _M_data() + __pos + __n, __how_much); ++ } ++ ++ _M_rep()->_M_set_length(__new_size); ++ } ++ ++ template<> ++ inline bool ++ __rc_string_base, ++ std::allocator >:: ++ _M_compare(const __rc_string_base& __rcs) const ++ { ++ if (_M_rep() == __rcs._M_rep()) ++ return true; ++ return false; ++ } ++ ++#ifdef _GLIBCXX_USE_WCHAR_T ++ template<> ++ inline bool ++ __rc_string_base, ++ std::allocator >:: ++ _M_compare(const __rc_string_base& __rcs) const ++ { ++ if (_M_rep() == __rcs._M_rep()) ++ return true; ++ return false; ++ } ++#endif ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif /* _RC_STRING_BASE_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/ropeimpl.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/ropeimpl.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/ropeimpl.h (revision 11967) +@@ -0,0 +1,1701 @@ ++// SGI's rope class implementation -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/* ++ * Copyright (c) 1997 ++ * Silicon Graphics Computer Systems, Inc. ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Silicon Graphics makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ */ ++ ++/** @file ropeimpl.h ++ * This is an internal header file, included by other library headers. ++ * You should not attempt to use it directly. ++ */ ++ ++#include ++#include ++#include ++ ++#include // For copy_n and lexicographical_compare_3way ++#include // For uninitialized_copy_n ++#include // For power ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::size_t; ++ using std::printf; ++ using std::basic_ostream; ++ using std::__throw_length_error; ++ using std::_Destroy; ++ using std::uninitialized_fill_n; ++ ++ // Set buf_start, buf_end, and buf_ptr appropriately, filling tmp_buf ++ // if necessary. Assumes _M_path_end[leaf_index] and leaf_pos are correct. ++ // Results in a valid buf_ptr if the iterator can be legitimately ++ // dereferenced. ++ template ++ void ++ _Rope_iterator_base<_CharT, _Alloc>:: ++ _S_setbuf(_Rope_iterator_base<_CharT, _Alloc>& __x) ++ { ++ const _RopeRep* __leaf = __x._M_path_end[__x._M_leaf_index]; ++ size_t __leaf_pos = __x._M_leaf_pos; ++ size_t __pos = __x._M_current_pos; ++ ++ switch(__leaf->_M_tag) ++ { ++ case __detail::_S_leaf: ++ __x._M_buf_start = ((_Rope_RopeLeaf<_CharT, _Alloc>*)__leaf)->_M_data; ++ __x._M_buf_ptr = __x._M_buf_start + (__pos - __leaf_pos); ++ __x._M_buf_end = __x._M_buf_start + __leaf->_M_size; ++ break; ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ { ++ size_t __len = _S_iterator_buf_len; ++ size_t __buf_start_pos = __leaf_pos; ++ size_t __leaf_end = __leaf_pos + __leaf->_M_size; ++ char_producer<_CharT>* __fn = ((_Rope_RopeFunction<_CharT, ++ _Alloc>*)__leaf)->_M_fn; ++ if (__buf_start_pos + __len <= __pos) ++ { ++ __buf_start_pos = __pos - __len / 4; ++ if (__buf_start_pos + __len > __leaf_end) ++ __buf_start_pos = __leaf_end - __len; ++ } ++ if (__buf_start_pos + __len > __leaf_end) ++ __len = __leaf_end - __buf_start_pos; ++ (*__fn)(__buf_start_pos - __leaf_pos, __len, __x._M_tmp_buf); ++ __x._M_buf_ptr = __x._M_tmp_buf + (__pos - __buf_start_pos); ++ __x._M_buf_start = __x._M_tmp_buf; ++ __x._M_buf_end = __x._M_tmp_buf + __len; ++ } ++ break; ++ default: ++ break; ++ } ++ } ++ ++ // Set path and buffer inside a rope iterator. We assume that ++ // pos and root are already set. ++ template ++ void ++ _Rope_iterator_base<_CharT, _Alloc>:: ++ _S_setcache(_Rope_iterator_base<_CharT, _Alloc>& __x) ++ { ++ const _RopeRep* __path[int(__detail::_S_max_rope_depth) + 1]; ++ const _RopeRep* __curr_rope; ++ int __curr_depth = -1; /* index into path */ ++ size_t __curr_start_pos = 0; ++ size_t __pos = __x._M_current_pos; ++ unsigned char __dirns = 0; // Bit vector marking right turns in the path ++ ++ if (__pos >= __x._M_root->_M_size) ++ { ++ __x._M_buf_ptr = 0; ++ return; ++ } ++ __curr_rope = __x._M_root; ++ if (0 != __curr_rope->_M_c_string) ++ { ++ /* Treat the root as a leaf. */ ++ __x._M_buf_start = __curr_rope->_M_c_string; ++ __x._M_buf_end = __curr_rope->_M_c_string + __curr_rope->_M_size; ++ __x._M_buf_ptr = __curr_rope->_M_c_string + __pos; ++ __x._M_path_end[0] = __curr_rope; ++ __x._M_leaf_index = 0; ++ __x._M_leaf_pos = 0; ++ return; ++ } ++ for(;;) ++ { ++ ++__curr_depth; ++ __path[__curr_depth] = __curr_rope; ++ switch(__curr_rope->_M_tag) ++ { ++ case __detail::_S_leaf: ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ __x._M_leaf_pos = __curr_start_pos; ++ goto done; ++ case __detail::_S_concat: ++ { ++ _Rope_RopeConcatenation<_CharT, _Alloc>* __c = ++ (_Rope_RopeConcatenation<_CharT, _Alloc>*)__curr_rope; ++ _RopeRep* __left = __c->_M_left; ++ size_t __left_len = __left->_M_size; ++ ++ __dirns <<= 1; ++ if (__pos >= __curr_start_pos + __left_len) ++ { ++ __dirns |= 1; ++ __curr_rope = __c->_M_right; ++ __curr_start_pos += __left_len; ++ } ++ else ++ __curr_rope = __left; ++ } ++ break; ++ } ++ } ++ done: ++ // Copy last section of path into _M_path_end. ++ { ++ int __i = -1; ++ int __j = __curr_depth + 1 - int(_S_path_cache_len); ++ ++ if (__j < 0) __j = 0; ++ while (__j <= __curr_depth) ++ __x._M_path_end[++__i] = __path[__j++]; ++ __x._M_leaf_index = __i; ++ } ++ __x._M_path_directions = __dirns; ++ _S_setbuf(__x); ++ } ++ ++ // Specialized version of the above. Assumes that ++ // the path cache is valid for the previous position. ++ template ++ void ++ _Rope_iterator_base<_CharT, _Alloc>:: ++ _S_setcache_for_incr(_Rope_iterator_base<_CharT, _Alloc>& __x) ++ { ++ int __current_index = __x._M_leaf_index; ++ const _RopeRep* __current_node = __x._M_path_end[__current_index]; ++ size_t __len = __current_node->_M_size; ++ size_t __node_start_pos = __x._M_leaf_pos; ++ unsigned char __dirns = __x._M_path_directions; ++ _Rope_RopeConcatenation<_CharT, _Alloc>* __c; ++ ++ if (__x._M_current_pos - __node_start_pos < __len) ++ { ++ /* More stuff in this leaf, we just didn't cache it. */ ++ _S_setbuf(__x); ++ return; ++ } ++ // node_start_pos is starting position of last_node. ++ while (--__current_index >= 0) ++ { ++ if (!(__dirns & 1) /* Path turned left */) ++ break; ++ __current_node = __x._M_path_end[__current_index]; ++ __c = (_Rope_RopeConcatenation<_CharT, _Alloc>*)__current_node; ++ // Otherwise we were in the right child. Thus we should pop ++ // the concatenation node. ++ __node_start_pos -= __c->_M_left->_M_size; ++ __dirns >>= 1; ++ } ++ if (__current_index < 0) ++ { ++ // We underflowed the cache. Punt. ++ _S_setcache(__x); ++ return; ++ } ++ __current_node = __x._M_path_end[__current_index]; ++ __c = (_Rope_RopeConcatenation<_CharT, _Alloc>*)__current_node; ++ // current_node is a concatenation node. We are positioned on the first ++ // character in its right child. ++ // node_start_pos is starting position of current_node. ++ __node_start_pos += __c->_M_left->_M_size; ++ __current_node = __c->_M_right; ++ __x._M_path_end[++__current_index] = __current_node; ++ __dirns |= 1; ++ while (__detail::_S_concat == __current_node->_M_tag) ++ { ++ ++__current_index; ++ if (int(_S_path_cache_len) == __current_index) ++ { ++ int __i; ++ for (__i = 0; __i < int(_S_path_cache_len) - 1; __i++) ++ __x._M_path_end[__i] = __x._M_path_end[__i+1]; ++ --__current_index; ++ } ++ __current_node = ++ ((_Rope_RopeConcatenation<_CharT, _Alloc>*)__current_node)->_M_left; ++ __x._M_path_end[__current_index] = __current_node; ++ __dirns <<= 1; ++ // node_start_pos is unchanged. ++ } ++ __x._M_leaf_index = __current_index; ++ __x._M_leaf_pos = __node_start_pos; ++ __x._M_path_directions = __dirns; ++ _S_setbuf(__x); ++ } ++ ++ template ++ void ++ _Rope_iterator_base<_CharT, _Alloc>:: ++ _M_incr(size_t __n) ++ { ++ _M_current_pos += __n; ++ if (0 != _M_buf_ptr) ++ { ++ size_t __chars_left = _M_buf_end - _M_buf_ptr; ++ if (__chars_left > __n) ++ _M_buf_ptr += __n; ++ else if (__chars_left == __n) ++ { ++ _M_buf_ptr += __n; ++ _S_setcache_for_incr(*this); ++ } ++ else ++ _M_buf_ptr = 0; ++ } ++ } ++ ++ template ++ void ++ _Rope_iterator_base<_CharT, _Alloc>:: ++ _M_decr(size_t __n) ++ { ++ if (0 != _M_buf_ptr) ++ { ++ size_t __chars_left = _M_buf_ptr - _M_buf_start; ++ if (__chars_left >= __n) ++ _M_buf_ptr -= __n; ++ else ++ _M_buf_ptr = 0; ++ } ++ _M_current_pos -= __n; ++ } ++ ++ template ++ void ++ _Rope_iterator<_CharT, _Alloc>:: ++ _M_check() ++ { ++ if (_M_root_rope->_M_tree_ptr != this->_M_root) ++ { ++ // _Rope was modified. Get things fixed up. ++ _RopeRep::_S_unref(this->_M_root); ++ this->_M_root = _M_root_rope->_M_tree_ptr; ++ _RopeRep::_S_ref(this->_M_root); ++ this->_M_buf_ptr = 0; ++ } ++ } ++ ++ template ++ inline ++ _Rope_const_iterator<_CharT, _Alloc>:: ++ _Rope_const_iterator(const _Rope_iterator<_CharT, _Alloc>& __x) ++ : _Rope_iterator_base<_CharT, _Alloc>(__x) ++ { } ++ ++ template ++ inline ++ _Rope_iterator<_CharT, _Alloc>:: ++ _Rope_iterator(rope<_CharT, _Alloc>& __r, size_t __pos) ++ : _Rope_iterator_base<_CharT,_Alloc>(__r._M_tree_ptr, __pos), ++ _M_root_rope(&__r) ++ { _RopeRep::_S_ref(this->_M_root); } ++ ++ template ++ inline size_t ++ rope<_CharT, _Alloc>:: ++ _S_char_ptr_len(const _CharT* __s) ++ { ++ const _CharT* __p = __s; ++ ++ while (!_S_is0(*__p)) ++ ++__p; ++ return (__p - __s); ++ } ++ ++ ++#ifndef __GC ++ ++ template ++ inline void ++ _Rope_RopeRep<_CharT, _Alloc>:: ++ _M_free_c_string() ++ { ++ _CharT* __cstr = _M_c_string; ++ if (0 != __cstr) ++ { ++ size_t __size = this->_M_size + 1; ++ _Destroy(__cstr, __cstr + __size, _M_get_allocator()); ++ this->_Data_deallocate(__cstr, __size); ++ } ++ } ++ ++ template ++ inline void ++ _Rope_RopeRep<_CharT, _Alloc>:: ++ _S_free_string(_CharT* __s, size_t __n, allocator_type& __a) ++ { ++ if (!_S_is_basic_char_type((_CharT*)0)) ++ _Destroy(__s, __s + __n, __a); ++ ++ // This has to be a static member, so this gets a bit messy ++ __a.deallocate(__s, ++ _Rope_RopeLeaf<_CharT, _Alloc>::_S_rounded_up_size(__n)); ++ } ++ ++ // There are several reasons for not doing this with virtual destructors ++ // and a class specific delete operator: ++ // - A class specific delete operator can't easily get access to ++ // allocator instances if we need them. ++ // - Any virtual function would need a 4 or byte vtable pointer; ++ // this only requires a one byte tag per object. ++ template ++ void ++ _Rope_RopeRep<_CharT, _Alloc>:: ++ _M_free_tree() ++ { ++ switch(_M_tag) ++ { ++ case __detail::_S_leaf: ++ { ++ _Rope_RopeLeaf<_CharT, _Alloc>* __l ++ = (_Rope_RopeLeaf<_CharT, _Alloc>*)this; ++ __l->_Rope_RopeLeaf<_CharT, _Alloc>::~_Rope_RopeLeaf(); ++ _L_deallocate(__l, 1); ++ break; ++ } ++ case __detail::_S_concat: ++ { ++ _Rope_RopeConcatenation<_CharT,_Alloc>* __c ++ = (_Rope_RopeConcatenation<_CharT, _Alloc>*)this; ++ __c->_Rope_RopeConcatenation<_CharT, _Alloc>:: ++ ~_Rope_RopeConcatenation(); ++ _C_deallocate(__c, 1); ++ break; ++ } ++ case __detail::_S_function: ++ { ++ _Rope_RopeFunction<_CharT, _Alloc>* __f ++ = (_Rope_RopeFunction<_CharT, _Alloc>*)this; ++ __f->_Rope_RopeFunction<_CharT, _Alloc>::~_Rope_RopeFunction(); ++ _F_deallocate(__f, 1); ++ break; ++ } ++ case __detail::_S_substringfn: ++ { ++ _Rope_RopeSubstring<_CharT, _Alloc>* __ss = ++ (_Rope_RopeSubstring<_CharT, _Alloc>*)this; ++ __ss->_Rope_RopeSubstring<_CharT, _Alloc>:: ++ ~_Rope_RopeSubstring(); ++ _S_deallocate(__ss, 1); ++ break; ++ } ++ } ++ } ++#else ++ ++ template ++ inline void ++ _Rope_RopeRep<_CharT, _Alloc>:: ++ _S_free_string(const _CharT*, size_t, allocator_type) ++ { } ++ ++#endif ++ ++ // Concatenate a C string onto a leaf rope by copying the rope data. ++ // Used for short ropes. ++ template ++ typename rope<_CharT, _Alloc>::_RopeLeaf* ++ rope<_CharT, _Alloc>:: ++ _S_leaf_concat_char_iter(_RopeLeaf* __r, const _CharT* __iter, size_t __len) ++ { ++ size_t __old_len = __r->_M_size; ++ _CharT* __new_data = (_CharT*) ++ _Data_allocate(_S_rounded_up_size(__old_len + __len)); ++ _RopeLeaf* __result; ++ ++ uninitialized_copy_n(__r->_M_data, __old_len, __new_data); ++ uninitialized_copy_n(__iter, __len, __new_data + __old_len); ++ _S_cond_store_eos(__new_data[__old_len + __len]); ++ __try ++ { ++ __result = _S_new_RopeLeaf(__new_data, __old_len + __len, ++ __r->_M_get_allocator()); ++ } ++ __catch(...) ++ { ++ _RopeRep::__STL_FREE_STRING(__new_data, __old_len + __len, ++ __r->_M_get_allocator()); ++ __throw_exception_again; ++ } ++ return __result; ++ } ++ ++#ifndef __GC ++ // As above, but it's OK to clobber original if refcount is 1 ++ template ++ typename rope<_CharT,_Alloc>::_RopeLeaf* ++ rope<_CharT, _Alloc>:: ++ _S_destr_leaf_concat_char_iter(_RopeLeaf* __r, const _CharT* __iter, ++ size_t __len) ++ { ++ if (__r->_M_ref_count > 1) ++ return _S_leaf_concat_char_iter(__r, __iter, __len); ++ size_t __old_len = __r->_M_size; ++ if (_S_allocated_capacity(__old_len) >= __old_len + __len) ++ { ++ // The space has been partially initialized for the standard ++ // character types. But that doesn't matter for those types. ++ uninitialized_copy_n(__iter, __len, __r->_M_data + __old_len); ++ if (_S_is_basic_char_type((_CharT*)0)) ++ _S_cond_store_eos(__r->_M_data[__old_len + __len]); ++ else if (__r->_M_c_string != __r->_M_data && 0 != __r->_M_c_string) ++ { ++ __r->_M_free_c_string(); ++ __r->_M_c_string = 0; ++ } ++ __r->_M_size = __old_len + __len; ++ __r->_M_ref_count = 2; ++ return __r; ++ } ++ else ++ { ++ _RopeLeaf* __result = _S_leaf_concat_char_iter(__r, __iter, __len); ++ return __result; ++ } ++ } ++#endif ++ ++ // Assumes left and right are not 0. ++ // Does not increment (nor decrement on exception) child reference counts. ++ // Result has ref count 1. ++ template ++ typename rope<_CharT, _Alloc>::_RopeRep* ++ rope<_CharT, _Alloc>:: ++ _S_tree_concat(_RopeRep* __left, _RopeRep* __right) ++ { ++ _RopeConcatenation* __result = _S_new_RopeConcatenation(__left, __right, ++ __left-> ++ _M_get_allocator()); ++ size_t __depth = __result->_M_depth; ++ ++ if (__depth > 20 ++ && (__result->_M_size < 1000 ++ || __depth > size_t(__detail::_S_max_rope_depth))) ++ { ++ _RopeRep* __balanced; ++ ++ __try ++ { ++ __balanced = _S_balance(__result); ++ __result->_M_unref_nonnil(); ++ } ++ __catch(...) ++ { ++ _C_deallocate(__result,1); ++ __throw_exception_again; ++ } ++ // In case of exception, we need to deallocate ++ // otherwise dangling result node. But caller ++ // still owns its children. Thus unref is ++ // inappropriate. ++ return __balanced; ++ } ++ else ++ return __result; ++ } ++ ++ template ++ typename rope<_CharT, _Alloc>::_RopeRep* ++ rope<_CharT, _Alloc>:: ++ _S_concat_char_iter(_RopeRep* __r, const _CharT*__s, size_t __slen) ++ { ++ _RopeRep* __result; ++ if (0 == __slen) ++ { ++ _S_ref(__r); ++ return __r; ++ } ++ if (0 == __r) ++ return __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __slen, ++ __r->_M_get_allocator()); ++ if (__r->_M_tag == __detail::_S_leaf ++ && __r->_M_size + __slen <= size_t(_S_copy_max)) ++ { ++ __result = _S_leaf_concat_char_iter((_RopeLeaf*)__r, __s, __slen); ++ return __result; ++ } ++ if (__detail::_S_concat == __r->_M_tag ++ && __detail::_S_leaf == ((_RopeConcatenation*) __r)->_M_right->_M_tag) ++ { ++ _RopeLeaf* __right = ++ (_RopeLeaf* )(((_RopeConcatenation* )__r)->_M_right); ++ if (__right->_M_size + __slen <= size_t(_S_copy_max)) ++ { ++ _RopeRep* __left = ((_RopeConcatenation*)__r)->_M_left; ++ _RopeRep* __nright = ++ _S_leaf_concat_char_iter((_RopeLeaf*)__right, __s, __slen); ++ __left->_M_ref_nonnil(); ++ __try ++ { __result = _S_tree_concat(__left, __nright); } ++ __catch(...) ++ { ++ _S_unref(__left); ++ _S_unref(__nright); ++ __throw_exception_again; ++ } ++ return __result; ++ } ++ } ++ _RopeRep* __nright = ++ __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __slen, __r->_M_get_allocator()); ++ __try ++ { ++ __r->_M_ref_nonnil(); ++ __result = _S_tree_concat(__r, __nright); ++ } ++ __catch(...) ++ { ++ _S_unref(__r); ++ _S_unref(__nright); ++ __throw_exception_again; ++ } ++ return __result; ++ } ++ ++#ifndef __GC ++ template ++ typename rope<_CharT,_Alloc>::_RopeRep* ++ rope<_CharT,_Alloc>:: ++ _S_destr_concat_char_iter(_RopeRep* __r, const _CharT* __s, size_t __slen) ++ { ++ _RopeRep* __result; ++ if (0 == __r) ++ return __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __slen, ++ __r->_M_get_allocator()); ++ size_t __count = __r->_M_ref_count; ++ size_t __orig_size = __r->_M_size; ++ if (__count > 1) ++ return _S_concat_char_iter(__r, __s, __slen); ++ if (0 == __slen) ++ { ++ __r->_M_ref_count = 2; // One more than before ++ return __r; ++ } ++ if (__orig_size + __slen <= size_t(_S_copy_max) ++ && __detail::_S_leaf == __r->_M_tag) ++ { ++ __result = _S_destr_leaf_concat_char_iter((_RopeLeaf*)__r, __s, ++ __slen); ++ return __result; ++ } ++ if (__detail::_S_concat == __r->_M_tag) ++ { ++ _RopeLeaf* __right = (_RopeLeaf*)(((_RopeConcatenation*) ++ __r)->_M_right); ++ if (__detail::_S_leaf == __right->_M_tag ++ && __right->_M_size + __slen <= size_t(_S_copy_max)) ++ { ++ _RopeRep* __new_right = ++ _S_destr_leaf_concat_char_iter(__right, __s, __slen); ++ if (__right == __new_right) ++ __new_right->_M_ref_count = 1; ++ else ++ __right->_M_unref_nonnil(); ++ __r->_M_ref_count = 2; // One more than before. ++ ((_RopeConcatenation*)__r)->_M_right = __new_right; ++ __r->_M_size = __orig_size + __slen; ++ if (0 != __r->_M_c_string) ++ { ++ __r->_M_free_c_string(); ++ __r->_M_c_string = 0; ++ } ++ return __r; ++ } ++ } ++ _RopeRep* __right = ++ __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __slen, __r->_M_get_allocator()); ++ __r->_M_ref_nonnil(); ++ __try ++ { __result = _S_tree_concat(__r, __right); } ++ __catch(...) ++ { ++ _S_unref(__r); ++ _S_unref(__right); ++ __throw_exception_again; ++ } ++ return __result; ++ } ++#endif /* !__GC */ ++ ++ template ++ typename rope<_CharT, _Alloc>::_RopeRep* ++ rope<_CharT, _Alloc>:: ++ _S_concat(_RopeRep* __left, _RopeRep* __right) ++ { ++ if (0 == __left) ++ { ++ _S_ref(__right); ++ return __right; ++ } ++ if (0 == __right) ++ { ++ __left->_M_ref_nonnil(); ++ return __left; ++ } ++ if (__detail::_S_leaf == __right->_M_tag) ++ { ++ if (__detail::_S_leaf == __left->_M_tag) ++ { ++ if (__right->_M_size + __left->_M_size <= size_t(_S_copy_max)) ++ return _S_leaf_concat_char_iter((_RopeLeaf*)__left, ++ ((_RopeLeaf*)__right)->_M_data, ++ __right->_M_size); ++ } ++ else if (__detail::_S_concat == __left->_M_tag ++ && __detail::_S_leaf == ((_RopeConcatenation*) ++ __left)->_M_right->_M_tag) ++ { ++ _RopeLeaf* __leftright = ++ (_RopeLeaf*)(((_RopeConcatenation*)__left)->_M_right); ++ if (__leftright->_M_size ++ + __right->_M_size <= size_t(_S_copy_max)) ++ { ++ _RopeRep* __leftleft = ((_RopeConcatenation*)__left)->_M_left; ++ _RopeRep* __rest = _S_leaf_concat_char_iter(__leftright, ++ ((_RopeLeaf*) ++ __right)-> ++ _M_data, ++ __right->_M_size); ++ __leftleft->_M_ref_nonnil(); ++ __try ++ { return(_S_tree_concat(__leftleft, __rest)); } ++ __catch(...) ++ { ++ _S_unref(__leftleft); ++ _S_unref(__rest); ++ __throw_exception_again; ++ } ++ } ++ } ++ } ++ __left->_M_ref_nonnil(); ++ __right->_M_ref_nonnil(); ++ __try ++ { return(_S_tree_concat(__left, __right)); } ++ __catch(...) ++ { ++ _S_unref(__left); ++ _S_unref(__right); ++ __throw_exception_again; ++ } ++ } ++ ++ template ++ typename rope<_CharT, _Alloc>::_RopeRep* ++ rope<_CharT, _Alloc>:: ++ _S_substring(_RopeRep* __base, size_t __start, size_t __endp1) ++ { ++ if (0 == __base) ++ return 0; ++ size_t __len = __base->_M_size; ++ size_t __adj_endp1; ++ const size_t __lazy_threshold = 128; ++ ++ if (__endp1 >= __len) ++ { ++ if (0 == __start) ++ { ++ __base->_M_ref_nonnil(); ++ return __base; ++ } ++ else ++ __adj_endp1 = __len; ++ ++ } ++ else ++ __adj_endp1 = __endp1; ++ ++ switch(__base->_M_tag) ++ { ++ case __detail::_S_concat: ++ { ++ _RopeConcatenation* __c = (_RopeConcatenation*)__base; ++ _RopeRep* __left = __c->_M_left; ++ _RopeRep* __right = __c->_M_right; ++ size_t __left_len = __left->_M_size; ++ _RopeRep* __result; ++ ++ if (__adj_endp1 <= __left_len) ++ return _S_substring(__left, __start, __endp1); ++ else if (__start >= __left_len) ++ return _S_substring(__right, __start - __left_len, ++ __adj_endp1 - __left_len); ++ _Self_destruct_ptr __left_result(_S_substring(__left, ++ __start, ++ __left_len)); ++ _Self_destruct_ptr __right_result(_S_substring(__right, 0, ++ __endp1 ++ - __left_len)); ++ __result = _S_concat(__left_result, __right_result); ++ return __result; ++ } ++ case __detail::_S_leaf: ++ { ++ _RopeLeaf* __l = (_RopeLeaf*)__base; ++ _RopeLeaf* __result; ++ size_t __result_len; ++ if (__start >= __adj_endp1) ++ return 0; ++ __result_len = __adj_endp1 - __start; ++ if (__result_len > __lazy_threshold) ++ goto lazy; ++#ifdef __GC ++ const _CharT* __section = __l->_M_data + __start; ++ __result = _S_new_RopeLeaf(__section, __result_len, ++ __base->_M_get_allocator()); ++ __result->_M_c_string = 0; // Not eos terminated. ++#else ++ // We should sometimes create substring node instead. ++ __result = __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__l->_M_data + __start, ++ __result_len, ++ __base-> ++ _M_get_allocator()); ++#endif ++ return __result; ++ } ++ case __detail::_S_substringfn: ++ // Avoid introducing multiple layers of substring nodes. ++ { ++ _RopeSubstring* __old = (_RopeSubstring*)__base; ++ size_t __result_len; ++ if (__start >= __adj_endp1) ++ return 0; ++ __result_len = __adj_endp1 - __start; ++ if (__result_len > __lazy_threshold) ++ { ++ _RopeSubstring* __result = ++ _S_new_RopeSubstring(__old->_M_base, ++ __start + __old->_M_start, ++ __adj_endp1 - __start, ++ __base->_M_get_allocator()); ++ return __result; ++ ++ } // *** else fall through: *** ++ } ++ case __detail::_S_function: ++ { ++ _RopeFunction* __f = (_RopeFunction*)__base; ++ _CharT* __section; ++ size_t __result_len; ++ if (__start >= __adj_endp1) ++ return 0; ++ __result_len = __adj_endp1 - __start; ++ ++ if (__result_len > __lazy_threshold) ++ goto lazy; ++ __section = (_CharT*) ++ _Data_allocate(_S_rounded_up_size(__result_len)); ++ __try ++ { (*(__f->_M_fn))(__start, __result_len, __section); } ++ __catch(...) ++ { ++ _RopeRep::__STL_FREE_STRING(__section, __result_len, ++ __base->_M_get_allocator()); ++ __throw_exception_again; ++ } ++ _S_cond_store_eos(__section[__result_len]); ++ return _S_new_RopeLeaf(__section, __result_len, ++ __base->_M_get_allocator()); ++ } ++ } ++ lazy: ++ { ++ // Create substring node. ++ return _S_new_RopeSubstring(__base, __start, __adj_endp1 - __start, ++ __base->_M_get_allocator()); ++ } ++ } ++ ++ template ++ class _Rope_flatten_char_consumer ++ : public _Rope_char_consumer<_CharT> ++ { ++ private: ++ _CharT* _M_buf_ptr; ++ public: ++ ++ _Rope_flatten_char_consumer(_CharT* __buffer) ++ { _M_buf_ptr = __buffer; }; ++ ++ ~_Rope_flatten_char_consumer() {} ++ ++ bool ++ operator()(const _CharT* __leaf, size_t __n) ++ { ++ uninitialized_copy_n(__leaf, __n, _M_buf_ptr); ++ _M_buf_ptr += __n; ++ return true; ++ } ++ }; ++ ++ template ++ class _Rope_find_char_char_consumer ++ : public _Rope_char_consumer<_CharT> ++ { ++ private: ++ _CharT _M_pattern; ++ public: ++ size_t _M_count; // Number of nonmatching characters ++ ++ _Rope_find_char_char_consumer(_CharT __p) ++ : _M_pattern(__p), _M_count(0) {} ++ ++ ~_Rope_find_char_char_consumer() {} ++ ++ bool ++ operator()(const _CharT* __leaf, size_t __n) ++ { ++ size_t __i; ++ for (__i = 0; __i < __n; __i++) ++ { ++ if (__leaf[__i] == _M_pattern) ++ { ++ _M_count += __i; ++ return false; ++ } ++ } ++ _M_count += __n; return true; ++ } ++ }; ++ ++ template ++ // Here _CharT is both the stream and rope character type. ++ class _Rope_insert_char_consumer ++ : public _Rope_char_consumer<_CharT> ++ { ++ private: ++ typedef basic_ostream<_CharT,_Traits> _Insert_ostream; ++ _Insert_ostream& _M_o; ++ public: ++ _Rope_insert_char_consumer(_Insert_ostream& __writer) ++ : _M_o(__writer) {}; ++ ~_Rope_insert_char_consumer() { }; ++ // Caller is presumed to own the ostream ++ bool operator() (const _CharT* __leaf, size_t __n); ++ // Returns true to continue traversal. ++ }; ++ ++ template ++ bool ++ _Rope_insert_char_consumer<_CharT, _Traits>:: ++ operator()(const _CharT* __leaf, size_t __n) ++ { ++ size_t __i; ++ // We assume that formatting is set up correctly for each element. ++ for (__i = 0; __i < __n; __i++) ++ _M_o.put(__leaf[__i]); ++ return true; ++ } ++ ++ template ++ bool ++ rope<_CharT, _Alloc>:: ++ _S_apply_to_pieces(_Rope_char_consumer<_CharT>& __c, ++ const _RopeRep* __r, size_t __begin, size_t __end) ++ { ++ if (0 == __r) ++ return true; ++ switch(__r->_M_tag) ++ { ++ case __detail::_S_concat: ++ { ++ _RopeConcatenation* __conc = (_RopeConcatenation*)__r; ++ _RopeRep* __left = __conc->_M_left; ++ size_t __left_len = __left->_M_size; ++ if (__begin < __left_len) ++ { ++ size_t __left_end = std::min(__left_len, __end); ++ if (!_S_apply_to_pieces(__c, __left, __begin, __left_end)) ++ return false; ++ } ++ if (__end > __left_len) ++ { ++ _RopeRep* __right = __conc->_M_right; ++ size_t __right_start = std::max(__left_len, __begin); ++ if (!_S_apply_to_pieces(__c, __right, ++ __right_start - __left_len, ++ __end - __left_len)) ++ return false; ++ } ++ } ++ return true; ++ case __detail::_S_leaf: ++ { ++ _RopeLeaf* __l = (_RopeLeaf*)__r; ++ return __c(__l->_M_data + __begin, __end - __begin); ++ } ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ { ++ _RopeFunction* __f = (_RopeFunction*)__r; ++ size_t __len = __end - __begin; ++ bool __result; ++ _CharT* __buffer = ++ (_CharT*)_Alloc().allocate(__len * sizeof(_CharT)); ++ __try ++ { ++ (*(__f->_M_fn))(__begin, __len, __buffer); ++ __result = __c(__buffer, __len); ++ _Alloc().deallocate(__buffer, __len * sizeof(_CharT)); ++ } ++ __catch(...) ++ { ++ _Alloc().deallocate(__buffer, __len * sizeof(_CharT)); ++ __throw_exception_again; ++ } ++ return __result; ++ } ++ default: ++ return false; ++ } ++ } ++ ++ template ++ inline void ++ _Rope_fill(basic_ostream<_CharT, _Traits>& __o, size_t __n) ++ { ++ char __f = __o.fill(); ++ size_t __i; ++ ++ for (__i = 0; __i < __n; __i++) ++ __o.put(__f); ++ } ++ ++ ++ template ++ inline bool ++ _Rope_is_simple(_CharT*) ++ { return false; } ++ ++ inline bool ++ _Rope_is_simple(char*) ++ { return true; } ++ ++ inline bool ++ _Rope_is_simple(wchar_t*) ++ { return true; } ++ ++ template ++ basic_ostream<_CharT, _Traits>& ++ operator<<(basic_ostream<_CharT, _Traits>& __o, ++ const rope<_CharT, _Alloc>& __r) ++ { ++ size_t __w = __o.width(); ++ bool __left = bool(__o.flags() & std::ios::left); ++ size_t __pad_len; ++ size_t __rope_len = __r.size(); ++ _Rope_insert_char_consumer<_CharT, _Traits> __c(__o); ++ bool __is_simple = _Rope_is_simple((_CharT*)0); ++ ++ if (__rope_len < __w) ++ __pad_len = __w - __rope_len; ++ else ++ __pad_len = 0; ++ ++ if (!__is_simple) ++ __o.width(__w / __rope_len); ++ __try ++ { ++ if (__is_simple && !__left && __pad_len > 0) ++ _Rope_fill(__o, __pad_len); ++ __r.apply_to_pieces(0, __r.size(), __c); ++ if (__is_simple && __left && __pad_len > 0) ++ _Rope_fill(__o, __pad_len); ++ if (!__is_simple) ++ __o.width(__w); ++ } ++ __catch(...) ++ { ++ if (!__is_simple) ++ __o.width(__w); ++ __throw_exception_again; ++ } ++ return __o; ++ } ++ ++ template ++ _CharT* ++ rope<_CharT, _Alloc>:: ++ _S_flatten(_RopeRep* __r, size_t __start, size_t __len, ++ _CharT* __buffer) ++ { ++ _Rope_flatten_char_consumer<_CharT> __c(__buffer); ++ _S_apply_to_pieces(__c, __r, __start, __start + __len); ++ return(__buffer + __len); ++ } ++ ++ template ++ size_t ++ rope<_CharT, _Alloc>:: ++ find(_CharT __pattern, size_t __start) const ++ { ++ _Rope_find_char_char_consumer<_CharT> __c(__pattern); ++ _S_apply_to_pieces(__c, this->_M_tree_ptr, __start, size()); ++ size_type __result_pos = __start + __c._M_count; ++#ifndef __STL_OLD_ROPE_SEMANTICS ++ if (__result_pos == size()) ++ __result_pos = npos; ++#endif ++ return __result_pos; ++ } ++ ++ template ++ _CharT* ++ rope<_CharT, _Alloc>:: ++ _S_flatten(_RopeRep* __r, _CharT* __buffer) ++ { ++ if (0 == __r) ++ return __buffer; ++ switch(__r->_M_tag) ++ { ++ case __detail::_S_concat: ++ { ++ _RopeConcatenation* __c = (_RopeConcatenation*)__r; ++ _RopeRep* __left = __c->_M_left; ++ _RopeRep* __right = __c->_M_right; ++ _CharT* __rest = _S_flatten(__left, __buffer); ++ return _S_flatten(__right, __rest); ++ } ++ case __detail::_S_leaf: ++ { ++ _RopeLeaf* __l = (_RopeLeaf*)__r; ++ return copy_n(__l->_M_data, __l->_M_size, __buffer).second; ++ } ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ // We don't yet do anything with substring nodes. ++ // This needs to be fixed before ropefiles will work well. ++ { ++ _RopeFunction* __f = (_RopeFunction*)__r; ++ (*(__f->_M_fn))(0, __f->_M_size, __buffer); ++ return __buffer + __f->_M_size; ++ } ++ default: ++ return 0; ++ } ++ } ++ ++ // This needs work for _CharT != char ++ template ++ void ++ rope<_CharT, _Alloc>:: ++ _S_dump(_RopeRep* __r, int __indent) ++ { ++ for (int __i = 0; __i < __indent; __i++) ++ putchar(' '); ++ if (0 == __r) ++ { ++ printf("NULL\n"); ++ return; ++ } ++ if (_S_concat == __r->_M_tag) ++ { ++ _RopeConcatenation* __c = (_RopeConcatenation*)__r; ++ _RopeRep* __left = __c->_M_left; ++ _RopeRep* __right = __c->_M_right; ++ ++#ifdef __GC ++ printf("Concatenation %p (depth = %d, len = %ld, %s balanced)\n", ++ __r, __r->_M_depth, __r->_M_size, ++ __r->_M_is_balanced? "" : "not"); ++#else ++ printf("Concatenation %p (rc = %ld, depth = %d, " ++ "len = %ld, %s balanced)\n", ++ __r, __r->_M_ref_count, __r->_M_depth, __r->_M_size, ++ __r->_M_is_balanced? "" : "not"); ++#endif ++ _S_dump(__left, __indent + 2); ++ _S_dump(__right, __indent + 2); ++ return; ++ } ++ else ++ { ++ char* __kind; ++ ++ switch (__r->_M_tag) ++ { ++ case __detail::_S_leaf: ++ __kind = "Leaf"; ++ break; ++ case __detail::_S_function: ++ __kind = "Function"; ++ break; ++ case __detail::_S_substringfn: ++ __kind = "Function representing substring"; ++ break; ++ default: ++ __kind = "(corrupted kind field!)"; ++ } ++#ifdef __GC ++ printf("%s %p (depth = %d, len = %ld) ", ++ __kind, __r, __r->_M_depth, __r->_M_size); ++#else ++ printf("%s %p (rc = %ld, depth = %d, len = %ld) ", ++ __kind, __r, __r->_M_ref_count, __r->_M_depth, __r->_M_size); ++#endif ++ if (_S_is_one_byte_char_type((_CharT*)0)) ++ { ++ const int __max_len = 40; ++ _Self_destruct_ptr __prefix(_S_substring(__r, 0, __max_len)); ++ _CharT __buffer[__max_len + 1]; ++ bool __too_big = __r->_M_size > __prefix->_M_size; ++ ++ _S_flatten(__prefix, __buffer); ++ __buffer[__prefix->_M_size] = _S_eos((_CharT*)0); ++ printf("%s%s\n", (char*)__buffer, ++ __too_big? "...\n" : "\n"); ++ } ++ else ++ printf("\n"); ++ } ++ } ++ ++ template ++ const unsigned long ++ rope<_CharT, _Alloc>:: ++ _S_min_len[int(__detail::_S_max_rope_depth) + 1] = { ++ /* 0 */1, /* 1 */2, /* 2 */3, /* 3 */5, /* 4 */8, /* 5 */13, /* 6 */21, ++ /* 7 */34, /* 8 */55, /* 9 */89, /* 10 */144, /* 11 */233, /* 12 */377, ++ /* 13 */610, /* 14 */987, /* 15 */1597, /* 16 */2584, /* 17 */4181, ++ /* 18 */6765, /* 19 */10946, /* 20 */17711, /* 21 */28657, /* 22 */46368, ++ /* 23 */75025, /* 24 */121393, /* 25 */196418, /* 26 */317811, ++ /* 27 */514229, /* 28 */832040, /* 29 */1346269, /* 30 */2178309, ++ /* 31 */3524578, /* 32 */5702887, /* 33 */9227465, /* 34 */14930352, ++ /* 35 */24157817, /* 36 */39088169, /* 37 */63245986, /* 38 */102334155, ++ /* 39 */165580141, /* 40 */267914296, /* 41 */433494437, ++ /* 42 */701408733, /* 43 */1134903170, /* 44 */1836311903, ++ /* 45 */2971215073u }; ++ // These are Fibonacci numbers < 2**32. ++ ++ template ++ typename rope<_CharT, _Alloc>::_RopeRep* ++ rope<_CharT, _Alloc>:: ++ _S_balance(_RopeRep* __r) ++ { ++ _RopeRep* __forest[int(__detail::_S_max_rope_depth) + 1]; ++ _RopeRep* __result = 0; ++ int __i; ++ // Invariant: ++ // The concatenation of forest in descending order is equal to __r. ++ // __forest[__i]._M_size >= _S_min_len[__i] ++ // __forest[__i]._M_depth = __i ++ // References from forest are included in refcount. ++ ++ for (__i = 0; __i <= int(__detail::_S_max_rope_depth); ++__i) ++ __forest[__i] = 0; ++ __try ++ { ++ _S_add_to_forest(__r, __forest); ++ for (__i = 0; __i <= int(__detail::_S_max_rope_depth); ++__i) ++ if (0 != __forest[__i]) ++ { ++#ifndef __GC ++ _Self_destruct_ptr __old(__result); ++#endif ++ __result = _S_concat(__forest[__i], __result); ++ __forest[__i]->_M_unref_nonnil(); ++#if !defined(__GC) && defined(__EXCEPTIONS) ++ __forest[__i] = 0; ++#endif ++ } ++ } ++ __catch(...) ++ { ++ for(__i = 0; __i <= int(__detail::_S_max_rope_depth); __i++) ++ _S_unref(__forest[__i]); ++ __throw_exception_again; ++ } ++ ++ if (__result->_M_depth > int(__detail::_S_max_rope_depth)) ++ __throw_length_error(__N("rope::_S_balance")); ++ return(__result); ++ } ++ ++ template ++ void ++ rope<_CharT, _Alloc>:: ++ _S_add_to_forest(_RopeRep* __r, _RopeRep** __forest) ++ { ++ if (__r->_M_is_balanced) ++ { ++ _S_add_leaf_to_forest(__r, __forest); ++ return; ++ } ++ ++ { ++ _RopeConcatenation* __c = (_RopeConcatenation*)__r; ++ ++ _S_add_to_forest(__c->_M_left, __forest); ++ _S_add_to_forest(__c->_M_right, __forest); ++ } ++ } ++ ++ ++ template ++ void ++ rope<_CharT, _Alloc>:: ++ _S_add_leaf_to_forest(_RopeRep* __r, _RopeRep** __forest) ++ { ++ _RopeRep* __insertee; // included in refcount ++ _RopeRep* __too_tiny = 0; // included in refcount ++ int __i; // forest[0..__i-1] is empty ++ size_t __s = __r->_M_size; ++ ++ for (__i = 0; __s >= _S_min_len[__i+1]/* not this bucket */; ++__i) ++ { ++ if (0 != __forest[__i]) ++ { ++#ifndef __GC ++ _Self_destruct_ptr __old(__too_tiny); ++#endif ++ __too_tiny = _S_concat_and_set_balanced(__forest[__i], ++ __too_tiny); ++ __forest[__i]->_M_unref_nonnil(); ++ __forest[__i] = 0; ++ } ++ } ++ { ++#ifndef __GC ++ _Self_destruct_ptr __old(__too_tiny); ++#endif ++ __insertee = _S_concat_and_set_balanced(__too_tiny, __r); ++ } ++ // Too_tiny dead, and no longer included in refcount. ++ // Insertee is live and included. ++ for (;; ++__i) ++ { ++ if (0 != __forest[__i]) ++ { ++#ifndef __GC ++ _Self_destruct_ptr __old(__insertee); ++#endif ++ __insertee = _S_concat_and_set_balanced(__forest[__i], ++ __insertee); ++ __forest[__i]->_M_unref_nonnil(); ++ __forest[__i] = 0; ++ } ++ if (__i == int(__detail::_S_max_rope_depth) ++ || __insertee->_M_size < _S_min_len[__i+1]) ++ { ++ __forest[__i] = __insertee; ++ // refcount is OK since __insertee is now dead. ++ return; ++ } ++ } ++ } ++ ++ template ++ _CharT ++ rope<_CharT, _Alloc>:: ++ _S_fetch(_RopeRep* __r, size_type __i) ++ { ++ __GC_CONST _CharT* __cstr = __r->_M_c_string; ++ ++ if (0 != __cstr) ++ return __cstr[__i]; ++ for(;;) ++ { ++ switch(__r->_M_tag) ++ { ++ case __detail::_S_concat: ++ { ++ _RopeConcatenation* __c = (_RopeConcatenation*)__r; ++ _RopeRep* __left = __c->_M_left; ++ size_t __left_len = __left->_M_size; ++ ++ if (__i >= __left_len) ++ { ++ __i -= __left_len; ++ __r = __c->_M_right; ++ } ++ else ++ __r = __left; ++ } ++ break; ++ case __detail::_S_leaf: ++ { ++ _RopeLeaf* __l = (_RopeLeaf*)__r; ++ return __l->_M_data[__i]; ++ } ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ { ++ _RopeFunction* __f = (_RopeFunction*)__r; ++ _CharT __result; ++ ++ (*(__f->_M_fn))(__i, 1, &__result); ++ return __result; ++ } ++ } ++ } ++ } ++ ++#ifndef __GC ++ // Return a uniquely referenced character slot for the given ++ // position, or 0 if that's not possible. ++ template ++ _CharT* ++ rope<_CharT, _Alloc>:: ++ _S_fetch_ptr(_RopeRep* __r, size_type __i) ++ { ++ _RopeRep* __clrstack[__detail::_S_max_rope_depth]; ++ size_t __csptr = 0; ++ ++ for(;;) ++ { ++ if (__r->_M_ref_count > 1) ++ return 0; ++ switch(__r->_M_tag) ++ { ++ case __detail::_S_concat: ++ { ++ _RopeConcatenation* __c = (_RopeConcatenation*)__r; ++ _RopeRep* __left = __c->_M_left; ++ size_t __left_len = __left->_M_size; ++ ++ if (__c->_M_c_string != 0) ++ __clrstack[__csptr++] = __c; ++ if (__i >= __left_len) ++ { ++ __i -= __left_len; ++ __r = __c->_M_right; ++ } ++ else ++ __r = __left; ++ } ++ break; ++ case __detail::_S_leaf: ++ { ++ _RopeLeaf* __l = (_RopeLeaf*)__r; ++ if (__l->_M_c_string != __l->_M_data && __l->_M_c_string != 0) ++ __clrstack[__csptr++] = __l; ++ while (__csptr > 0) ++ { ++ -- __csptr; ++ _RopeRep* __d = __clrstack[__csptr]; ++ __d->_M_free_c_string(); ++ __d->_M_c_string = 0; ++ } ++ return __l->_M_data + __i; ++ } ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ return 0; ++ } ++ } ++ } ++#endif /* __GC */ ++ ++ // The following could be implemented trivially using ++ // lexicographical_compare_3way. ++ // We do a little more work to avoid dealing with rope iterators for ++ // flat strings. ++ template ++ int ++ rope<_CharT, _Alloc>:: ++ _S_compare (const _RopeRep* __left, const _RopeRep* __right) ++ { ++ size_t __left_len; ++ size_t __right_len; ++ ++ if (0 == __right) ++ return 0 != __left; ++ if (0 == __left) ++ return -1; ++ __left_len = __left->_M_size; ++ __right_len = __right->_M_size; ++ if (__detail::_S_leaf == __left->_M_tag) ++ { ++ _RopeLeaf* __l = (_RopeLeaf*) __left; ++ if (__detail::_S_leaf == __right->_M_tag) ++ { ++ _RopeLeaf* __r = (_RopeLeaf*) __right; ++ return lexicographical_compare_3way(__l->_M_data, ++ __l->_M_data + __left_len, ++ __r->_M_data, __r->_M_data ++ + __right_len); ++ } ++ else ++ { ++ const_iterator __rstart(__right, 0); ++ const_iterator __rend(__right, __right_len); ++ return lexicographical_compare_3way(__l->_M_data, __l->_M_data ++ + __left_len, ++ __rstart, __rend); ++ } ++ } ++ else ++ { ++ const_iterator __lstart(__left, 0); ++ const_iterator __lend(__left, __left_len); ++ if (__detail::_S_leaf == __right->_M_tag) ++ { ++ _RopeLeaf* __r = (_RopeLeaf*) __right; ++ return lexicographical_compare_3way(__lstart, __lend, ++ __r->_M_data, __r->_M_data ++ + __right_len); ++ } ++ else ++ { ++ const_iterator __rstart(__right, 0); ++ const_iterator __rend(__right, __right_len); ++ return lexicographical_compare_3way(__lstart, __lend, ++ __rstart, __rend); ++ } ++ } ++ } ++ ++ // Assignment to reference proxies. ++ template ++ _Rope_char_ref_proxy<_CharT, _Alloc>& ++ _Rope_char_ref_proxy<_CharT, _Alloc>:: ++ operator=(_CharT __c) ++ { ++ _RopeRep* __old = _M_root->_M_tree_ptr; ++#ifndef __GC ++ // First check for the case in which everything is uniquely ++ // referenced. In that case we can do this destructively. ++ _CharT* __ptr = _My_rope::_S_fetch_ptr(__old, _M_pos); ++ if (0 != __ptr) ++ { ++ *__ptr = __c; ++ return *this; ++ } ++#endif ++ _Self_destruct_ptr __left(_My_rope::_S_substring(__old, 0, _M_pos)); ++ _Self_destruct_ptr __right(_My_rope::_S_substring(__old, _M_pos + 1, ++ __old->_M_size)); ++ _Self_destruct_ptr __result_left(_My_rope:: ++ _S_destr_concat_char_iter(__left, ++ &__c, 1)); ++ ++ _RopeRep* __result = _My_rope::_S_concat(__result_left, __right); ++#ifndef __GC ++ _RopeRep::_S_unref(__old); ++#endif ++ _M_root->_M_tree_ptr = __result; ++ return *this; ++ } ++ ++ template ++ inline _Rope_char_ref_proxy<_CharT, _Alloc>:: ++ operator _CharT() const ++ { ++ if (_M_current_valid) ++ return _M_current; ++ else ++ return _My_rope::_S_fetch(_M_root->_M_tree_ptr, _M_pos); ++ } ++ ++ template ++ _Rope_char_ptr_proxy<_CharT, _Alloc> ++ _Rope_char_ref_proxy<_CharT, _Alloc>:: ++ operator&() const ++ { return _Rope_char_ptr_proxy<_CharT, _Alloc>(*this); } ++ ++ template ++ rope<_CharT, _Alloc>:: ++ rope(size_t __n, _CharT __c, const allocator_type& __a) ++ : _Base(__a) ++ { ++ rope<_CharT,_Alloc> __result; ++ const size_t __exponentiate_threshold = 32; ++ size_t __exponent; ++ size_t __rest; ++ _CharT* __rest_buffer; ++ _RopeRep* __remainder; ++ rope<_CharT, _Alloc> __remainder_rope; ++ ++ if (0 == __n) ++ return; ++ ++ __exponent = __n / __exponentiate_threshold; ++ __rest = __n % __exponentiate_threshold; ++ if (0 == __rest) ++ __remainder = 0; ++ else ++ { ++ __rest_buffer = this->_Data_allocate(_S_rounded_up_size(__rest)); ++ __uninitialized_fill_n_a(__rest_buffer, __rest, __c, ++ _M_get_allocator()); ++ _S_cond_store_eos(__rest_buffer[__rest]); ++ __try ++ { __remainder = _S_new_RopeLeaf(__rest_buffer, __rest, ++ _M_get_allocator()); } ++ __catch(...) ++ { ++ _RopeRep::__STL_FREE_STRING(__rest_buffer, __rest, ++ _M_get_allocator()); ++ __throw_exception_again; ++ } ++ } ++ __remainder_rope._M_tree_ptr = __remainder; ++ if (__exponent != 0) ++ { ++ _CharT* __base_buffer = ++ this->_Data_allocate(_S_rounded_up_size(__exponentiate_threshold)); ++ _RopeLeaf* __base_leaf; ++ rope __base_rope; ++ __uninitialized_fill_n_a(__base_buffer, __exponentiate_threshold, __c, ++ _M_get_allocator()); ++ _S_cond_store_eos(__base_buffer[__exponentiate_threshold]); ++ __try ++ { ++ __base_leaf = _S_new_RopeLeaf(__base_buffer, ++ __exponentiate_threshold, ++ _M_get_allocator()); ++ } ++ __catch(...) ++ { ++ _RopeRep::__STL_FREE_STRING(__base_buffer, ++ __exponentiate_threshold, ++ _M_get_allocator()); ++ __throw_exception_again; ++ } ++ __base_rope._M_tree_ptr = __base_leaf; ++ if (1 == __exponent) ++ __result = __base_rope; ++ else ++ __result = power(__base_rope, __exponent, ++ _Rope_Concat_fn<_CharT, _Alloc>()); ++ ++ if (0 != __remainder) ++ __result += __remainder_rope; ++ } ++ else ++ __result = __remainder_rope; ++ ++ this->_M_tree_ptr = __result._M_tree_ptr; ++ this->_M_tree_ptr->_M_ref_nonnil(); ++ } ++ ++ template ++ _CharT ++ rope<_CharT, _Alloc>::_S_empty_c_str[1]; ++ ++ template ++ const _CharT* ++ rope<_CharT, _Alloc>:: ++ c_str() const ++ { ++ if (0 == this->_M_tree_ptr) ++ { ++ _S_empty_c_str[0] = _S_eos((_CharT*)0); // Possibly redundant, ++ // but probably fast. ++ return _S_empty_c_str; ++ } ++ __gthread_mutex_lock (&this->_M_tree_ptr->_M_c_string_lock); ++ __GC_CONST _CharT* __result = this->_M_tree_ptr->_M_c_string; ++ if (0 == __result) ++ { ++ size_t __s = size(); ++ __result = this->_Data_allocate(__s + 1); ++ _S_flatten(this->_M_tree_ptr, __result); ++ __result[__s] = _S_eos((_CharT*)0); ++ this->_M_tree_ptr->_M_c_string = __result; ++ } ++ __gthread_mutex_unlock (&this->_M_tree_ptr->_M_c_string_lock); ++ return(__result); ++ } ++ ++ template ++ const _CharT* rope<_CharT, _Alloc>:: ++ replace_with_c_str() ++ { ++ if (0 == this->_M_tree_ptr) ++ { ++ _S_empty_c_str[0] = _S_eos((_CharT*)0); ++ return _S_empty_c_str; ++ } ++ __GC_CONST _CharT* __old_c_string = this->_M_tree_ptr->_M_c_string; ++ if (__detail::_S_leaf == this->_M_tree_ptr->_M_tag ++ && 0 != __old_c_string) ++ return(__old_c_string); ++ size_t __s = size(); ++ _CharT* __result = this->_Data_allocate(_S_rounded_up_size(__s)); ++ _S_flatten(this->_M_tree_ptr, __result); ++ __result[__s] = _S_eos((_CharT*)0); ++ this->_M_tree_ptr->_M_unref_nonnil(); ++ this->_M_tree_ptr = _S_new_RopeLeaf(__result, __s, ++ this->_M_get_allocator()); ++ return(__result); ++ } ++ ++ // Algorithm specializations. More should be added. ++ ++ template // was templated on CharT and Alloc ++ void // VC++ workaround ++ _Rope_rotate(_Rope_iterator __first, ++ _Rope_iterator __middle, ++ _Rope_iterator __last) ++ { ++ typedef typename _Rope_iterator::value_type _CharT; ++ typedef typename _Rope_iterator::_allocator_type _Alloc; ++ ++ rope<_CharT, _Alloc>& __r(__first.container()); ++ rope<_CharT, _Alloc> __prefix = __r.substr(0, __first.index()); ++ rope<_CharT, _Alloc> __suffix = ++ __r.substr(__last.index(), __r.size() - __last.index()); ++ rope<_CharT, _Alloc> __part1 = ++ __r.substr(__middle.index(), __last.index() - __middle.index()); ++ rope<_CharT, _Alloc> __part2 = ++ __r.substr(__first.index(), __middle.index() - __first.index()); ++ __r = __prefix; ++ __r += __part1; ++ __r += __part2; ++ __r += __suffix; ++ } ++ ++#if !defined(__GNUC__) ++ // Appears to confuse g++ ++ inline void ++ rotate(_Rope_iterator __first, ++ _Rope_iterator __middle, ++ _Rope_iterator __last) ++ { _Rope_rotate(__first, __middle, __last); } ++#endif ++ ++# if 0 ++ // Probably not useful for several reasons: ++ // - for SGIs 7.1 compiler and probably some others, ++ // this forces lots of rope instantiations, creating a ++ // code bloat and compile time problem. (Fixed in 7.2.) ++ // - wchar_t is 4 bytes wide on most UNIX platforms, making it ++ // unattractive for unicode strings. Unsigned short may be a better ++ // character type. ++ inline void ++ rotate(_Rope_iterator __first, ++ _Rope_iterator __middle, ++ _Rope_iterator __last) ++ { _Rope_rotate(__first, __middle, __last); } ++# endif ++ ++_GLIBCXX_END_NAMESPACE +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/numeric_traits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/numeric_traits.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/numeric_traits.h (revision 11967) +@@ -0,0 +1,135 @@ ++// -*- C++ -*- ++ ++// Copyright (C) 2007, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the terms ++// of the GNU General Public License as published by the Free Software ++// Foundation; either version 3, or (at your option) any later ++// version. ++ ++// This library is distributed in the hope that it will be useful, but ++// WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++// General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/numeric_traits.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _EXT_NUMERIC_TRAITS ++#define _EXT_NUMERIC_TRAITS 1 ++ ++#pragma GCC system_header ++ ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ // Compile time constants for builtin types. ++ // Sadly std::numeric_limits member functions cannot be used for this. ++#define __glibcxx_signed(_Tp) ((_Tp)(-1) < 0) ++#define __glibcxx_digits(_Tp) \ ++ (sizeof(_Tp) * __CHAR_BIT__ - __glibcxx_signed(_Tp)) ++ ++#define __glibcxx_min(_Tp) \ ++ (__glibcxx_signed(_Tp) ? (_Tp)1 << __glibcxx_digits(_Tp) : (_Tp)0) ++ ++#define __glibcxx_max(_Tp) \ ++ (__glibcxx_signed(_Tp) ? \ ++ (((((_Tp)1 << (__glibcxx_digits(_Tp) - 1)) - 1) << 1) + 1) : ~(_Tp)0) ++ ++ template ++ struct __numeric_traits_integer ++ { ++ // Only integers for initialization of member constant. ++ static const _Value __min = __glibcxx_min(_Value); ++ static const _Value __max = __glibcxx_max(_Value); ++ ++ // NB: these two also available in std::numeric_limits as compile ++ // time constants, but is big and we avoid including it. ++ static const bool __is_signed = __glibcxx_signed(_Value); ++ static const int __digits = __glibcxx_digits(_Value); ++ }; ++ ++ template ++ const _Value __numeric_traits_integer<_Value>::__min; ++ ++ template ++ const _Value __numeric_traits_integer<_Value>::__max; ++ ++ template ++ const bool __numeric_traits_integer<_Value>::__is_signed; ++ ++ template ++ const int __numeric_traits_integer<_Value>::__digits; ++ ++#undef __glibcxx_signed ++#undef __glibcxx_digits ++#undef __glibcxx_min ++#undef __glibcxx_max ++ ++#define __glibcxx_floating(_Tp, _Fval, _Dval, _LDval) \ ++ (std::__are_same<_Tp, float>::__value ? _Fval \ ++ : std::__are_same<_Tp, double>::__value ? _Dval : _LDval) ++ ++#define __glibcxx_max_digits10(_Tp) \ ++ (2 + __glibcxx_floating(_Tp, __FLT_MANT_DIG__, __DBL_MANT_DIG__, \ ++ __LDBL_MANT_DIG__) * 3010 / 10000) ++ ++#define __glibcxx_digits10(_Tp) \ ++ __glibcxx_floating(_Tp, __FLT_DIG__, __DBL_DIG__, __LDBL_DIG__) ++ ++#define __glibcxx_max_exponent10(_Tp) \ ++ __glibcxx_floating(_Tp, __FLT_MAX_10_EXP__, __DBL_MAX_10_EXP__, \ ++ __LDBL_MAX_10_EXP__) ++ ++ template ++ struct __numeric_traits_floating ++ { ++ // Only floating point types. See N1822. ++ static const int __max_digits10 = __glibcxx_max_digits10(_Value); ++ ++ // See above comment... ++ static const bool __is_signed = true; ++ static const int __digits10 = __glibcxx_digits10(_Value); ++ static const int __max_exponent10 = __glibcxx_max_exponent10(_Value); ++ }; ++ ++ template ++ const int __numeric_traits_floating<_Value>::__max_digits10; ++ ++ template ++ const bool __numeric_traits_floating<_Value>::__is_signed; ++ ++ template ++ const int __numeric_traits_floating<_Value>::__digits10; ++ ++ template ++ const int __numeric_traits_floating<_Value>::__max_exponent10; ++ ++ template ++ struct __numeric_traits ++ : public __conditional_type::__value, ++ __numeric_traits_integer<_Value>, ++ __numeric_traits_floating<_Value> >::__type ++ { }; ++ ++_GLIBCXX_END_NAMESPACE ++ ++#undef __glibcxx_floating ++#undef __glibcxx_max_digits10 ++#undef __glibcxx_digits10 ++#undef __glibcxx_max_exponent10 ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/new_allocator.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/new_allocator.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/new_allocator.h (revision 11967) +@@ -0,0 +1,130 @@ ++// Allocator that wraps operator new -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/new_allocator.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _NEW_ALLOCATOR_H ++#define _NEW_ALLOCATOR_H 1 ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::size_t; ++ using std::ptrdiff_t; ++ ++ /** ++ * @brief An allocator that uses global new, as per [20.4]. ++ * @ingroup allocators ++ * ++ * This is precisely the allocator defined in the C++ Standard. ++ * - all allocation calls operator new ++ * - all deallocation calls operator delete ++ */ ++ template ++ class new_allocator ++ { ++ public: ++ typedef size_t size_type; ++ typedef ptrdiff_t difference_type; ++ typedef _Tp* pointer; ++ typedef const _Tp* const_pointer; ++ typedef _Tp& reference; ++ typedef const _Tp& const_reference; ++ typedef _Tp value_type; ++ ++ template ++ struct rebind ++ { typedef new_allocator<_Tp1> other; }; ++ ++ new_allocator() throw() { } ++ ++ new_allocator(const new_allocator&) throw() { } ++ ++ template ++ new_allocator(const new_allocator<_Tp1>&) throw() { } ++ ++ ~new_allocator() throw() { } ++ ++ pointer ++ address(reference __x) const { return &__x; } ++ ++ const_pointer ++ address(const_reference __x) const { return &__x; } ++ ++ // NB: __n is permitted to be 0. The C++ standard says nothing ++ // about what the return value is when __n == 0. ++ pointer ++ allocate(size_type __n, const void* = 0) ++ { ++ if (__builtin_expect(__n > this->max_size(), false)) ++ std::__throw_bad_alloc(); ++ ++ return static_cast<_Tp*>(::operator new(__n * sizeof(_Tp))); ++ } ++ ++ // __p is not permitted to be a null pointer. ++ void ++ deallocate(pointer __p, size_type) ++ { ::operator delete(__p); } ++ ++ size_type ++ max_size() const throw() ++ { return size_t(-1) / sizeof(_Tp); } ++ ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 402. wrong new expression in [some_] allocator::construct ++ void ++ construct(pointer __p, const _Tp& __val) ++ { ::new((void *)__p) _Tp(__val); } ++ ++#ifdef __GXX_EXPERIMENTAL_CXX0X__ ++ template ++ void ++ construct(pointer __p, _Args&&... __args) ++ { ::new((void *)__p) _Tp(std::forward<_Args>(__args)...); } ++#endif ++ ++ void ++ destroy(pointer __p) { __p->~_Tp(); } ++ }; ++ ++ template ++ inline bool ++ operator==(const new_allocator<_Tp>&, const new_allocator<_Tp>&) ++ { return true; } ++ ++ template ++ inline bool ++ operator!=(const new_allocator<_Tp>&, const new_allocator<_Tp>&) ++ { return false; } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/hash_map +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/hash_map (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/hash_map (revision 11967) +@@ -0,0 +1,593 @@ ++// Hashing map implementation -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2004, 2005, 2006, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/* ++ * Copyright (c) 1996 ++ * Silicon Graphics Computer Systems, Inc. ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Silicon Graphics makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ * ++ * ++ * Copyright (c) 1994 ++ * Hewlett-Packard Company ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Hewlett-Packard Company makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ * ++ */ ++ ++/** @file backward/hash_map ++ * This file is a GNU extension to the Standard C++ Library (possibly ++ * containing extensions from the HP/SGI STL subset). ++ */ ++ ++#ifndef _HASH_MAP ++#define _HASH_MAP 1 ++ ++#ifndef _GLIBCXX_PERMIT_BACKWARD_HASH ++#include "backward_warning.h" ++#endif ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::equal_to; ++ using std::allocator; ++ using std::pair; ++ using std::_Select1st; ++ ++ /** ++ * This is an SGI extension. ++ * @ingroup SGIextensions ++ * @doctodo ++ */ ++ template, ++ class _EqualKey = equal_to<_Key>, class _Alloc = allocator<_Tp> > ++ class hash_map ++ { ++ private: ++ typedef hashtable,_Key, _HashFn, ++ _Select1st >, ++ _EqualKey, _Alloc> _Ht; ++ ++ _Ht _M_ht; ++ ++ public: ++ typedef typename _Ht::key_type key_type; ++ typedef _Tp data_type; ++ typedef _Tp mapped_type; ++ typedef typename _Ht::value_type value_type; ++ typedef typename _Ht::hasher hasher; ++ typedef typename _Ht::key_equal key_equal; ++ ++ typedef typename _Ht::size_type size_type; ++ typedef typename _Ht::difference_type difference_type; ++ typedef typename _Ht::pointer pointer; ++ typedef typename _Ht::const_pointer const_pointer; ++ typedef typename _Ht::reference reference; ++ typedef typename _Ht::const_reference const_reference; ++ ++ typedef typename _Ht::iterator iterator; ++ typedef typename _Ht::const_iterator const_iterator; ++ ++ typedef typename _Ht::allocator_type allocator_type; ++ ++ hasher ++ hash_funct() const ++ { return _M_ht.hash_funct(); } ++ ++ key_equal ++ key_eq() const ++ { return _M_ht.key_eq(); } ++ ++ allocator_type ++ get_allocator() const ++ { return _M_ht.get_allocator(); } ++ ++ hash_map() ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) {} ++ ++ explicit ++ hash_map(size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) {} ++ ++ hash_map(size_type __n, const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) {} ++ ++ hash_map(size_type __n, const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) {} ++ ++ template ++ hash_map(_InputIterator __f, _InputIterator __l) ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ template ++ hash_map(_InputIterator __f, _InputIterator __l, size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ template ++ hash_map(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ template ++ hash_map(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ size_type ++ size() const ++ { return _M_ht.size(); } ++ ++ size_type ++ max_size() const ++ { return _M_ht.max_size(); } ++ ++ bool ++ empty() const ++ { return _M_ht.empty(); } ++ ++ void ++ swap(hash_map& __hs) ++ { _M_ht.swap(__hs._M_ht); } ++ ++ template ++ friend bool ++ operator== (const hash_map<_K1, _T1, _HF, _EqK, _Al>&, ++ const hash_map<_K1, _T1, _HF, _EqK, _Al>&); ++ ++ iterator ++ begin() ++ { return _M_ht.begin(); } ++ ++ iterator ++ end() ++ { return _M_ht.end(); } ++ ++ const_iterator ++ begin() const ++ { return _M_ht.begin(); } ++ ++ const_iterator ++ end() const ++ { return _M_ht.end(); } ++ ++ pair ++ insert(const value_type& __obj) ++ { return _M_ht.insert_unique(__obj); } ++ ++ template ++ void ++ insert(_InputIterator __f, _InputIterator __l) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ pair ++ insert_noresize(const value_type& __obj) ++ { return _M_ht.insert_unique_noresize(__obj); } ++ ++ iterator ++ find(const key_type& __key) ++ { return _M_ht.find(__key); } ++ ++ const_iterator ++ find(const key_type& __key) const ++ { return _M_ht.find(__key); } ++ ++ _Tp& ++ operator[](const key_type& __key) ++ { return _M_ht.find_or_insert(value_type(__key, _Tp())).second; } ++ ++ size_type ++ count(const key_type& __key) const ++ { return _M_ht.count(__key); } ++ ++ pair ++ equal_range(const key_type& __key) ++ { return _M_ht.equal_range(__key); } ++ ++ pair ++ equal_range(const key_type& __key) const ++ { return _M_ht.equal_range(__key); } ++ ++ size_type ++ erase(const key_type& __key) ++ {return _M_ht.erase(__key); } ++ ++ void ++ erase(iterator __it) ++ { _M_ht.erase(__it); } ++ ++ void ++ erase(iterator __f, iterator __l) ++ { _M_ht.erase(__f, __l); } ++ ++ void ++ clear() ++ { _M_ht.clear(); } ++ ++ void ++ resize(size_type __hint) ++ { _M_ht.resize(__hint); } ++ ++ size_type ++ bucket_count() const ++ { return _M_ht.bucket_count(); } ++ ++ size_type ++ max_bucket_count() const ++ { return _M_ht.max_bucket_count(); } ++ ++ size_type ++ elems_in_bucket(size_type __n) const ++ { return _M_ht.elems_in_bucket(__n); } ++ }; ++ ++ template ++ inline bool ++ operator==(const hash_map<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm1, ++ const hash_map<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm2) ++ { return __hm1._M_ht == __hm2._M_ht; } ++ ++ template ++ inline bool ++ operator!=(const hash_map<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm1, ++ const hash_map<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm2) ++ { return !(__hm1 == __hm2); } ++ ++ template ++ inline void ++ swap(hash_map<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm1, ++ hash_map<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm2) ++ { __hm1.swap(__hm2); } ++ ++ ++ /** ++ * This is an SGI extension. ++ * @ingroup SGIextensions ++ * @doctodo ++ */ ++ template, ++ class _EqualKey = equal_to<_Key>, ++ class _Alloc = allocator<_Tp> > ++ class hash_multimap ++ { ++ // concept requirements ++ __glibcxx_class_requires(_Key, _SGIAssignableConcept) ++ __glibcxx_class_requires(_Tp, _SGIAssignableConcept) ++ __glibcxx_class_requires3(_HashFn, size_t, _Key, _UnaryFunctionConcept) ++ __glibcxx_class_requires3(_EqualKey, _Key, _Key, _BinaryPredicateConcept) ++ ++ private: ++ typedef hashtable, _Key, _HashFn, ++ _Select1st >, _EqualKey, _Alloc> ++ _Ht; ++ ++ _Ht _M_ht; ++ ++ public: ++ typedef typename _Ht::key_type key_type; ++ typedef _Tp data_type; ++ typedef _Tp mapped_type; ++ typedef typename _Ht::value_type value_type; ++ typedef typename _Ht::hasher hasher; ++ typedef typename _Ht::key_equal key_equal; ++ ++ typedef typename _Ht::size_type size_type; ++ typedef typename _Ht::difference_type difference_type; ++ typedef typename _Ht::pointer pointer; ++ typedef typename _Ht::const_pointer const_pointer; ++ typedef typename _Ht::reference reference; ++ typedef typename _Ht::const_reference const_reference; ++ ++ typedef typename _Ht::iterator iterator; ++ typedef typename _Ht::const_iterator const_iterator; ++ ++ typedef typename _Ht::allocator_type allocator_type; ++ ++ hasher ++ hash_funct() const ++ { return _M_ht.hash_funct(); } ++ ++ key_equal ++ key_eq() const ++ { return _M_ht.key_eq(); } ++ ++ allocator_type ++ get_allocator() const ++ { return _M_ht.get_allocator(); } ++ ++ hash_multimap() ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) {} ++ ++ explicit ++ hash_multimap(size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) {} ++ ++ hash_multimap(size_type __n, const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) {} ++ ++ hash_multimap(size_type __n, const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) {} ++ ++ template ++ hash_multimap(_InputIterator __f, _InputIterator __l) ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ template ++ hash_multimap(_InputIterator __f, _InputIterator __l, size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ template ++ hash_multimap(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ template ++ hash_multimap(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ size_type ++ size() const ++ { return _M_ht.size(); } ++ ++ size_type ++ max_size() const ++ { return _M_ht.max_size(); } ++ ++ bool ++ empty() const ++ { return _M_ht.empty(); } ++ ++ void ++ swap(hash_multimap& __hs) ++ { _M_ht.swap(__hs._M_ht); } ++ ++ template ++ friend bool ++ operator==(const hash_multimap<_K1, _T1, _HF, _EqK, _Al>&, ++ const hash_multimap<_K1, _T1, _HF, _EqK, _Al>&); ++ ++ iterator ++ begin() ++ { return _M_ht.begin(); } ++ ++ iterator ++ end() ++ { return _M_ht.end(); } ++ ++ const_iterator ++ begin() const ++ { return _M_ht.begin(); } ++ ++ const_iterator ++ end() const ++ { return _M_ht.end(); } ++ ++ iterator ++ insert(const value_type& __obj) ++ { return _M_ht.insert_equal(__obj); } ++ ++ template ++ void ++ insert(_InputIterator __f, _InputIterator __l) ++ { _M_ht.insert_equal(__f,__l); } ++ ++ iterator ++ insert_noresize(const value_type& __obj) ++ { return _M_ht.insert_equal_noresize(__obj); } ++ ++ iterator ++ find(const key_type& __key) ++ { return _M_ht.find(__key); } ++ ++ const_iterator ++ find(const key_type& __key) const ++ { return _M_ht.find(__key); } ++ ++ size_type ++ count(const key_type& __key) const ++ { return _M_ht.count(__key); } ++ ++ pair ++ equal_range(const key_type& __key) ++ { return _M_ht.equal_range(__key); } ++ ++ pair ++ equal_range(const key_type& __key) const ++ { return _M_ht.equal_range(__key); } ++ ++ size_type ++ erase(const key_type& __key) ++ { return _M_ht.erase(__key); } ++ ++ void ++ erase(iterator __it) ++ { _M_ht.erase(__it); } ++ ++ void ++ erase(iterator __f, iterator __l) ++ { _M_ht.erase(__f, __l); } ++ ++ void ++ clear() ++ { _M_ht.clear(); } ++ ++ void ++ resize(size_type __hint) ++ { _M_ht.resize(__hint); } ++ ++ size_type ++ bucket_count() const ++ { return _M_ht.bucket_count(); } ++ ++ size_type ++ max_bucket_count() const ++ { return _M_ht.max_bucket_count(); } ++ ++ size_type ++ elems_in_bucket(size_type __n) const ++ { return _M_ht.elems_in_bucket(__n); } ++ }; ++ ++ template ++ inline bool ++ operator==(const hash_multimap<_Key, _Tp, _HF, _EqKey, _Alloc>& __hm1, ++ const hash_multimap<_Key, _Tp, _HF, _EqKey, _Alloc>& __hm2) ++ { return __hm1._M_ht == __hm2._M_ht; } ++ ++ template ++ inline bool ++ operator!=(const hash_multimap<_Key, _Tp, _HF, _EqKey, _Alloc>& __hm1, ++ const hash_multimap<_Key, _Tp, _HF, _EqKey, _Alloc>& __hm2) ++ { return !(__hm1 == __hm2); } ++ ++ template ++ inline void ++ swap(hash_multimap<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm1, ++ hash_multimap<_Key, _Tp, _HashFn, _EqlKey, _Alloc>& __hm2) ++ { __hm1.swap(__hm2); } ++ ++_GLIBCXX_END_NAMESPACE ++ ++_GLIBCXX_BEGIN_NAMESPACE(std) ++ ++ // Specialization of insert_iterator so that it will work for hash_map ++ // and hash_multimap. ++ template ++ class insert_iterator<__gnu_cxx::hash_map<_Key, _Tp, _HashFn, ++ _EqKey, _Alloc> > ++ { ++ protected: ++ typedef __gnu_cxx::hash_map<_Key, _Tp, _HashFn, _EqKey, _Alloc> ++ _Container; ++ _Container* container; ++ ++ public: ++ typedef _Container container_type; ++ typedef output_iterator_tag iterator_category; ++ typedef void value_type; ++ typedef void difference_type; ++ typedef void pointer; ++ typedef void reference; ++ ++ insert_iterator(_Container& __x) ++ : container(&__x) {} ++ ++ insert_iterator(_Container& __x, typename _Container::iterator) ++ : container(&__x) {} ++ ++ insert_iterator<_Container>& ++ operator=(const typename _Container::value_type& __value) ++ { ++ container->insert(__value); ++ return *this; ++ } ++ ++ insert_iterator<_Container>& ++ operator*() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++() { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++(int) ++ { return *this; } ++ }; ++ ++ template ++ class insert_iterator<__gnu_cxx::hash_multimap<_Key, _Tp, _HashFn, ++ _EqKey, _Alloc> > ++ { ++ protected: ++ typedef __gnu_cxx::hash_multimap<_Key, _Tp, _HashFn, _EqKey, _Alloc> ++ _Container; ++ _Container* container; ++ typename _Container::iterator iter; ++ ++ public: ++ typedef _Container container_type; ++ typedef output_iterator_tag iterator_category; ++ typedef void value_type; ++ typedef void difference_type; ++ typedef void pointer; ++ typedef void reference; ++ ++ insert_iterator(_Container& __x) ++ : container(&__x) {} ++ ++ insert_iterator(_Container& __x, typename _Container::iterator) ++ : container(&__x) {} ++ ++ insert_iterator<_Container>& ++ operator=(const typename _Container::value_type& __value) ++ { ++ container->insert(__value); ++ return *this; ++ } ++ ++ insert_iterator<_Container>& ++ operator*() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++(int) ++ { return *this; } ++ }; ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/vstring_fwd.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/vstring_fwd.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/vstring_fwd.h (revision 11967) +@@ -0,0 +1,87 @@ ++// Versatile string forward -*- C++ -*- ++ ++// Copyright (C) 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/vstring_fwd.h ++ * This file is a GNU extension to the Standard C++ Library. ++ * This is an internal header file, included by other library headers. ++ * You should not attempt to use it directly. ++ */ ++ ++#ifndef _VSTRING_FWD_H ++#define _VSTRING_FWD_H 1 ++ ++#pragma GCC system_header ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ template ++ class __sso_string_base; ++ ++ template ++ class __rc_string_base; ++ ++ template, ++ typename _Alloc = std::allocator<_CharT>, ++ template ++ class _Base = __sso_string_base> ++ class __versa_string; ++ ++ typedef __versa_string __vstring; ++ typedef __vstring __sso_string; ++ typedef ++ __versa_string, ++ std::allocator, __rc_string_base> __rc_string; ++ ++#ifdef _GLIBCXX_USE_WCHAR_T ++ typedef __versa_string __wvstring; ++ typedef __wvstring __wsso_string; ++ typedef ++ __versa_string, ++ std::allocator, __rc_string_base> __wrc_string; ++#endif ++ ++#if (defined(__GXX_EXPERIMENTAL_CXX0X__) \ ++ && defined(_GLIBCXX_USE_C99_STDINT_TR1)) ++ ++ typedef __versa_string __u16vstring; ++ typedef __u16vstring __u16sso_string; ++ typedef ++ __versa_string, ++ std::allocator, __rc_string_base> __u16rc_string; ++ ++ typedef __versa_string __u32vstring; ++ typedef __u32vstring __u32sso_string; ++ typedef ++ __versa_string, ++ std::allocator, __rc_string_base> __u32rc_string; ++ ++#endif ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif /* _VSTRING_FWD_H */ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/atomicity.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/atomicity.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/atomicity.h (revision 11967) +@@ -0,0 +1,113 @@ ++// Support for atomic operations -*- C++ -*- ++ ++// Copyright (C) 2004, 2005, 2006, 2008, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file atomicity.h ++ * This is an internal header file, included by other library headers. ++ * You should not attempt to use it directly. ++ */ ++ ++#ifndef _GLIBCXX_ATOMICITY_H ++#define _GLIBCXX_ATOMICITY_H 1 ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ // Functions for portable atomic access. ++ // To abstract locking primitives across all thread policies, use: ++ // __exchange_and_add_dispatch ++ // __atomic_add_dispatch ++#ifdef _GLIBCXX_ATOMIC_BUILTINS_4 ++ static inline _Atomic_word ++ __exchange_and_add(volatile _Atomic_word* __mem, int __val) ++ { return __sync_fetch_and_add(__mem, __val); } ++ ++ static inline void ++ __atomic_add(volatile _Atomic_word* __mem, int __val) ++ { __sync_fetch_and_add(__mem, __val); } ++#else ++ _Atomic_word ++ __attribute__ ((__unused__)) ++ __exchange_and_add(volatile _Atomic_word*, int); ++ ++ void ++ __attribute__ ((__unused__)) ++ __atomic_add(volatile _Atomic_word*, int); ++#endif ++ ++ static inline _Atomic_word ++ __exchange_and_add_single(_Atomic_word* __mem, int __val) ++ { ++ _Atomic_word __result = *__mem; ++ *__mem += __val; ++ return __result; ++ } ++ ++ static inline void ++ __atomic_add_single(_Atomic_word* __mem, int __val) ++ { *__mem += __val; } ++ ++ static inline _Atomic_word ++ __attribute__ ((__unused__)) ++ __exchange_and_add_dispatch(_Atomic_word* __mem, int __val) ++ { ++#ifdef __GTHREADS ++ if (__gthread_active_p()) ++ return __exchange_and_add(__mem, __val); ++ else ++ return __exchange_and_add_single(__mem, __val); ++#else ++ return __exchange_and_add_single(__mem, __val); ++#endif ++ } ++ ++ static inline void ++ __attribute__ ((__unused__)) ++ __atomic_add_dispatch(_Atomic_word* __mem, int __val) ++ { ++#ifdef __GTHREADS ++ if (__gthread_active_p()) ++ __atomic_add(__mem, __val); ++ else ++ __atomic_add_single(__mem, __val); ++#else ++ __atomic_add_single(__mem, __val); ++#endif ++ } ++ ++_GLIBCXX_END_NAMESPACE ++ ++// Even if the CPU doesn't need a memory barrier, we need to ensure ++// that the compiler doesn't reorder memory accesses across the ++// barriers. ++#ifndef _GLIBCXX_READ_MEM_BARRIER ++#define _GLIBCXX_READ_MEM_BARRIER __asm __volatile ("":::"memory") ++#endif ++#ifndef _GLIBCXX_WRITE_MEM_BARRIER ++#define _GLIBCXX_WRITE_MEM_BARRIER __asm __volatile ("":::"memory") ++#endif ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/iterator +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/iterator (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/iterator (revision 11967) +@@ -0,0 +1,113 @@ ++// HP/SGI iterator extensions -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2004, 2005, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/* ++ * ++ * Copyright (c) 1994 ++ * Hewlett-Packard Company ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Hewlett-Packard Company makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ * ++ * ++ * Copyright (c) 1996-1998 ++ * Silicon Graphics Computer Systems, Inc. ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Silicon Graphics makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ */ ++ ++/** @file ext/iterator ++ * This file is a GNU extension to the Standard C++ Library (possibly ++ * containing extensions from the HP/SGI STL subset). ++ */ ++ ++#ifndef _EXT_ITERATOR ++#define _EXT_ITERATOR 1 ++ ++#pragma GCC system_header ++ ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ // There are two signatures for distance. In addition to the one ++ // taking two iterators and returning a result, there is another ++ // taking two iterators and a reference-to-result variable, and ++ // returning nothing. The latter seems to be an SGI extension. ++ // -- pedwards ++ template ++ inline void ++ __distance(_InputIterator __first, _InputIterator __last, ++ _Distance& __n, std::input_iterator_tag) ++ { ++ // concept requirements ++ __glibcxx_function_requires(_InputIteratorConcept<_InputIterator>) ++ while (__first != __last) ++ { ++ ++__first; ++ ++__n; ++ } ++ } ++ ++ template ++ inline void ++ __distance(_RandomAccessIterator __first, _RandomAccessIterator __last, ++ _Distance& __n, std::random_access_iterator_tag) ++ { ++ // concept requirements ++ __glibcxx_function_requires(_RandomAccessIteratorConcept< ++ _RandomAccessIterator>) ++ __n += __last - __first; ++ } ++ ++ /** ++ * This is an SGI extension. ++ * @ingroup SGIextensions ++ * @doctodo ++ */ ++ template ++ inline void ++ distance(_InputIterator __first, _InputIterator __last, ++ _Distance& __n) ++ { ++ // concept requirements -- taken care of in __distance ++ __distance(__first, __last, __n, std::__iterator_category(__first)); ++ } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/pod_char_traits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/pod_char_traits.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/pod_char_traits.h (revision 11967) +@@ -0,0 +1,182 @@ ++// POD character, std::char_traits specialization -*- C++ -*- ++ ++// Copyright (C) 2002, 2003, 2004, 2005, 2007, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/pod_char_traits.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++// Gabriel Dos Reis ++// Benjamin Kosnik ++ ++#ifndef _POD_CHAR_TRAITS_H ++#define _POD_CHAR_TRAITS_H 1 ++ ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ // POD character abstraction. ++ // NB: The char_type parameter is a subset of int_type, as to allow ++ // int_type to properly hold the full range of char_type values as ++ // well as EOF. ++ /// @brief A POD class that serves as a character abstraction class. ++ template ++ struct character ++ { ++ typedef V value_type; ++ typedef I int_type; ++ typedef S state_type; ++ typedef character char_type; ++ ++ value_type value; ++ ++ template ++ static char_type ++ from(const V2& v) ++ { ++ char_type ret = { static_cast(v) }; ++ return ret; ++ } ++ ++ template ++ static V2 ++ to(const char_type& c) ++ { ++ V2 ret = { static_cast(c.value) }; ++ return ret; ++ } ++ ++ }; ++ ++ template ++ inline bool ++ operator==(const character& lhs, const character& rhs) ++ { return lhs.value == rhs.value; } ++ ++ template ++ inline bool ++ operator<(const character& lhs, const character& rhs) ++ { return lhs.value < rhs.value; } ++ ++_GLIBCXX_END_NAMESPACE ++ ++_GLIBCXX_BEGIN_NAMESPACE(std) ++ ++ /// char_traits<__gnu_cxx::character> specialization. ++ template ++ struct char_traits<__gnu_cxx::character > ++ { ++ typedef __gnu_cxx::character char_type; ++ typedef typename char_type::int_type int_type; ++ typedef typename char_type::state_type state_type; ++ typedef fpos pos_type; ++ typedef streamoff off_type; ++ ++ static void ++ assign(char_type& __c1, const char_type& __c2) ++ { __c1 = __c2; } ++ ++ static bool ++ eq(const char_type& __c1, const char_type& __c2) ++ { return __c1 == __c2; } ++ ++ static bool ++ lt(const char_type& __c1, const char_type& __c2) ++ { return __c1 < __c2; } ++ ++ static int ++ compare(const char_type* __s1, const char_type* __s2, size_t __n) ++ { ++ for (size_t __i = 0; __i < __n; ++__i) ++ if (!eq(__s1[__i], __s2[__i])) ++ return lt(__s1[__i], __s2[__i]) ? -1 : 1; ++ return 0; ++ } ++ ++ static size_t ++ length(const char_type* __s) ++ { ++ const char_type* __p = __s; ++ while (__p->value) ++ ++__p; ++ return (__p - __s); ++ } ++ ++ static const char_type* ++ find(const char_type* __s, size_t __n, const char_type& __a) ++ { ++ for (const char_type* __p = __s; size_t(__p - __s) < __n; ++__p) ++ if (*__p == __a) ++ return __p; ++ return 0; ++ } ++ ++ static char_type* ++ move(char_type* __s1, const char_type* __s2, size_t __n) ++ { ++ return static_cast ++ (__builtin_memmove(__s1, __s2, __n * sizeof(char_type))); ++ } ++ ++ static char_type* ++ copy(char_type* __s1, const char_type* __s2, size_t __n) ++ { ++ std::copy(__s2, __s2 + __n, __s1); ++ return __s1; ++ } ++ ++ static char_type* ++ assign(char_type* __s, size_t __n, char_type __a) ++ { ++ std::fill_n(__s, __n, __a); ++ return __s; ++ } ++ ++ static char_type ++ to_char_type(const int_type& __i) ++ { return char_type::template from(__i); } ++ ++ static int_type ++ to_int_type(const char_type& __c) ++ { return char_type::template to(__c); } ++ ++ static bool ++ eq_int_type(const int_type& __c1, const int_type& __c2) ++ { return __c1 == __c2; } ++ ++ static int_type ++ eof() ++ { ++ int_type __r = { -1 }; ++ return __r; ++ } ++ ++ static int_type ++ not_eof(const int_type& __c) ++ { return eq_int_type(__c, eof()) ? int_type() : __c; } ++ }; ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/concurrence.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/concurrence.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/concurrence.h (revision 11967) +@@ -0,0 +1,322 @@ ++// Support for concurrent programing -*- C++ -*- ++ ++// Copyright (C) 2003, 2004, 2005, 2006, 2007, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file concurrence.h ++ * This is an internal header file, included by other library headers. ++ * You should not attempt to use it directly. ++ */ ++ ++#ifndef _CONCURRENCE_H ++#define _CONCURRENCE_H 1 ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ // Available locking policies: ++ // _S_single single-threaded code that doesn't need to be locked. ++ // _S_mutex multi-threaded code that requires additional support ++ // from gthr.h or abstraction layers in concurrence.h. ++ // _S_atomic multi-threaded code using atomic operations. ++ enum _Lock_policy { _S_single, _S_mutex, _S_atomic }; ++ ++ // Compile time constant that indicates prefered locking policy in ++ // the current configuration. ++ static const _Lock_policy __default_lock_policy = ++#ifdef __GTHREADS ++#if (defined(__GCC_HAVE_SYNC_COMPARE_AND_SWAP_2) \ ++ && defined(__GCC_HAVE_SYNC_COMPARE_AND_SWAP_4)) ++ _S_atomic; ++#else ++ _S_mutex; ++#endif ++#else ++ _S_single; ++#endif ++ ++ // NB: As this is used in libsupc++, need to only depend on ++ // exception. No stdexception classes, no use of std::string. ++ class __concurrence_lock_error : public std::exception ++ { ++ public: ++ virtual char const* ++ what() const throw() ++ { return "__gnu_cxx::__concurrence_lock_error"; } ++ }; ++ ++ class __concurrence_unlock_error : public std::exception ++ { ++ public: ++ virtual char const* ++ what() const throw() ++ { return "__gnu_cxx::__concurrence_unlock_error"; } ++ }; ++ ++ class __concurrence_broadcast_error : public std::exception ++ { ++ public: ++ virtual char const* ++ what() const throw() ++ { return "__gnu_cxx::__concurrence_broadcast_error"; } ++ }; ++ ++ class __concurrence_wait_error : public std::exception ++ { ++ public: ++ virtual char const* ++ what() const throw() ++ { return "__gnu_cxx::__concurrence_wait_error"; } ++ }; ++ ++ // Substitute for concurrence_error object in the case of -fno-exceptions. ++ inline void ++ __throw_concurrence_lock_error() ++ { ++#if __EXCEPTIONS ++ throw __concurrence_lock_error(); ++#else ++ __builtin_abort(); ++#endif ++ } ++ ++ inline void ++ __throw_concurrence_unlock_error() ++ { ++#if __EXCEPTIONS ++ throw __concurrence_unlock_error(); ++#else ++ __builtin_abort(); ++#endif ++ } ++ ++#ifdef __GTHREAD_HAS_COND ++ inline void ++ __throw_concurrence_broadcast_error() ++ { ++#if __EXCEPTIONS ++ throw __concurrence_broadcast_error(); ++#else ++ __builtin_abort(); ++#endif ++ } ++ ++ inline void ++ __throw_concurrence_wait_error() ++ { ++#if __EXCEPTIONS ++ throw __concurrence_wait_error(); ++#else ++ __builtin_abort(); ++#endif ++ } ++#endif ++ ++ class __mutex ++ { ++ private: ++ __gthread_mutex_t _M_mutex; ++ ++ __mutex(const __mutex&); ++ __mutex& operator=(const __mutex&); ++ ++ public: ++ __mutex() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++#if defined __GTHREAD_MUTEX_INIT ++ __gthread_mutex_t __tmp = __GTHREAD_MUTEX_INIT; ++ _M_mutex = __tmp; ++#else ++ __GTHREAD_MUTEX_INIT_FUNCTION(&_M_mutex); ++#endif ++ } ++#endif ++ } ++ ++ void lock() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++ if (__gthread_mutex_lock(&_M_mutex) != 0) ++ __throw_concurrence_lock_error(); ++ } ++#endif ++ } ++ ++ void unlock() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++ if (__gthread_mutex_unlock(&_M_mutex) != 0) ++ __throw_concurrence_unlock_error(); ++ } ++#endif ++ } ++ ++ __gthread_mutex_t* gthread_mutex(void) ++ { return &_M_mutex; } ++ }; ++ ++ class __recursive_mutex ++ { ++ private: ++ __gthread_recursive_mutex_t _M_mutex; ++ ++ __recursive_mutex(const __recursive_mutex&); ++ __recursive_mutex& operator=(const __recursive_mutex&); ++ ++ public: ++ __recursive_mutex() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++#if defined __GTHREAD_RECURSIVE_MUTEX_INIT ++ __gthread_recursive_mutex_t __tmp = __GTHREAD_RECURSIVE_MUTEX_INIT; ++ _M_mutex = __tmp; ++#else ++ __GTHREAD_RECURSIVE_MUTEX_INIT_FUNCTION(&_M_mutex); ++#endif ++ } ++#endif ++ } ++ ++ void lock() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++ if (__gthread_recursive_mutex_lock(&_M_mutex) != 0) ++ __throw_concurrence_lock_error(); ++ } ++#endif ++ } ++ ++ void unlock() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++ if (__gthread_recursive_mutex_unlock(&_M_mutex) != 0) ++ __throw_concurrence_unlock_error(); ++ } ++#endif ++ } ++ ++ __gthread_recursive_mutex_t* gthread_recursive_mutex(void) ++ { return &_M_mutex; } ++ }; ++ ++ /// Scoped lock idiom. ++ // Acquire the mutex here with a constructor call, then release with ++ // the destructor call in accordance with RAII style. ++ class __scoped_lock ++ { ++ public: ++ typedef __mutex __mutex_type; ++ ++ private: ++ __mutex_type& _M_device; ++ ++ __scoped_lock(const __scoped_lock&); ++ __scoped_lock& operator=(const __scoped_lock&); ++ ++ public: ++ explicit __scoped_lock(__mutex_type& __name) : _M_device(__name) ++ { _M_device.lock(); } ++ ++ ~__scoped_lock() throw() ++ { _M_device.unlock(); } ++ }; ++ ++#ifdef __GTHREAD_HAS_COND ++ class __cond ++ { ++ private: ++ __gthread_cond_t _M_cond; ++ ++ __cond(const __cond&); ++ __cond& operator=(const __cond&); ++ ++ public: ++ __cond() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++#if defined __GTHREAD_COND_INIT ++ __gthread_cond_t __tmp = __GTHREAD_COND_INIT; ++ _M_cond = __tmp; ++#else ++ __GTHREAD_COND_INIT_FUNCTION(&_M_cond); ++#endif ++ } ++#endif ++ } ++ ++ void broadcast() ++ { ++#if __GTHREADS ++ if (__gthread_active_p()) ++ { ++ if (__gthread_cond_broadcast(&_M_cond) != 0) ++ __throw_concurrence_broadcast_error(); ++ } ++#endif ++ } ++ ++ void wait(__mutex *mutex) ++ { ++#if __GTHREADS ++ { ++ if (__gthread_cond_wait(&_M_cond, mutex->gthread_mutex()) != 0) ++ __throw_concurrence_wait_error(); ++ } ++#endif ++ } ++ ++ void wait_recursive(__recursive_mutex *mutex) ++ { ++#if __GTHREADS ++ { ++ if (__gthread_cond_wait_recursive(&_M_cond, ++ mutex->gthread_recursive_mutex()) ++ != 0) ++ __throw_concurrence_wait_error(); ++ } ++#endif ++ } ++ }; ++#endif ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/type_traits.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/type_traits.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/type_traits.h (revision 11967) +@@ -0,0 +1,204 @@ ++// -*- C++ -*- ++ ++// Copyright (C) 2005, 2006, 2007, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the terms ++// of the GNU General Public License as published by the Free Software ++// Foundation; either version 3, or (at your option) any later ++// version. ++ ++// This library is distributed in the hope that it will be useful, but ++// WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++// General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/type_traits.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _EXT_TYPE_TRAITS ++#define _EXT_TYPE_TRAITS 1 ++ ++#pragma GCC system_header ++ ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ // Define a nested type if some predicate holds. ++ template ++ struct __enable_if ++ { }; ++ ++ template ++ struct __enable_if ++ { typedef _Tp __type; }; ++ ++ ++ // Conditional expression for types. If true, first, if false, second. ++ template ++ struct __conditional_type ++ { typedef _Iftrue __type; }; ++ ++ template ++ struct __conditional_type ++ { typedef _Iffalse __type; }; ++ ++ ++ // Given an integral builtin type, return the corresponding unsigned type. ++ template ++ struct __add_unsigned ++ { ++ private: ++ typedef __enable_if::__value, _Tp> __if_type; ++ ++ public: ++ typedef typename __if_type::__type __type; ++ }; ++ ++ template<> ++ struct __add_unsigned ++ { typedef unsigned char __type; }; ++ ++ template<> ++ struct __add_unsigned ++ { typedef unsigned char __type; }; ++ ++ template<> ++ struct __add_unsigned ++ { typedef unsigned short __type; }; ++ ++ template<> ++ struct __add_unsigned ++ { typedef unsigned int __type; }; ++ ++ template<> ++ struct __add_unsigned ++ { typedef unsigned long __type; }; ++ ++ template<> ++ struct __add_unsigned ++ { typedef unsigned long long __type; }; ++ ++ // Declare but don't define. ++ template<> ++ struct __add_unsigned; ++ ++ template<> ++ struct __add_unsigned; ++ ++ ++ // Given an integral builtin type, return the corresponding signed type. ++ template ++ struct __remove_unsigned ++ { ++ private: ++ typedef __enable_if::__value, _Tp> __if_type; ++ ++ public: ++ typedef typename __if_type::__type __type; ++ }; ++ ++ template<> ++ struct __remove_unsigned ++ { typedef signed char __type; }; ++ ++ template<> ++ struct __remove_unsigned ++ { typedef signed char __type; }; ++ ++ template<> ++ struct __remove_unsigned ++ { typedef short __type; }; ++ ++ template<> ++ struct __remove_unsigned ++ { typedef int __type; }; ++ ++ template<> ++ struct __remove_unsigned ++ { typedef long __type; }; ++ ++ template<> ++ struct __remove_unsigned ++ { typedef long long __type; }; ++ ++ // Declare but don't define. ++ template<> ++ struct __remove_unsigned; ++ ++ template<> ++ struct __remove_unsigned; ++ ++ ++ // For use in string and vstring. ++ template ++ inline bool ++ __is_null_pointer(_Type* __ptr) ++ { return __ptr == 0; } ++ ++ template ++ inline bool ++ __is_null_pointer(_Type) ++ { return false; } ++ ++ ++ // For complex and cmath ++ template::__value> ++ struct __promote ++ { typedef double __type; }; ++ ++ template ++ struct __promote<_Tp, false> ++ { typedef _Tp __type; }; ++ ++ template ++ struct __promote_2 ++ { ++ private: ++ typedef typename __promote<_Tp>::__type __type1; ++ typedef typename __promote<_Up>::__type __type2; ++ ++ public: ++ typedef __typeof__(__type1() + __type2()) __type; ++ }; ++ ++ template ++ struct __promote_3 ++ { ++ private: ++ typedef typename __promote<_Tp>::__type __type1; ++ typedef typename __promote<_Up>::__type __type2; ++ typedef typename __promote<_Vp>::__type __type3; ++ ++ public: ++ typedef __typeof__(__type1() + __type2() + __type3()) __type; ++ }; ++ ++ template ++ struct __promote_4 ++ { ++ private: ++ typedef typename __promote<_Tp>::__type __type1; ++ typedef typename __promote<_Up>::__type __type2; ++ typedef typename __promote<_Vp>::__type __type3; ++ typedef typename __promote<_Wp>::__type __type4; ++ ++ public: ++ typedef __typeof__(__type1() + __type2() + __type3() + __type4()) __type; ++ }; ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/malloc_allocator.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/malloc_allocator.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/malloc_allocator.h (revision 11967) +@@ -0,0 +1,134 @@ ++// Allocator that wraps "C" malloc -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/malloc_allocator.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _MALLOC_ALLOCATOR_H ++#define _MALLOC_ALLOCATOR_H 1 ++ ++#include ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::size_t; ++ using std::ptrdiff_t; ++ ++ /** ++ * @brief An allocator that uses malloc. ++ * @ingroup allocators ++ * ++ * This is precisely the allocator defined in the C++ Standard. ++ * - all allocation calls malloc ++ * - all deallocation calls free ++ */ ++ template ++ class malloc_allocator ++ { ++ public: ++ typedef size_t size_type; ++ typedef ptrdiff_t difference_type; ++ typedef _Tp* pointer; ++ typedef const _Tp* const_pointer; ++ typedef _Tp& reference; ++ typedef const _Tp& const_reference; ++ typedef _Tp value_type; ++ ++ template ++ struct rebind ++ { typedef malloc_allocator<_Tp1> other; }; ++ ++ malloc_allocator() throw() { } ++ ++ malloc_allocator(const malloc_allocator&) throw() { } ++ ++ template ++ malloc_allocator(const malloc_allocator<_Tp1>&) throw() { } ++ ++ ~malloc_allocator() throw() { } ++ ++ pointer ++ address(reference __x) const { return &__x; } ++ ++ const_pointer ++ address(const_reference __x) const { return &__x; } ++ ++ // NB: __n is permitted to be 0. The C++ standard says nothing ++ // about what the return value is when __n == 0. ++ pointer ++ allocate(size_type __n, const void* = 0) ++ { ++ if (__builtin_expect(__n > this->max_size(), false)) ++ std::__throw_bad_alloc(); ++ ++ pointer __ret = static_cast<_Tp*>(std::malloc(__n * sizeof(_Tp))); ++ if (!__ret) ++ std::__throw_bad_alloc(); ++ return __ret; ++ } ++ ++ // __p is not permitted to be a null pointer. ++ void ++ deallocate(pointer __p, size_type) ++ { std::free(static_cast(__p)); } ++ ++ size_type ++ max_size() const throw() ++ { return size_t(-1) / sizeof(_Tp); } ++ ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 402. wrong new expression in [some_] allocator::construct ++ void ++ construct(pointer __p, const _Tp& __val) ++ { ::new((void *)__p) value_type(__val); } ++ ++#ifdef __GXX_EXPERIMENTAL_CXX0X__ ++ template ++ void ++ construct(pointer __p, _Args&&... __args) ++ { ::new((void *)__p) _Tp(std::forward<_Args>(__args)...); } ++#endif ++ ++ void ++ destroy(pointer __p) { __p->~_Tp(); } ++ }; ++ ++ template ++ inline bool ++ operator==(const malloc_allocator<_Tp>&, const malloc_allocator<_Tp>&) ++ { return true; } ++ ++ template ++ inline bool ++ operator!=(const malloc_allocator<_Tp>&, const malloc_allocator<_Tp>&) ++ { return false; } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/hash_set +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/hash_set (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/hash_set (revision 11967) +@@ -0,0 +1,561 @@ ++// Hashing set implementation -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2004, 2005, 2006, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/* ++ * Copyright (c) 1996 ++ * Silicon Graphics Computer Systems, Inc. ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Silicon Graphics makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ * ++ * ++ * Copyright (c) 1994 ++ * Hewlett-Packard Company ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Hewlett-Packard Company makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ * ++ */ ++ ++/** @file backward/hash_set ++ * This file is a GNU extension to the Standard C++ Library (possibly ++ * containing extensions from the HP/SGI STL subset). ++ */ ++ ++#ifndef _HASH_SET ++#define _HASH_SET 1 ++ ++#ifndef _GLIBCXX_PERMIT_BACKWARD_HASH ++#include "backward_warning.h" ++#endif ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::equal_to; ++ using std::allocator; ++ using std::pair; ++ using std::_Identity; ++ ++ /** ++ * This is an SGI extension. ++ * @ingroup SGIextensions ++ * @doctodo ++ */ ++ template, ++ class _EqualKey = equal_to<_Value>, ++ class _Alloc = allocator<_Value> > ++ class hash_set ++ { ++ // concept requirements ++ __glibcxx_class_requires(_Value, _SGIAssignableConcept) ++ __glibcxx_class_requires3(_HashFcn, size_t, _Value, _UnaryFunctionConcept) ++ __glibcxx_class_requires3(_EqualKey, _Value, _Value, _BinaryPredicateConcept) ++ ++ private: ++ typedef hashtable<_Value, _Value, _HashFcn, _Identity<_Value>, ++ _EqualKey, _Alloc> _Ht; ++ _Ht _M_ht; ++ ++ public: ++ typedef typename _Ht::key_type key_type; ++ typedef typename _Ht::value_type value_type; ++ typedef typename _Ht::hasher hasher; ++ typedef typename _Ht::key_equal key_equal; ++ ++ typedef typename _Ht::size_type size_type; ++ typedef typename _Ht::difference_type difference_type; ++ typedef typename _Alloc::pointer pointer; ++ typedef typename _Alloc::const_pointer const_pointer; ++ typedef typename _Alloc::reference reference; ++ typedef typename _Alloc::const_reference const_reference; ++ ++ typedef typename _Ht::const_iterator iterator; ++ typedef typename _Ht::const_iterator const_iterator; ++ ++ typedef typename _Ht::allocator_type allocator_type; ++ ++ hasher ++ hash_funct() const ++ { return _M_ht.hash_funct(); } ++ ++ key_equal ++ key_eq() const ++ { return _M_ht.key_eq(); } ++ ++ allocator_type ++ get_allocator() const ++ { return _M_ht.get_allocator(); } ++ ++ hash_set() ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) {} ++ ++ explicit ++ hash_set(size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) {} ++ ++ hash_set(size_type __n, const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) {} ++ ++ hash_set(size_type __n, const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) {} ++ ++ template ++ hash_set(_InputIterator __f, _InputIterator __l) ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ template ++ hash_set(_InputIterator __f, _InputIterator __l, size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ template ++ hash_set(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ template ++ hash_set(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ size_type ++ size() const ++ { return _M_ht.size(); } ++ ++ size_type ++ max_size() const ++ { return _M_ht.max_size(); } ++ ++ bool ++ empty() const ++ { return _M_ht.empty(); } ++ ++ void ++ swap(hash_set& __hs) ++ { _M_ht.swap(__hs._M_ht); } ++ ++ template ++ friend bool ++ operator==(const hash_set<_Val, _HF, _EqK, _Al>&, ++ const hash_set<_Val, _HF, _EqK, _Al>&); ++ ++ iterator ++ begin() const ++ { return _M_ht.begin(); } ++ ++ iterator ++ end() const ++ { return _M_ht.end(); } ++ ++ pair ++ insert(const value_type& __obj) ++ { ++ pair __p = _M_ht.insert_unique(__obj); ++ return pair(__p.first, __p.second); ++ } ++ ++ template ++ void ++ insert(_InputIterator __f, _InputIterator __l) ++ { _M_ht.insert_unique(__f, __l); } ++ ++ pair ++ insert_noresize(const value_type& __obj) ++ { ++ pair __p ++ = _M_ht.insert_unique_noresize(__obj); ++ return pair(__p.first, __p.second); ++ } ++ ++ iterator ++ find(const key_type& __key) const ++ { return _M_ht.find(__key); } ++ ++ size_type ++ count(const key_type& __key) const ++ { return _M_ht.count(__key); } ++ ++ pair ++ equal_range(const key_type& __key) const ++ { return _M_ht.equal_range(__key); } ++ ++ size_type ++ erase(const key_type& __key) ++ {return _M_ht.erase(__key); } ++ ++ void ++ erase(iterator __it) ++ { _M_ht.erase(__it); } ++ ++ void ++ erase(iterator __f, iterator __l) ++ { _M_ht.erase(__f, __l); } ++ ++ void ++ clear() ++ { _M_ht.clear(); } ++ ++ void ++ resize(size_type __hint) ++ { _M_ht.resize(__hint); } ++ ++ size_type ++ bucket_count() const ++ { return _M_ht.bucket_count(); } ++ ++ size_type ++ max_bucket_count() const ++ { return _M_ht.max_bucket_count(); } ++ ++ size_type ++ elems_in_bucket(size_type __n) const ++ { return _M_ht.elems_in_bucket(__n); } ++ }; ++ ++ template ++ inline bool ++ operator==(const hash_set<_Value, _HashFcn, _EqualKey, _Alloc>& __hs1, ++ const hash_set<_Value, _HashFcn, _EqualKey, _Alloc>& __hs2) ++ { return __hs1._M_ht == __hs2._M_ht; } ++ ++ template ++ inline bool ++ operator!=(const hash_set<_Value, _HashFcn, _EqualKey, _Alloc>& __hs1, ++ const hash_set<_Value, _HashFcn, _EqualKey, _Alloc>& __hs2) ++ { return !(__hs1 == __hs2); } ++ ++ template ++ inline void ++ swap(hash_set<_Val, _HashFcn, _EqualKey, _Alloc>& __hs1, ++ hash_set<_Val, _HashFcn, _EqualKey, _Alloc>& __hs2) ++ { __hs1.swap(__hs2); } ++ ++ ++ /** ++ * This is an SGI extension. ++ * @ingroup SGIextensions ++ * @doctodo ++ */ ++ template, ++ class _EqualKey = equal_to<_Value>, ++ class _Alloc = allocator<_Value> > ++ class hash_multiset ++ { ++ // concept requirements ++ __glibcxx_class_requires(_Value, _SGIAssignableConcept) ++ __glibcxx_class_requires3(_HashFcn, size_t, _Value, _UnaryFunctionConcept) ++ __glibcxx_class_requires3(_EqualKey, _Value, _Value, _BinaryPredicateConcept) ++ ++ private: ++ typedef hashtable<_Value, _Value, _HashFcn, _Identity<_Value>, ++ _EqualKey, _Alloc> _Ht; ++ _Ht _M_ht; ++ ++ public: ++ typedef typename _Ht::key_type key_type; ++ typedef typename _Ht::value_type value_type; ++ typedef typename _Ht::hasher hasher; ++ typedef typename _Ht::key_equal key_equal; ++ ++ typedef typename _Ht::size_type size_type; ++ typedef typename _Ht::difference_type difference_type; ++ typedef typename _Alloc::pointer pointer; ++ typedef typename _Alloc::const_pointer const_pointer; ++ typedef typename _Alloc::reference reference; ++ typedef typename _Alloc::const_reference const_reference; ++ ++ typedef typename _Ht::const_iterator iterator; ++ typedef typename _Ht::const_iterator const_iterator; ++ ++ typedef typename _Ht::allocator_type allocator_type; ++ ++ hasher ++ hash_funct() const ++ { return _M_ht.hash_funct(); } ++ ++ key_equal ++ key_eq() const ++ { return _M_ht.key_eq(); } ++ ++ allocator_type ++ get_allocator() const ++ { return _M_ht.get_allocator(); } ++ ++ hash_multiset() ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) {} ++ ++ explicit ++ hash_multiset(size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) {} ++ ++ hash_multiset(size_type __n, const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) {} ++ ++ hash_multiset(size_type __n, const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) {} ++ ++ template ++ hash_multiset(_InputIterator __f, _InputIterator __l) ++ : _M_ht(100, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ template ++ hash_multiset(_InputIterator __f, _InputIterator __l, size_type __n) ++ : _M_ht(__n, hasher(), key_equal(), allocator_type()) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ template ++ hash_multiset(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf) ++ : _M_ht(__n, __hf, key_equal(), allocator_type()) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ template ++ hash_multiset(_InputIterator __f, _InputIterator __l, size_type __n, ++ const hasher& __hf, const key_equal& __eql, ++ const allocator_type& __a = allocator_type()) ++ : _M_ht(__n, __hf, __eql, __a) ++ { _M_ht.insert_equal(__f, __l); } ++ ++ size_type ++ size() const ++ { return _M_ht.size(); } ++ ++ size_type ++ max_size() const ++ { return _M_ht.max_size(); } ++ ++ bool ++ empty() const ++ { return _M_ht.empty(); } ++ ++ void ++ swap(hash_multiset& hs) ++ { _M_ht.swap(hs._M_ht); } ++ ++ template ++ friend bool ++ operator==(const hash_multiset<_Val, _HF, _EqK, _Al>&, ++ const hash_multiset<_Val, _HF, _EqK, _Al>&); ++ ++ iterator ++ begin() const ++ { return _M_ht.begin(); } ++ ++ iterator ++ end() const ++ { return _M_ht.end(); } ++ ++ iterator ++ insert(const value_type& __obj) ++ { return _M_ht.insert_equal(__obj); } ++ ++ template ++ void ++ insert(_InputIterator __f, _InputIterator __l) ++ { _M_ht.insert_equal(__f,__l); } ++ ++ iterator ++ insert_noresize(const value_type& __obj) ++ { return _M_ht.insert_equal_noresize(__obj); } ++ ++ iterator ++ find(const key_type& __key) const ++ { return _M_ht.find(__key); } ++ ++ size_type ++ count(const key_type& __key) const ++ { return _M_ht.count(__key); } ++ ++ pair ++ equal_range(const key_type& __key) const ++ { return _M_ht.equal_range(__key); } ++ ++ size_type ++ erase(const key_type& __key) ++ { return _M_ht.erase(__key); } ++ ++ void ++ erase(iterator __it) ++ { _M_ht.erase(__it); } ++ ++ void ++ erase(iterator __f, iterator __l) ++ { _M_ht.erase(__f, __l); } ++ ++ void ++ clear() ++ { _M_ht.clear(); } ++ ++ void ++ resize(size_type __hint) ++ { _M_ht.resize(__hint); } ++ ++ size_type ++ bucket_count() const ++ { return _M_ht.bucket_count(); } ++ ++ size_type ++ max_bucket_count() const ++ { return _M_ht.max_bucket_count(); } ++ ++ size_type ++ elems_in_bucket(size_type __n) const ++ { return _M_ht.elems_in_bucket(__n); } ++ }; ++ ++ template ++ inline bool ++ operator==(const hash_multiset<_Val, _HashFcn, _EqualKey, _Alloc>& __hs1, ++ const hash_multiset<_Val, _HashFcn, _EqualKey, _Alloc>& __hs2) ++ { return __hs1._M_ht == __hs2._M_ht; } ++ ++ template ++ inline bool ++ operator!=(const hash_multiset<_Val, _HashFcn, _EqualKey, _Alloc>& __hs1, ++ const hash_multiset<_Val, _HashFcn, _EqualKey, _Alloc>& __hs2) ++ { return !(__hs1 == __hs2); } ++ ++ template ++ inline void ++ swap(hash_multiset<_Val, _HashFcn, _EqualKey, _Alloc>& __hs1, ++ hash_multiset<_Val, _HashFcn, _EqualKey, _Alloc>& __hs2) ++ { __hs1.swap(__hs2); } ++ ++_GLIBCXX_END_NAMESPACE ++ ++_GLIBCXX_BEGIN_NAMESPACE(std) ++ ++ // Specialization of insert_iterator so that it will work for hash_set ++ // and hash_multiset. ++ template ++ class insert_iterator<__gnu_cxx::hash_set<_Value, _HashFcn, ++ _EqualKey, _Alloc> > ++ { ++ protected: ++ typedef __gnu_cxx::hash_set<_Value, _HashFcn, _EqualKey, _Alloc> ++ _Container; ++ _Container* container; ++ ++ public: ++ typedef _Container container_type; ++ typedef output_iterator_tag iterator_category; ++ typedef void value_type; ++ typedef void difference_type; ++ typedef void pointer; ++ typedef void reference; ++ ++ insert_iterator(_Container& __x) ++ : container(&__x) {} ++ ++ insert_iterator(_Container& __x, typename _Container::iterator) ++ : container(&__x) {} ++ ++ insert_iterator<_Container>& ++ operator=(const typename _Container::value_type& __value) ++ { ++ container->insert(__value); ++ return *this; ++ } ++ ++ insert_iterator<_Container>& ++ operator*() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++(int) ++ { return *this; } ++ }; ++ ++ template ++ class insert_iterator<__gnu_cxx::hash_multiset<_Value, _HashFcn, ++ _EqualKey, _Alloc> > ++ { ++ protected: ++ typedef __gnu_cxx::hash_multiset<_Value, _HashFcn, _EqualKey, _Alloc> ++ _Container; ++ _Container* container; ++ typename _Container::iterator iter; ++ ++ public: ++ typedef _Container container_type; ++ typedef output_iterator_tag iterator_category; ++ typedef void value_type; ++ typedef void difference_type; ++ typedef void pointer; ++ typedef void reference; ++ ++ insert_iterator(_Container& __x) ++ : container(&__x) {} ++ ++ insert_iterator(_Container& __x, typename _Container::iterator) ++ : container(&__x) {} ++ ++ insert_iterator<_Container>& ++ operator=(const typename _Container::value_type& __value) ++ { ++ container->insert(__value); ++ return *this; ++ } ++ ++ insert_iterator<_Container>& ++ operator*() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++() ++ { return *this; } ++ ++ insert_iterator<_Container>& ++ operator++(int) { return *this; } ++ }; ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/codecvt_specializations.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/codecvt_specializations.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/codecvt_specializations.h (revision 11967) +@@ -0,0 +1,507 @@ ++// Locale support (codecvt) -*- C++ -*- ++ ++// Copyright (C) 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++// ++// ISO C++ 14882: 22.2.1.5 Template class codecvt ++// ++ ++// Written by Benjamin Kosnik ++ ++/** @file ext/codecvt_specializations.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _EXT_CODECVT_SPECIALIZATIONS_H ++#define _EXT_CODECVT_SPECIALIZATIONS_H 1 ++ ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ /// Extension to use iconv for dealing with character encodings. ++ // This includes conversions and comparisons between various character ++ // sets. This object encapsulates data that may need to be shared between ++ // char_traits, codecvt and ctype. ++ class encoding_state ++ { ++ public: ++ // Types: ++ // NB: A conversion descriptor subsumes and enhances the ++ // functionality of a simple state type such as mbstate_t. ++ typedef iconv_t descriptor_type; ++ ++ protected: ++ // Name of internal character set encoding. ++ std::string _M_int_enc; ++ ++ // Name of external character set encoding. ++ std::string _M_ext_enc; ++ ++ // Conversion descriptor between external encoding to internal encoding. ++ descriptor_type _M_in_desc; ++ ++ // Conversion descriptor between internal encoding to external encoding. ++ descriptor_type _M_out_desc; ++ ++ // The byte-order marker for the external encoding, if necessary. ++ int _M_ext_bom; ++ ++ // The byte-order marker for the internal encoding, if necessary. ++ int _M_int_bom; ++ ++ // Number of external bytes needed to construct one complete ++ // character in the internal encoding. ++ // NB: -1 indicates variable, or stateful, encodings. ++ int _M_bytes; ++ ++ public: ++ explicit ++ encoding_state() ++ : _M_in_desc(0), _M_out_desc(0), _M_ext_bom(0), _M_int_bom(0), _M_bytes(0) ++ { } ++ ++ explicit ++ encoding_state(const char* __int, const char* __ext, ++ int __ibom = 0, int __ebom = 0, int __bytes = 1) ++ : _M_int_enc(__int), _M_ext_enc(__ext), _M_in_desc(0), _M_out_desc(0), ++ _M_ext_bom(__ebom), _M_int_bom(__ibom), _M_bytes(__bytes) ++ { init(); } ++ ++ // 21.1.2 traits typedefs ++ // p4 ++ // typedef STATE_T state_type ++ // requires: state_type shall meet the requirements of ++ // CopyConstructible types (20.1.3) ++ // NB: This does not preserve the actual state of the conversion ++ // descriptor member, but it does duplicate the encoding ++ // information. ++ encoding_state(const encoding_state& __obj) : _M_in_desc(0), _M_out_desc(0) ++ { construct(__obj); } ++ ++ // Need assignment operator as well. ++ encoding_state& ++ operator=(const encoding_state& __obj) ++ { ++ construct(__obj); ++ return *this; ++ } ++ ++ ~encoding_state() ++ { destroy(); } ++ ++ bool ++ good() const throw() ++ { ++ const descriptor_type __err = (iconv_t)(-1); ++ bool __test = _M_in_desc && _M_in_desc != __err; ++ __test &= _M_out_desc && _M_out_desc != __err; ++ return __test; ++ } ++ ++ int ++ character_ratio() const ++ { return _M_bytes; } ++ ++ const std::string ++ internal_encoding() const ++ { return _M_int_enc; } ++ ++ int ++ internal_bom() const ++ { return _M_int_bom; } ++ ++ const std::string ++ external_encoding() const ++ { return _M_ext_enc; } ++ ++ int ++ external_bom() const ++ { return _M_ext_bom; } ++ ++ const descriptor_type& ++ in_descriptor() const ++ { return _M_in_desc; } ++ ++ const descriptor_type& ++ out_descriptor() const ++ { return _M_out_desc; } ++ ++ protected: ++ void ++ init() ++ { ++ const descriptor_type __err = (iconv_t)(-1); ++ const bool __have_encodings = _M_int_enc.size() && _M_ext_enc.size(); ++ if (!_M_in_desc && __have_encodings) ++ { ++ _M_in_desc = iconv_open(_M_int_enc.c_str(), _M_ext_enc.c_str()); ++ if (_M_in_desc == __err) ++ std::__throw_runtime_error(__N("encoding_state::_M_init " ++ "creating iconv input descriptor failed")); ++ } ++ if (!_M_out_desc && __have_encodings) ++ { ++ _M_out_desc = iconv_open(_M_ext_enc.c_str(), _M_int_enc.c_str()); ++ if (_M_out_desc == __err) ++ std::__throw_runtime_error(__N("encoding_state::_M_init " ++ "creating iconv output descriptor failed")); ++ } ++ } ++ ++ void ++ construct(const encoding_state& __obj) ++ { ++ destroy(); ++ _M_int_enc = __obj._M_int_enc; ++ _M_ext_enc = __obj._M_ext_enc; ++ _M_ext_bom = __obj._M_ext_bom; ++ _M_int_bom = __obj._M_int_bom; ++ _M_bytes = __obj._M_bytes; ++ init(); ++ } ++ ++ void ++ destroy() throw() ++ { ++ const descriptor_type __err = (iconv_t)(-1); ++ if (_M_in_desc && _M_in_desc != __err) ++ { ++ iconv_close(_M_in_desc); ++ _M_in_desc = 0; ++ } ++ if (_M_out_desc && _M_out_desc != __err) ++ { ++ iconv_close(_M_out_desc); ++ _M_out_desc = 0; ++ } ++ } ++ }; ++ ++ /// encoding_char_traits ++ // Custom traits type with encoding_state for the state type, and the ++ // associated fpos for the position type, all other ++ // bits equivalent to the required char_traits instantiations. ++ template ++ struct encoding_char_traits : public std::char_traits<_CharT> ++ { ++ typedef encoding_state state_type; ++ typedef typename std::fpos pos_type; ++ }; ++ ++_GLIBCXX_END_NAMESPACE ++ ++ ++_GLIBCXX_BEGIN_NAMESPACE(std) ++ ++ using __gnu_cxx::encoding_state; ++ ++ /// codecvt specialization. ++ // This partial specialization takes advantage of iconv to provide ++ // code conversions between a large number of character encodings. ++ template ++ class codecvt<_InternT, _ExternT, encoding_state> ++ : public __codecvt_abstract_base<_InternT, _ExternT, encoding_state> ++ { ++ public: ++ // Types: ++ typedef codecvt_base::result result; ++ typedef _InternT intern_type; ++ typedef _ExternT extern_type; ++ typedef __gnu_cxx::encoding_state state_type; ++ typedef state_type::descriptor_type descriptor_type; ++ ++ // Data Members: ++ static locale::id id; ++ ++ explicit ++ codecvt(size_t __refs = 0) ++ : __codecvt_abstract_base(__refs) ++ { } ++ ++ explicit ++ codecvt(state_type& __enc, size_t __refs = 0) ++ : __codecvt_abstract_base(__refs) ++ { } ++ ++ protected: ++ virtual ++ ~codecvt() { } ++ ++ virtual result ++ do_out(state_type& __state, const intern_type* __from, ++ const intern_type* __from_end, const intern_type*& __from_next, ++ extern_type* __to, extern_type* __to_end, ++ extern_type*& __to_next) const; ++ ++ virtual result ++ do_unshift(state_type& __state, extern_type* __to, ++ extern_type* __to_end, extern_type*& __to_next) const; ++ ++ virtual result ++ do_in(state_type& __state, const extern_type* __from, ++ const extern_type* __from_end, const extern_type*& __from_next, ++ intern_type* __to, intern_type* __to_end, ++ intern_type*& __to_next) const; ++ ++ virtual int ++ do_encoding() const throw(); ++ ++ virtual bool ++ do_always_noconv() const throw(); ++ ++ virtual int ++ do_length(state_type&, const extern_type* __from, ++ const extern_type* __end, size_t __max) const; ++ ++ virtual int ++ do_max_length() const throw(); ++ }; ++ ++ template ++ locale::id ++ codecvt<_InternT, _ExternT, encoding_state>::id; ++ ++ // This adaptor works around the signature problems of the second ++ // argument to iconv(): SUSv2 and others use 'const char**', but glibc 2.2 ++ // uses 'char**', which matches the POSIX 1003.1-2001 standard. ++ // Using this adaptor, g++ will do the work for us. ++ template ++ inline size_t ++ __iconv_adaptor(size_t(*__func)(iconv_t, _Tp, size_t*, char**, size_t*), ++ iconv_t __cd, char** __inbuf, size_t* __inbytes, ++ char** __outbuf, size_t* __outbytes) ++ { return __func(__cd, (_Tp)__inbuf, __inbytes, __outbuf, __outbytes); } ++ ++ template ++ codecvt_base::result ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_out(state_type& __state, const intern_type* __from, ++ const intern_type* __from_end, const intern_type*& __from_next, ++ extern_type* __to, extern_type* __to_end, ++ extern_type*& __to_next) const ++ { ++ result __ret = codecvt_base::error; ++ if (__state.good()) ++ { ++ const descriptor_type& __desc = __state.out_descriptor(); ++ const size_t __fmultiple = sizeof(intern_type); ++ size_t __fbytes = __fmultiple * (__from_end - __from); ++ const size_t __tmultiple = sizeof(extern_type); ++ size_t __tbytes = __tmultiple * (__to_end - __to); ++ ++ // Argument list for iconv specifies a byte sequence. Thus, ++ // all to/from arrays must be brutally casted to char*. ++ char* __cto = reinterpret_cast(__to); ++ char* __cfrom; ++ size_t __conv; ++ ++ // Some encodings need a byte order marker as the first item ++ // in the byte stream, to designate endian-ness. The default ++ // value for the byte order marker is NULL, so if this is ++ // the case, it's not necessary and we can just go on our ++ // merry way. ++ int __int_bom = __state.internal_bom(); ++ if (__int_bom) ++ { ++ size_t __size = __from_end - __from; ++ intern_type* __cfixed = static_cast ++ (__builtin_alloca(sizeof(intern_type) * (__size + 1))); ++ __cfixed[0] = static_cast(__int_bom); ++ char_traits::copy(__cfixed + 1, __from, __size); ++ __cfrom = reinterpret_cast(__cfixed); ++ __conv = __iconv_adaptor(iconv, __desc, &__cfrom, ++ &__fbytes, &__cto, &__tbytes); ++ } ++ else ++ { ++ intern_type* __cfixed = const_cast(__from); ++ __cfrom = reinterpret_cast(__cfixed); ++ __conv = __iconv_adaptor(iconv, __desc, &__cfrom, &__fbytes, ++ &__cto, &__tbytes); ++ } ++ ++ if (__conv != size_t(-1)) ++ { ++ __from_next = reinterpret_cast(__cfrom); ++ __to_next = reinterpret_cast(__cto); ++ __ret = codecvt_base::ok; ++ } ++ else ++ { ++ if (__fbytes < __fmultiple * (__from_end - __from)) ++ { ++ __from_next = reinterpret_cast(__cfrom); ++ __to_next = reinterpret_cast(__cto); ++ __ret = codecvt_base::partial; ++ } ++ else ++ __ret = codecvt_base::error; ++ } ++ } ++ return __ret; ++ } ++ ++ template ++ codecvt_base::result ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_unshift(state_type& __state, extern_type* __to, ++ extern_type* __to_end, extern_type*& __to_next) const ++ { ++ result __ret = codecvt_base::error; ++ if (__state.good()) ++ { ++ const descriptor_type& __desc = __state.in_descriptor(); ++ const size_t __tmultiple = sizeof(intern_type); ++ size_t __tlen = __tmultiple * (__to_end - __to); ++ ++ // Argument list for iconv specifies a byte sequence. Thus, ++ // all to/from arrays must be brutally casted to char*. ++ char* __cto = reinterpret_cast(__to); ++ size_t __conv = __iconv_adaptor(iconv,__desc, NULL, NULL, ++ &__cto, &__tlen); ++ ++ if (__conv != size_t(-1)) ++ { ++ __to_next = reinterpret_cast(__cto); ++ if (__tlen == __tmultiple * (__to_end - __to)) ++ __ret = codecvt_base::noconv; ++ else if (__tlen == 0) ++ __ret = codecvt_base::ok; ++ else ++ __ret = codecvt_base::partial; ++ } ++ else ++ __ret = codecvt_base::error; ++ } ++ return __ret; ++ } ++ ++ template ++ codecvt_base::result ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_in(state_type& __state, const extern_type* __from, ++ const extern_type* __from_end, const extern_type*& __from_next, ++ intern_type* __to, intern_type* __to_end, ++ intern_type*& __to_next) const ++ { ++ result __ret = codecvt_base::error; ++ if (__state.good()) ++ { ++ const descriptor_type& __desc = __state.in_descriptor(); ++ const size_t __fmultiple = sizeof(extern_type); ++ size_t __flen = __fmultiple * (__from_end - __from); ++ const size_t __tmultiple = sizeof(intern_type); ++ size_t __tlen = __tmultiple * (__to_end - __to); ++ ++ // Argument list for iconv specifies a byte sequence. Thus, ++ // all to/from arrays must be brutally casted to char*. ++ char* __cto = reinterpret_cast(__to); ++ char* __cfrom; ++ size_t __conv; ++ ++ // Some encodings need a byte order marker as the first item ++ // in the byte stream, to designate endian-ness. The default ++ // value for the byte order marker is NULL, so if this is ++ // the case, it's not necessary and we can just go on our ++ // merry way. ++ int __ext_bom = __state.external_bom(); ++ if (__ext_bom) ++ { ++ size_t __size = __from_end - __from; ++ extern_type* __cfixed = static_cast ++ (__builtin_alloca(sizeof(extern_type) * (__size + 1))); ++ __cfixed[0] = static_cast(__ext_bom); ++ char_traits::copy(__cfixed + 1, __from, __size); ++ __cfrom = reinterpret_cast(__cfixed); ++ __conv = __iconv_adaptor(iconv, __desc, &__cfrom, ++ &__flen, &__cto, &__tlen); ++ } ++ else ++ { ++ extern_type* __cfixed = const_cast(__from); ++ __cfrom = reinterpret_cast(__cfixed); ++ __conv = __iconv_adaptor(iconv, __desc, &__cfrom, ++ &__flen, &__cto, &__tlen); ++ } ++ ++ ++ if (__conv != size_t(-1)) ++ { ++ __from_next = reinterpret_cast(__cfrom); ++ __to_next = reinterpret_cast(__cto); ++ __ret = codecvt_base::ok; ++ } ++ else ++ { ++ if (__flen < static_cast(__from_end - __from)) ++ { ++ __from_next = reinterpret_cast(__cfrom); ++ __to_next = reinterpret_cast(__cto); ++ __ret = codecvt_base::partial; ++ } ++ else ++ __ret = codecvt_base::error; ++ } ++ } ++ return __ret; ++ } ++ ++ template ++ int ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_encoding() const throw() ++ { ++ int __ret = 0; ++ if (sizeof(_ExternT) <= sizeof(_InternT)) ++ __ret = sizeof(_InternT) / sizeof(_ExternT); ++ return __ret; ++ } ++ ++ template ++ bool ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_always_noconv() const throw() ++ { return false; } ++ ++ template ++ int ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_length(state_type&, const extern_type* __from, ++ const extern_type* __end, size_t __max) const ++ { return std::min(__max, static_cast(__end - __from)); } ++ ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 74. Garbled text for codecvt::do_max_length ++ template ++ int ++ codecvt<_InternT, _ExternT, encoding_state>:: ++ do_max_length() const throw() ++ { return 1; } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/stdio_sync_filebuf.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/stdio_sync_filebuf.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/stdio_sync_filebuf.h (revision 11967) +@@ -0,0 +1,279 @@ ++// Iostreams wrapper for stdio FILE* -*- C++ -*- ++ ++// Copyright (C) 2003, 2004, 2005, 2006, 2007, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/stdio_sync_filebuf.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _STDIO_SYNC_FILEBUF_H ++#define _STDIO_SYNC_FILEBUF_H 1 ++ ++#pragma GCC system_header ++ ++#include ++#include ++#include ++#include // For __c_file ++ ++#ifdef _GLIBCXX_USE_WCHAR_T ++#include ++#endif ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ /// class stdio_sync_filebuf. ++ template > ++ class stdio_sync_filebuf : public std::basic_streambuf<_CharT, _Traits> ++ { ++ public: ++ // Types: ++ typedef _CharT char_type; ++ typedef _Traits traits_type; ++ typedef typename traits_type::int_type int_type; ++ typedef typename traits_type::pos_type pos_type; ++ typedef typename traits_type::off_type off_type; ++ ++ private: ++ // Underlying stdio FILE ++ std::__c_file* const _M_file; ++ ++ // Last character gotten. This is used when pbackfail is ++ // called from basic_streambuf::sungetc() ++ int_type _M_unget_buf; ++ ++ public: ++ explicit ++ stdio_sync_filebuf(std::__c_file* __f) ++ : _M_file(__f), _M_unget_buf(traits_type::eof()) ++ { } ++ ++ /** ++ * @return The underlying FILE*. ++ * ++ * This function can be used to access the underlying "C" file pointer. ++ * Note that there is no way for the library to track what you do ++ * with the file, so be careful. ++ */ ++ std::__c_file* const ++ file() { return this->_M_file; } ++ ++ protected: ++ int_type ++ syncgetc(); ++ ++ int_type ++ syncungetc(int_type __c); ++ ++ int_type ++ syncputc(int_type __c); ++ ++ virtual int_type ++ underflow() ++ { ++ int_type __c = this->syncgetc(); ++ return this->syncungetc(__c); ++ } ++ ++ virtual int_type ++ uflow() ++ { ++ // Store the gotten character in case we need to unget it. ++ _M_unget_buf = this->syncgetc(); ++ return _M_unget_buf; ++ } ++ ++ virtual int_type ++ pbackfail(int_type __c = traits_type::eof()) ++ { ++ int_type __ret; ++ const int_type __eof = traits_type::eof(); ++ ++ // Check if the unget or putback was requested ++ if (traits_type::eq_int_type(__c, __eof)) // unget ++ { ++ if (!traits_type::eq_int_type(_M_unget_buf, __eof)) ++ __ret = this->syncungetc(_M_unget_buf); ++ else // buffer invalid, fail. ++ __ret = __eof; ++ } ++ else // putback ++ __ret = this->syncungetc(__c); ++ ++ // The buffered character is no longer valid, discard it. ++ _M_unget_buf = __eof; ++ return __ret; ++ } ++ ++ virtual std::streamsize ++ xsgetn(char_type* __s, std::streamsize __n); ++ ++ virtual int_type ++ overflow(int_type __c = traits_type::eof()) ++ { ++ int_type __ret; ++ if (traits_type::eq_int_type(__c, traits_type::eof())) ++ { ++ if (std::fflush(_M_file)) ++ __ret = traits_type::eof(); ++ else ++ __ret = traits_type::not_eof(__c); ++ } ++ else ++ __ret = this->syncputc(__c); ++ return __ret; ++ } ++ ++ virtual std::streamsize ++ xsputn(const char_type* __s, std::streamsize __n); ++ ++ virtual int ++ sync() ++ { return std::fflush(_M_file); } ++ ++ virtual std::streampos ++ seekoff(std::streamoff __off, std::ios_base::seekdir __dir, ++ std::ios_base::openmode = std::ios_base::in | std::ios_base::out) ++ { ++ std::streampos __ret(std::streamoff(-1)); ++ int __whence; ++ if (__dir == std::ios_base::beg) ++ __whence = SEEK_SET; ++ else if (__dir == std::ios_base::cur) ++ __whence = SEEK_CUR; ++ else ++ __whence = SEEK_END; ++#ifdef _GLIBCXX_USE_LFS ++ if (!fseeko64(_M_file, __off, __whence)) ++ __ret = std::streampos(ftello64(_M_file)); ++#else ++ if (!fseek(_M_file, __off, __whence)) ++ __ret = std::streampos(std::ftell(_M_file)); ++#endif ++ return __ret; ++ } ++ ++ virtual std::streampos ++ seekpos(std::streampos __pos, ++ std::ios_base::openmode __mode = ++ std::ios_base::in | std::ios_base::out) ++ { return seekoff(std::streamoff(__pos), std::ios_base::beg, __mode); } ++ }; ++ ++ template<> ++ inline stdio_sync_filebuf::int_type ++ stdio_sync_filebuf::syncgetc() ++ { return std::getc(_M_file); } ++ ++ template<> ++ inline stdio_sync_filebuf::int_type ++ stdio_sync_filebuf::syncungetc(int_type __c) ++ { return std::ungetc(__c, _M_file); } ++ ++ template<> ++ inline stdio_sync_filebuf::int_type ++ stdio_sync_filebuf::syncputc(int_type __c) ++ { return std::putc(__c, _M_file); } ++ ++ template<> ++ inline std::streamsize ++ stdio_sync_filebuf::xsgetn(char* __s, std::streamsize __n) ++ { ++ std::streamsize __ret = std::fread(__s, 1, __n, _M_file); ++ if (__ret > 0) ++ _M_unget_buf = traits_type::to_int_type(__s[__ret - 1]); ++ else ++ _M_unget_buf = traits_type::eof(); ++ return __ret; ++ } ++ ++ template<> ++ inline std::streamsize ++ stdio_sync_filebuf::xsputn(const char* __s, std::streamsize __n) ++ { return std::fwrite(__s, 1, __n, _M_file); } ++ ++#ifdef _GLIBCXX_USE_WCHAR_T ++ template<> ++ inline stdio_sync_filebuf::int_type ++ stdio_sync_filebuf::syncgetc() ++ { return std::getwc(_M_file); } ++ ++ template<> ++ inline stdio_sync_filebuf::int_type ++ stdio_sync_filebuf::syncungetc(int_type __c) ++ { return std::ungetwc(__c, _M_file); } ++ ++ template<> ++ inline stdio_sync_filebuf::int_type ++ stdio_sync_filebuf::syncputc(int_type __c) ++ { return std::putwc(__c, _M_file); } ++ ++ template<> ++ inline std::streamsize ++ stdio_sync_filebuf::xsgetn(wchar_t* __s, std::streamsize __n) ++ { ++ std::streamsize __ret = 0; ++ const int_type __eof = traits_type::eof(); ++ while (__n--) ++ { ++ int_type __c = this->syncgetc(); ++ if (traits_type::eq_int_type(__c, __eof)) ++ break; ++ __s[__ret] = traits_type::to_char_type(__c); ++ ++__ret; ++ } ++ ++ if (__ret > 0) ++ _M_unget_buf = traits_type::to_int_type(__s[__ret - 1]); ++ else ++ _M_unget_buf = traits_type::eof(); ++ return __ret; ++ } ++ ++ template<> ++ inline std::streamsize ++ stdio_sync_filebuf::xsputn(const wchar_t* __s, ++ std::streamsize __n) ++ { ++ std::streamsize __ret = 0; ++ const int_type __eof = traits_type::eof(); ++ while (__n--) ++ { ++ if (traits_type::eq_int_type(this->syncputc(*__s++), __eof)) ++ break; ++ ++__ret; ++ } ++ return __ret; ++ } ++#endif ++ ++#if _GLIBCXX_EXTERN_TEMPLATE ++ extern template class stdio_sync_filebuf; ++#ifdef _GLIBCXX_USE_WCHAR_T ++ extern template class stdio_sync_filebuf; ++#endif ++#endif ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/functional +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/functional (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/functional (revision 11967) +@@ -0,0 +1,425 @@ ++// Functional extensions -*- C++ -*- ++ ++// Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/* ++ * ++ * Copyright (c) 1994 ++ * Hewlett-Packard Company ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Hewlett-Packard Company makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ * ++ * ++ * Copyright (c) 1996 ++ * Silicon Graphics Computer Systems, Inc. ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Silicon Graphics makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ */ ++ ++/** @file ext/functional ++ * This file is a GNU extension to the Standard C++ Library (possibly ++ * containing extensions from the HP/SGI STL subset). ++ */ ++ ++#ifndef _EXT_FUNCTIONAL ++#define _EXT_FUNCTIONAL 1 ++ ++#pragma GCC system_header ++ ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::size_t; ++ using std::unary_function; ++ using std::binary_function; ++ using std::mem_fun1_t; ++ using std::const_mem_fun1_t; ++ using std::mem_fun1_ref_t; ++ using std::const_mem_fun1_ref_t; ++ ++ /** The @c identity_element functions are not part of the C++ ++ * standard; SGI provided them as an extension. Its argument is an ++ * operation, and its return value is the identity element for that ++ * operation. It is overloaded for addition and multiplication, ++ * and you can overload it for your own nefarious operations. ++ * ++ * @addtogroup SGIextensions ++ * @{ ++ */ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline _Tp ++ identity_element(std::plus<_Tp>) ++ { return _Tp(0); } ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline _Tp ++ identity_element(std::multiplies<_Tp>) ++ { return _Tp(1); } ++ /** @} */ ++ ++ /** As an extension to the binders, SGI provided composition functors and ++ * wrapper functions to aid in their creation. The @c unary_compose ++ * functor is constructed from two functions/functors, @c f and @c g. ++ * Calling @c operator() with a single argument @c x returns @c f(g(x)). ++ * The function @c compose1 takes the two functions and constructs a ++ * @c unary_compose variable for you. ++ * ++ * @c binary_compose is constructed from three functors, @c f, @c g1, ++ * and @c g2. Its @c operator() returns @c f(g1(x),g2(x)). The function ++ * @compose2 takes f, g1, and g2, and constructs the @c binary_compose ++ * instance for you. For example, if @c f returns an int, then ++ * \code ++ * int answer = (compose2(f,g1,g2))(x); ++ * \endcode ++ * is equivalent to ++ * \code ++ * int temp1 = g1(x); ++ * int temp2 = g2(x); ++ * int answer = f(temp1,temp2); ++ * \endcode ++ * But the first form is more compact, and can be passed around as a ++ * functor to other algorithms. ++ * ++ * @addtogroup SGIextensions ++ * @{ ++ */ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ class unary_compose ++ : public unary_function ++ { ++ protected: ++ _Operation1 _M_fn1; ++ _Operation2 _M_fn2; ++ ++ public: ++ unary_compose(const _Operation1& __x, const _Operation2& __y) ++ : _M_fn1(__x), _M_fn2(__y) {} ++ ++ typename _Operation1::result_type ++ operator()(const typename _Operation2::argument_type& __x) const ++ { return _M_fn1(_M_fn2(__x)); } ++ }; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline unary_compose<_Operation1, _Operation2> ++ compose1(const _Operation1& __fn1, const _Operation2& __fn2) ++ { return unary_compose<_Operation1,_Operation2>(__fn1, __fn2); } ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ class binary_compose ++ : public unary_function ++ { ++ protected: ++ _Operation1 _M_fn1; ++ _Operation2 _M_fn2; ++ _Operation3 _M_fn3; ++ ++ public: ++ binary_compose(const _Operation1& __x, const _Operation2& __y, ++ const _Operation3& __z) ++ : _M_fn1(__x), _M_fn2(__y), _M_fn3(__z) { } ++ ++ typename _Operation1::result_type ++ operator()(const typename _Operation2::argument_type& __x) const ++ { return _M_fn1(_M_fn2(__x), _M_fn3(__x)); } ++ }; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline binary_compose<_Operation1, _Operation2, _Operation3> ++ compose2(const _Operation1& __fn1, const _Operation2& __fn2, ++ const _Operation3& __fn3) ++ { return binary_compose<_Operation1, _Operation2, _Operation3> ++ (__fn1, __fn2, __fn3); } ++ /** @} */ ++ ++ /** As an extension, SGI provided a functor called @c identity. When a ++ * functor is required but no operations are desired, this can be used as a ++ * pass-through. Its @c operator() returns its argument unchanged. ++ * ++ * @addtogroup SGIextensions ++ */ ++ template ++ struct identity : public std::_Identity<_Tp> {}; ++ ++ /** @c select1st and @c select2nd are extensions provided by SGI. Their ++ * @c operator()s ++ * take a @c std::pair as an argument, and return either the first member ++ * or the second member, respectively. They can be used (especially with ++ * the composition functors) to "strip" data from a sequence before ++ * performing the remainder of an algorithm. ++ * ++ * @addtogroup SGIextensions ++ * @{ ++ */ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct select1st : public std::_Select1st<_Pair> {}; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct select2nd : public std::_Select2nd<_Pair> {}; ++ /** @} */ ++ ++ // extension documented next ++ template ++ struct _Project1st : public binary_function<_Arg1, _Arg2, _Arg1> ++ { ++ _Arg1 ++ operator()(const _Arg1& __x, const _Arg2&) const ++ { return __x; } ++ }; ++ ++ template ++ struct _Project2nd : public binary_function<_Arg1, _Arg2, _Arg2> ++ { ++ _Arg2 ++ operator()(const _Arg1&, const _Arg2& __y) const ++ { return __y; } ++ }; ++ ++ /** The @c operator() of the @c project1st functor takes two arbitrary ++ * arguments and returns the first one, while @c project2nd returns the ++ * second one. They are extensions provided by SGI. ++ * ++ * @addtogroup SGIextensions ++ * @{ ++ */ ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct project1st : public _Project1st<_Arg1, _Arg2> {}; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct project2nd : public _Project2nd<_Arg1, _Arg2> {}; ++ /** @} */ ++ ++ // extension documented next ++ template ++ struct _Constant_void_fun ++ { ++ typedef _Result result_type; ++ result_type _M_val; ++ ++ _Constant_void_fun(const result_type& __v) : _M_val(__v) {} ++ ++ const result_type& ++ operator()() const ++ { return _M_val; } ++ }; ++ ++ template ++ struct _Constant_unary_fun ++ { ++ typedef _Argument argument_type; ++ typedef _Result result_type; ++ result_type _M_val; ++ ++ _Constant_unary_fun(const result_type& __v) : _M_val(__v) {} ++ ++ const result_type& ++ operator()(const _Argument&) const ++ { return _M_val; } ++ }; ++ ++ template ++ struct _Constant_binary_fun ++ { ++ typedef _Arg1 first_argument_type; ++ typedef _Arg2 second_argument_type; ++ typedef _Result result_type; ++ _Result _M_val; ++ ++ _Constant_binary_fun(const _Result& __v) : _M_val(__v) {} ++ ++ const result_type& ++ operator()(const _Arg1&, const _Arg2&) const ++ { return _M_val; } ++ }; ++ ++ /** These three functors are each constructed from a single arbitrary ++ * variable/value. Later, their @c operator()s completely ignore any ++ * arguments passed, and return the stored value. ++ * - @c constant_void_fun's @c operator() takes no arguments ++ * - @c constant_unary_fun's @c operator() takes one argument (ignored) ++ * - @c constant_binary_fun's @c operator() takes two arguments (ignored) ++ * ++ * The helper creator functions @c constant0, @c constant1, and ++ * @c constant2 each take a "result" argument and construct variables of ++ * the appropriate functor type. ++ * ++ * @addtogroup SGIextensions ++ * @{ ++ */ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct constant_void_fun ++ : public _Constant_void_fun<_Result> ++ { ++ constant_void_fun(const _Result& __v) ++ : _Constant_void_fun<_Result>(__v) {} ++ }; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct constant_unary_fun : public _Constant_unary_fun<_Result, _Argument> ++ { ++ constant_unary_fun(const _Result& __v) ++ : _Constant_unary_fun<_Result, _Argument>(__v) {} ++ }; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ struct constant_binary_fun ++ : public _Constant_binary_fun<_Result, _Arg1, _Arg2> ++ { ++ constant_binary_fun(const _Result& __v) ++ : _Constant_binary_fun<_Result, _Arg1, _Arg2>(__v) {} ++ }; ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline constant_void_fun<_Result> ++ constant0(const _Result& __val) ++ { return constant_void_fun<_Result>(__val); } ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline constant_unary_fun<_Result, _Result> ++ constant1(const _Result& __val) ++ { return constant_unary_fun<_Result, _Result>(__val); } ++ ++ /// An \link SGIextensions SGI extension \endlink. ++ template ++ inline constant_binary_fun<_Result,_Result,_Result> ++ constant2(const _Result& __val) ++ { return constant_binary_fun<_Result, _Result, _Result>(__val); } ++ /** @} */ ++ ++ /** The @c subtractive_rng class is documented on ++ * SGI's site. ++ * Note that this code assumes that @c int is 32 bits. ++ * ++ * @ingroup SGIextensions ++ */ ++ class subtractive_rng ++ : public unary_function ++ { ++ private: ++ unsigned int _M_table[55]; ++ size_t _M_index1; ++ size_t _M_index2; ++ ++ public: ++ /// Returns a number less than the argument. ++ unsigned int ++ operator()(unsigned int __limit) ++ { ++ _M_index1 = (_M_index1 + 1) % 55; ++ _M_index2 = (_M_index2 + 1) % 55; ++ _M_table[_M_index1] = _M_table[_M_index1] - _M_table[_M_index2]; ++ return _M_table[_M_index1] % __limit; ++ } ++ ++ void ++ _M_initialize(unsigned int __seed) ++ { ++ unsigned int __k = 1; ++ _M_table[54] = __seed; ++ size_t __i; ++ for (__i = 0; __i < 54; __i++) ++ { ++ size_t __ii = (21 * (__i + 1) % 55) - 1; ++ _M_table[__ii] = __k; ++ __k = __seed - __k; ++ __seed = _M_table[__ii]; ++ } ++ for (int __loop = 0; __loop < 4; __loop++) ++ { ++ for (__i = 0; __i < 55; __i++) ++ _M_table[__i] = _M_table[__i] - _M_table[(1 + __i + 30) % 55]; ++ } ++ _M_index1 = 0; ++ _M_index2 = 31; ++ } ++ ++ /// Ctor allowing you to initialize the seed. ++ subtractive_rng(unsigned int __seed) ++ { _M_initialize(__seed); } ++ ++ /// Default ctor; initializes its state with some number you don't see. ++ subtractive_rng() ++ { _M_initialize(161803398u); } ++ }; ++ ++ // Mem_fun adaptor helper functions mem_fun1 and mem_fun1_ref, ++ // provided for backward compatibility, they are no longer part of ++ // the C++ standard. ++ ++ template ++ inline mem_fun1_t<_Ret, _Tp, _Arg> ++ mem_fun1(_Ret (_Tp::*__f)(_Arg)) ++ { return mem_fun1_t<_Ret, _Tp, _Arg>(__f); } ++ ++ template ++ inline const_mem_fun1_t<_Ret, _Tp, _Arg> ++ mem_fun1(_Ret (_Tp::*__f)(_Arg) const) ++ { return const_mem_fun1_t<_Ret, _Tp, _Arg>(__f); } ++ ++ template ++ inline mem_fun1_ref_t<_Ret, _Tp, _Arg> ++ mem_fun1_ref(_Ret (_Tp::*__f)(_Arg)) ++ { return mem_fun1_ref_t<_Ret, _Tp, _Arg>(__f); } ++ ++ template ++ inline const_mem_fun1_ref_t<_Ret, _Tp, _Arg> ++ mem_fun1_ref(_Ret (_Tp::*__f)(_Arg) const) ++ { return const_mem_fun1_ref_t<_Ret, _Tp, _Arg>(__f); } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/typelist.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/typelist.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/typelist.h (revision 11967) +@@ -0,0 +1,544 @@ ++// -*- C++ -*- ++ ++// Copyright (C) 2005, 2006, 2008, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++// Copyright (C) 2004 Ami Tavory and Vladimir Dreizin, IBM-HRL. ++ ++// Permission to use, copy, modify, sell, and distribute this software ++// is hereby granted without fee, provided that the above copyright ++// notice appears in all copies, and that both that copyright notice and ++// this permission notice appear in supporting documentation. None of ++// the above authors, nor IBM Haifa Research Laboratories, make any ++// representation about the suitability of this software for any ++// purpose. It is provided "as is" without express or implied warranty. ++ ++/** ++ * @file typelist.h ++ * Contains typelist_chain definitions. ++ * Typelists are an idea by Andrei Alexandrescu. ++ */ ++ ++#ifndef _TYPELIST_H ++#define _TYPELIST_H 1 ++ ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++/** @namespace __gnu_cxx::typelist ++ * @brief GNU typelist extensions for public compile-time use. ++*/ ++namespace typelist ++{ ++ struct null_type { }; ++ ++ template ++ struct node ++ { ++ typedef Root root; ++ }; ++ ++ // Forward declarations of functors. ++ template ++ struct chain ++ { ++ typedef Hd head; ++ typedef Typelist tail; ++ }; ++ ++ // Apply all typelist types to unary functor. ++ template ++ void ++ apply(Fn&, Typelist); ++ ++ /// Apply all typelist types to generator functor. ++ template ++ void ++ apply_generator(Gn&, Typelist); ++ ++ // Apply all typelist types and values to generator functor. ++ template ++ void ++ apply_generator(Gn&, TypelistT, TypelistV); ++ ++ template ++ struct append; ++ ++ template ++ struct append_typelist; ++ ++ template ++ struct contains; ++ ++ template class Pred> ++ struct filter; ++ ++ template ++ struct at_index; ++ ++ template class Transform> ++ struct transform; ++ ++ template ++ struct flatten; ++ ++ template ++ struct from_first; ++ ++ template ++ struct create1; ++ ++ template ++ struct create2; ++ ++ template ++ struct create3; ++ ++ template ++ struct create4; ++ ++ template ++ struct create5; ++ ++ template ++ struct create6; ++} // namespace typelist ++ ++_GLIBCXX_END_NAMESPACE ++ ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++namespace typelist ++{ ++namespace detail ++{ ++ template ++ struct apply_; ++ ++ template ++ struct apply_ > ++ { ++ void ++ operator()(Fn& f) ++ { ++ f.operator()(Hd()); ++ apply_ next; ++ next(f); ++ } ++ }; ++ ++ template ++ struct apply_ ++ { ++ void ++ operator()(Fn&) { } ++ }; ++ ++ template ++ struct apply_generator1_; ++ ++ template ++ struct apply_generator1_ > ++ { ++ void ++ operator()(Gn& g) ++ { ++ g.template operator()(); ++ apply_generator1_ next; ++ next(g); ++ } ++ }; ++ ++ template ++ struct apply_generator1_ ++ { ++ void ++ operator()(Gn&) { } ++ }; ++ ++ template ++ struct apply_generator2_; ++ ++ template ++ struct apply_generator2_, chain > ++ { ++ void ++ operator()(Gn& g) ++ { ++ g.template operator()(); ++ apply_generator2_ next; ++ next(g); ++ } ++ }; ++ ++ template ++ struct apply_generator2_ ++ { ++ void ++ operator()(Gn&) { } ++ }; ++ ++ template ++ struct append_; ++ ++ template ++ struct append_, Typelist_Chain> ++ { ++ private: ++ typedef append_ append_type; ++ ++ public: ++ typedef chain type; ++ }; ++ ++ template ++ struct append_ ++ { ++ typedef Typelist_Chain type; ++ }; ++ ++ template ++ struct append_ ++ { ++ typedef Typelist_Chain type; ++ }; ++ ++ template<> ++ struct append_ ++ { ++ typedef null_type type; ++ }; ++ ++ template ++ struct append_typelist_; ++ ++ template ++ struct append_typelist_ > ++ { ++ typedef chain type; ++ }; ++ ++ template ++ struct append_typelist_ > ++ { ++ private: ++ typedef typename append_typelist_::type rest_type; ++ ++ public: ++ typedef typename append >::type::root type; ++ }; ++ ++ template ++ struct contains_; ++ ++ template ++ struct contains_ ++ { ++ enum ++ { ++ value = false ++ }; ++ }; ++ ++ template ++ struct contains_, T> ++ { ++ enum ++ { ++ value = contains_::value ++ }; ++ }; ++ ++ template ++ struct contains_, T> ++ { ++ enum ++ { ++ value = true ++ }; ++ }; ++ ++ template class Pred> ++ struct chain_filter_; ++ ++ template class Pred> ++ struct chain_filter_ ++ { ++ typedef null_type type; ++ }; ++ ++ template class Pred> ++ struct chain_filter_, Pred> ++ { ++ private: ++ enum ++ { ++ include_hd = Pred::value ++ }; ++ ++ typedef typename chain_filter_::type rest_type; ++ typedef chain chain_type; ++ ++ public: ++ typedef typename __conditional_type::__type type; ++ }; ++ ++ template ++ struct chain_at_index_; ++ ++ template ++ struct chain_at_index_, 0> ++ { ++ typedef Hd type; ++ }; ++ ++ template ++ struct chain_at_index_, i> ++ { ++ typedef typename chain_at_index_::type type; ++ }; ++ ++ template class Transform> ++ struct chain_transform_; ++ ++ template class Transform> ++ struct chain_transform_ ++ { ++ typedef null_type type; ++ }; ++ ++ template class Transform> ++ struct chain_transform_, Transform> ++ { ++ private: ++ typedef typename chain_transform_::type rest_type; ++ typedef typename Transform::type transform_type; ++ ++ public: ++ typedef chain type; ++ }; ++ ++ template ++ struct chain_flatten_; ++ ++ template ++ struct chain_flatten_ > ++ { ++ typedef typename Hd_Tl::root type; ++ }; ++ ++ template ++ struct chain_flatten_ > ++ { ++ private: ++ typedef typename chain_flatten_::type rest_type; ++ typedef append > append_type; ++ public: ++ typedef typename append_type::type::root type; ++ }; ++} // namespace detail ++} // namespace typelist ++ ++_GLIBCXX_END_NAMESPACE ++ ++#define _GLIBCXX_TYPELIST_CHAIN1(X0) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN2(X0, X1) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN3(X0, X1, X2) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN4(X0, X1, X2, X3) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN5(X0, X1, X2, X3, X4) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN6(X0, X1, X2, X3, X4, X5) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN7(X0, X1, X2, X3, X4, X5, X6) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN8(X0, X1, X2, X3, X4, X5, X6, X7) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN9(X0, X1, X2, X3, X4, X5, X6, X7, X8) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN10(X0, X1, X2, X3, X4, X5, X6, X7, X8, X9) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN11(X0, X1, X2, X3, X4, X5, X6, X7, X8, X9, X10) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN12(X0, X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN13(X0, X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN14(X0, X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13) __gnu_cxx::typelist::chain ++#define _GLIBCXX_TYPELIST_CHAIN15(X0, X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X14) __gnu_cxx::typelist::chain ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++namespace typelist ++{ ++ template ++ void ++ apply(Fn& fn, Typelist) ++ { ++ detail::apply_ a; ++ a(fn); ++ } ++ ++ template ++ void ++ apply_generator(Fn& fn, Typelist) ++ { ++ detail::apply_generator1_ a; ++ a(fn); ++ } ++ ++ template ++ void ++ apply_generator(Fn& fn, TypelistT, TypelistV) ++ { ++ typedef typename TypelistT::root rootT; ++ typedef typename TypelistV::root rootV; ++ detail::apply_generator2_ a; ++ a(fn); ++ } ++ ++ template ++ struct append ++ { ++ private: ++ typedef typename Typelist0::root root0_type; ++ typedef typename Typelist1::root root1_type; ++ typedef detail::append_ append_type; ++ ++ public: ++ typedef node type; ++ }; ++ ++ template ++ struct append_typelist ++ { ++ private: ++ typedef typename Typelist_Typelist::root root_type; ++ typedef detail::append_typelist_ append_type; ++ ++ public: ++ typedef node type; ++ }; ++ ++ template ++ struct contains ++ { ++ private: ++ typedef typename Typelist::root root_type; ++ ++ public: ++ enum ++ { ++ value = detail::contains_::value ++ }; ++ }; ++ ++ template class Pred> ++ struct filter ++ { ++ private: ++ typedef typename Typelist::root root_type; ++ typedef detail::chain_filter_ filter_type; ++ ++ public: ++ typedef node type; ++ }; ++ ++ template ++ struct at_index ++ { ++ private: ++ typedef typename Typelist::root root_type; ++ typedef detail::chain_at_index_ index_type; ++ ++ public: ++ typedef typename index_type::type type; ++ }; ++ ++ template class Transform> ++ struct transform ++ { ++ private: ++ typedef typename Typelist::root root_type; ++ typedef detail::chain_transform_ transform_type; ++ ++ public: ++ typedef node type; ++ }; ++ ++ template ++ struct flatten ++ { ++ private: ++ typedef typename Typelist_Typelist::root root_type; ++ typedef typename detail::chain_flatten_::type flatten_type; ++ ++ public: ++ typedef node type; ++ }; ++ ++ template ++ struct from_first ++ { ++ private: ++ typedef typename at_index::type first_type; ++ ++ public: ++ typedef node > type; ++ }; ++ ++ template ++ struct create1 ++ { ++ typedef node<_GLIBCXX_TYPELIST_CHAIN1(T1)> type; ++ }; ++ ++ template ++ struct create2 ++ { ++ typedef node<_GLIBCXX_TYPELIST_CHAIN2(T1,T2)> type; ++ }; ++ ++ template ++ struct create3 ++ { ++ typedef node<_GLIBCXX_TYPELIST_CHAIN3(T1,T2,T3)> type; ++ }; ++ ++ template ++ struct create4 ++ { ++ typedef node<_GLIBCXX_TYPELIST_CHAIN4(T1,T2,T3,T4)> type; ++ }; ++ ++ template ++ struct create5 ++ { ++ typedef node<_GLIBCXX_TYPELIST_CHAIN5(T1,T2,T3,T4,T5)> type; ++ }; ++ ++ template ++ struct create6 ++ { ++ typedef node<_GLIBCXX_TYPELIST_CHAIN6(T1,T2,T3,T4,T5,T6)> type; ++ }; ++} // namespace typelist ++_GLIBCXX_END_NAMESPACE ++ ++ ++#endif ++ +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/array_allocator.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/array_allocator.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/array_allocator.h (revision 11967) +@@ -0,0 +1,154 @@ ++// array allocator -*- C++ -*- ++ ++// Copyright (C) 2004, 2005, 2006, 2007, 2008, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/array_allocator.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _ARRAY_ALLOCATOR_H ++#define _ARRAY_ALLOCATOR_H 1 ++ ++#include ++#include ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::size_t; ++ using std::ptrdiff_t; ++ ++ /// Base class. ++ template ++ class array_allocator_base ++ { ++ public: ++ typedef size_t size_type; ++ typedef ptrdiff_t difference_type; ++ typedef _Tp* pointer; ++ typedef const _Tp* const_pointer; ++ typedef _Tp& reference; ++ typedef const _Tp& const_reference; ++ typedef _Tp value_type; ++ ++ pointer ++ address(reference __x) const { return &__x; } ++ ++ const_pointer ++ address(const_reference __x) const { return &__x; } ++ ++ void ++ deallocate(pointer, size_type) ++ { ++ // Does nothing. ++ } ++ ++ size_type ++ max_size() const throw() ++ { return size_t(-1) / sizeof(_Tp); } ++ ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 402. wrong new expression in [some_] allocator::construct ++ void ++ construct(pointer __p, const _Tp& __val) ++ { ::new((void *)__p) value_type(__val); } ++ ++#ifdef __GXX_EXPERIMENTAL_CXX0X__ ++ template ++ void ++ construct(pointer __p, _Args&&... __args) ++ { ::new((void *)__p) _Tp(std::forward<_Args>(__args)...); } ++#endif ++ ++ void ++ destroy(pointer __p) { __p->~_Tp(); } ++ }; ++ ++ /** ++ * @brief An allocator that uses previously allocated memory. ++ * This memory can be externally, globally, or otherwise allocated. ++ * @ingroup allocators ++ */ ++ template > ++ class array_allocator : public array_allocator_base<_Tp> ++ { ++ public: ++ typedef size_t size_type; ++ typedef ptrdiff_t difference_type; ++ typedef _Tp* pointer; ++ typedef const _Tp* const_pointer; ++ typedef _Tp& reference; ++ typedef const _Tp& const_reference; ++ typedef _Tp value_type; ++ typedef _Array array_type; ++ ++ private: ++ array_type* _M_array; ++ size_type _M_used; ++ ++ public: ++ template ++ struct rebind ++ { typedef array_allocator<_Tp1, _Array1> other; }; ++ ++ array_allocator(array_type* __array = NULL) throw() ++ : _M_array(__array), _M_used(size_type()) { } ++ ++ array_allocator(const array_allocator& __o) throw() ++ : _M_array(__o._M_array), _M_used(__o._M_used) { } ++ ++ template ++ array_allocator(const array_allocator<_Tp1, _Array1>&) throw() ++ : _M_array(NULL), _M_used(size_type()) { } ++ ++ ~array_allocator() throw() { } ++ ++ pointer ++ allocate(size_type __n, const void* = 0) ++ { ++ if (_M_array == 0 || _M_used + __n > _M_array->size()) ++ std::__throw_bad_alloc(); ++ pointer __ret = _M_array->begin() + _M_used; ++ _M_used += __n; ++ return __ret; ++ } ++ }; ++ ++ template ++ inline bool ++ operator==(const array_allocator<_Tp, _Array>&, ++ const array_allocator<_Tp, _Array>&) ++ { return true; } ++ ++ template ++ inline bool ++ operator!=(const array_allocator<_Tp, _Array>&, ++ const array_allocator<_Tp, _Array>&) ++ { return false; } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/vstring.tcc +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/vstring.tcc (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/vstring.tcc (revision 11967) +@@ -0,0 +1,696 @@ ++// Versatile string -*- C++ -*- ++ ++// Copyright (C) 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/vstring.tcc ++ * This file is a GNU extension to the Standard C++ Library. ++ * This is an internal header file, included by other library headers. ++ * You should not attempt to use it directly. ++ */ ++ ++#ifndef _VSTRING_TCC ++#define _VSTRING_TCC 1 ++ ++#pragma GCC system_header ++ ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ template class _Base> ++ const typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>::npos; ++ ++ template class _Base> ++ void ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ resize(size_type __n, _CharT __c) ++ { ++ const size_type __size = this->size(); ++ if (__size < __n) ++ this->append(__n - __size, __c); ++ else if (__n < __size) ++ this->_M_erase(__n, __size - __n); ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base>& ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ _M_append(const _CharT* __s, size_type __n) ++ { ++ const size_type __len = __n + this->size(); ++ ++ if (__len <= this->capacity() && !this->_M_is_shared()) ++ { ++ if (__n) ++ this->_S_copy(this->_M_data() + this->size(), __s, __n); ++ } ++ else ++ this->_M_mutate(this->size(), size_type(0), __s, __n); ++ ++ this->_M_set_length(__len); ++ return *this; ++ } ++ ++ template class _Base> ++ template ++ __versa_string<_CharT, _Traits, _Alloc, _Base>& ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ _M_replace_dispatch(iterator __i1, iterator __i2, _InputIterator __k1, ++ _InputIterator __k2, std::__false_type) ++ { ++ const __versa_string __s(__k1, __k2); ++ const size_type __n1 = __i2 - __i1; ++ return _M_replace(__i1 - _M_ibegin(), __n1, __s._M_data(), ++ __s.size()); ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base>& ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ _M_replace_aux(size_type __pos1, size_type __n1, size_type __n2, ++ _CharT __c) ++ { ++ _M_check_length(__n1, __n2, "__versa_string::_M_replace_aux"); ++ ++ const size_type __old_size = this->size(); ++ const size_type __new_size = __old_size + __n2 - __n1; ++ ++ if (__new_size <= this->capacity() && !this->_M_is_shared()) ++ { ++ _CharT* __p = this->_M_data() + __pos1; ++ ++ const size_type __how_much = __old_size - __pos1 - __n1; ++ if (__how_much && __n1 != __n2) ++ this->_S_move(__p + __n2, __p + __n1, __how_much); ++ } ++ else ++ this->_M_mutate(__pos1, __n1, 0, __n2); ++ ++ if (__n2) ++ this->_S_assign(this->_M_data() + __pos1, __n2, __c); ++ ++ this->_M_set_length(__new_size); ++ return *this; ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base>& ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ _M_replace(size_type __pos, size_type __len1, const _CharT* __s, ++ const size_type __len2) ++ { ++ _M_check_length(__len1, __len2, "__versa_string::_M_replace"); ++ ++ const size_type __old_size = this->size(); ++ const size_type __new_size = __old_size + __len2 - __len1; ++ ++ if (__new_size <= this->capacity() && !this->_M_is_shared()) ++ { ++ _CharT* __p = this->_M_data() + __pos; ++ ++ const size_type __how_much = __old_size - __pos - __len1; ++ if (_M_disjunct(__s)) ++ { ++ if (__how_much && __len1 != __len2) ++ this->_S_move(__p + __len2, __p + __len1, __how_much); ++ if (__len2) ++ this->_S_copy(__p, __s, __len2); ++ } ++ else ++ { ++ // Work in-place. ++ if (__len2 && __len2 <= __len1) ++ this->_S_move(__p, __s, __len2); ++ if (__how_much && __len1 != __len2) ++ this->_S_move(__p + __len2, __p + __len1, __how_much); ++ if (__len2 > __len1) ++ { ++ if (__s + __len2 <= __p + __len1) ++ this->_S_move(__p, __s, __len2); ++ else if (__s >= __p + __len1) ++ this->_S_copy(__p, __s + __len2 - __len1, __len2); ++ else ++ { ++ const size_type __nleft = (__p + __len1) - __s; ++ this->_S_move(__p, __s, __nleft); ++ this->_S_copy(__p + __nleft, __p + __len2, ++ __len2 - __nleft); ++ } ++ } ++ } ++ } ++ else ++ this->_M_mutate(__pos, __len1, __s, __len2); ++ ++ this->_M_set_length(__new_size); ++ return *this; ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base> ++ operator+(const __versa_string<_CharT, _Traits, _Alloc, _Base>& __lhs, ++ const __versa_string<_CharT, _Traits, _Alloc, _Base>& __rhs) ++ { ++ __versa_string<_CharT, _Traits, _Alloc, _Base> __str; ++ __str.reserve(__lhs.size() + __rhs.size()); ++ __str.append(__lhs); ++ __str.append(__rhs); ++ return __str; ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base> ++ operator+(const _CharT* __lhs, ++ const __versa_string<_CharT, _Traits, _Alloc, _Base>& __rhs) ++ { ++ __glibcxx_requires_string(__lhs); ++ typedef __versa_string<_CharT, _Traits, _Alloc, _Base> __string_type; ++ typedef typename __string_type::size_type __size_type; ++ const __size_type __len = _Traits::length(__lhs); ++ __string_type __str; ++ __str.reserve(__len + __rhs.size()); ++ __str.append(__lhs, __len); ++ __str.append(__rhs); ++ return __str; ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base> ++ operator+(_CharT __lhs, ++ const __versa_string<_CharT, _Traits, _Alloc, _Base>& __rhs) ++ { ++ __versa_string<_CharT, _Traits, _Alloc, _Base> __str; ++ __str.reserve(__rhs.size() + 1); ++ __str.push_back(__lhs); ++ __str.append(__rhs); ++ return __str; ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base> ++ operator+(const __versa_string<_CharT, _Traits, _Alloc, _Base>& __lhs, ++ const _CharT* __rhs) ++ { ++ __glibcxx_requires_string(__rhs); ++ typedef __versa_string<_CharT, _Traits, _Alloc, _Base> __string_type; ++ typedef typename __string_type::size_type __size_type; ++ const __size_type __len = _Traits::length(__rhs); ++ __string_type __str; ++ __str.reserve(__lhs.size() + __len); ++ __str.append(__lhs); ++ __str.append(__rhs, __len); ++ return __str; ++ } ++ ++ template class _Base> ++ __versa_string<_CharT, _Traits, _Alloc, _Base> ++ operator+(const __versa_string<_CharT, _Traits, _Alloc, _Base>& __lhs, ++ _CharT __rhs) ++ { ++ __versa_string<_CharT, _Traits, _Alloc, _Base> __str; ++ __str.reserve(__lhs.size() + 1); ++ __str.append(__lhs); ++ __str.push_back(__rhs); ++ return __str; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ copy(_CharT* __s, size_type __n, size_type __pos) const ++ { ++ _M_check(__pos, "__versa_string::copy"); ++ __n = _M_limit(__pos, __n); ++ __glibcxx_requires_string_len(__s, __n); ++ if (__n) ++ this->_S_copy(__s, this->_M_data() + __pos, __n); ++ // 21.3.5.7 par 3: do not append null. (good.) ++ return __n; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find(const _CharT* __s, size_type __pos, size_type __n) const ++ { ++ __glibcxx_requires_string_len(__s, __n); ++ const size_type __size = this->size(); ++ const _CharT* __data = this->_M_data(); ++ ++ if (__n == 0) ++ return __pos <= __size ? __pos : npos; ++ ++ if (__n <= __size) ++ { ++ for (; __pos <= __size - __n; ++__pos) ++ if (traits_type::eq(__data[__pos], __s[0]) ++ && traits_type::compare(__data + __pos + 1, ++ __s + 1, __n - 1) == 0) ++ return __pos; ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find(_CharT __c, size_type __pos) const ++ { ++ size_type __ret = npos; ++ const size_type __size = this->size(); ++ if (__pos < __size) ++ { ++ const _CharT* __data = this->_M_data(); ++ const size_type __n = __size - __pos; ++ const _CharT* __p = traits_type::find(__data + __pos, __n, __c); ++ if (__p) ++ __ret = __p - __data; ++ } ++ return __ret; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ rfind(const _CharT* __s, size_type __pos, size_type __n) const ++ { ++ __glibcxx_requires_string_len(__s, __n); ++ const size_type __size = this->size(); ++ if (__n <= __size) ++ { ++ __pos = std::min(size_type(__size - __n), __pos); ++ const _CharT* __data = this->_M_data(); ++ do ++ { ++ if (traits_type::compare(__data + __pos, __s, __n) == 0) ++ return __pos; ++ } ++ while (__pos-- > 0); ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ rfind(_CharT __c, size_type __pos) const ++ { ++ size_type __size = this->size(); ++ if (__size) ++ { ++ if (--__size > __pos) ++ __size = __pos; ++ for (++__size; __size-- > 0; ) ++ if (traits_type::eq(this->_M_data()[__size], __c)) ++ return __size; ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find_first_of(const _CharT* __s, size_type __pos, size_type __n) const ++ { ++ __glibcxx_requires_string_len(__s, __n); ++ for (; __n && __pos < this->size(); ++__pos) ++ { ++ const _CharT* __p = traits_type::find(__s, __n, ++ this->_M_data()[__pos]); ++ if (__p) ++ return __pos; ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find_last_of(const _CharT* __s, size_type __pos, size_type __n) const ++ { ++ __glibcxx_requires_string_len(__s, __n); ++ size_type __size = this->size(); ++ if (__size && __n) ++ { ++ if (--__size > __pos) ++ __size = __pos; ++ do ++ { ++ if (traits_type::find(__s, __n, this->_M_data()[__size])) ++ return __size; ++ } ++ while (__size-- != 0); ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find_first_not_of(const _CharT* __s, size_type __pos, size_type __n) const ++ { ++ __glibcxx_requires_string_len(__s, __n); ++ for (; __pos < this->size(); ++__pos) ++ if (!traits_type::find(__s, __n, this->_M_data()[__pos])) ++ return __pos; ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find_first_not_of(_CharT __c, size_type __pos) const ++ { ++ for (; __pos < this->size(); ++__pos) ++ if (!traits_type::eq(this->_M_data()[__pos], __c)) ++ return __pos; ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find_last_not_of(const _CharT* __s, size_type __pos, size_type __n) const ++ { ++ __glibcxx_requires_string_len(__s, __n); ++ size_type __size = this->size(); ++ if (__size) ++ { ++ if (--__size > __pos) ++ __size = __pos; ++ do ++ { ++ if (!traits_type::find(__s, __n, this->_M_data()[__size])) ++ return __size; ++ } ++ while (__size--); ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ typename __versa_string<_CharT, _Traits, _Alloc, _Base>::size_type ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ find_last_not_of(_CharT __c, size_type __pos) const ++ { ++ size_type __size = this->size(); ++ if (__size) ++ { ++ if (--__size > __pos) ++ __size = __pos; ++ do ++ { ++ if (!traits_type::eq(this->_M_data()[__size], __c)) ++ return __size; ++ } ++ while (__size--); ++ } ++ return npos; ++ } ++ ++ template class _Base> ++ int ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ compare(size_type __pos, size_type __n, const __versa_string& __str) const ++ { ++ _M_check(__pos, "__versa_string::compare"); ++ __n = _M_limit(__pos, __n); ++ const size_type __osize = __str.size(); ++ const size_type __len = std::min(__n, __osize); ++ int __r = traits_type::compare(this->_M_data() + __pos, ++ __str.data(), __len); ++ if (!__r) ++ __r = this->_S_compare(__n, __osize); ++ return __r; ++ } ++ ++ template class _Base> ++ int ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ compare(size_type __pos1, size_type __n1, const __versa_string& __str, ++ size_type __pos2, size_type __n2) const ++ { ++ _M_check(__pos1, "__versa_string::compare"); ++ __str._M_check(__pos2, "__versa_string::compare"); ++ __n1 = _M_limit(__pos1, __n1); ++ __n2 = __str._M_limit(__pos2, __n2); ++ const size_type __len = std::min(__n1, __n2); ++ int __r = traits_type::compare(this->_M_data() + __pos1, ++ __str.data() + __pos2, __len); ++ if (!__r) ++ __r = this->_S_compare(__n1, __n2); ++ return __r; ++ } ++ ++ template class _Base> ++ int ++ __versa_string<_CharT, _Traits, _Alloc, _Base>:: ++ compare(const _CharT* __s) const ++ { ++ __glibcxx_requires_string(__s); ++ const size_type __size = this->size(); ++ const size_type __osize = traits_type::length(__s); ++ const size_type __len = std::min(__size, __osize); ++ int __r = traits_type::compare(this->_M_data(), __s, __len); ++ if (!__r) ++ __r = this->_S_compare(__size, __osize); ++ return __r; ++ } ++ ++ template class _Base> ++ int ++ __versa_string <_CharT, _Traits, _Alloc, _Base>:: ++ compare(size_type __pos, size_type __n1, const _CharT* __s) const ++ { ++ __glibcxx_requires_string(__s); ++ _M_check(__pos, "__versa_string::compare"); ++ __n1 = _M_limit(__pos, __n1); ++ const size_type __osize = traits_type::length(__s); ++ const size_type __len = std::min(__n1, __osize); ++ int __r = traits_type::compare(this->_M_data() + __pos, __s, __len); ++ if (!__r) ++ __r = this->_S_compare(__n1, __osize); ++ return __r; ++ } ++ ++ template class _Base> ++ int ++ __versa_string <_CharT, _Traits, _Alloc, _Base>:: ++ compare(size_type __pos, size_type __n1, const _CharT* __s, ++ size_type __n2) const ++ { ++ __glibcxx_requires_string_len(__s, __n2); ++ _M_check(__pos, "__versa_string::compare"); ++ __n1 = _M_limit(__pos, __n1); ++ const size_type __len = std::min(__n1, __n2); ++ int __r = traits_type::compare(this->_M_data() + __pos, __s, __len); ++ if (!__r) ++ __r = this->_S_compare(__n1, __n2); ++ return __r; ++ } ++ ++_GLIBCXX_END_NAMESPACE ++ ++_GLIBCXX_BEGIN_NAMESPACE(std) ++ ++ template class _Base> ++ basic_istream<_CharT, _Traits>& ++ operator>>(basic_istream<_CharT, _Traits>& __in, ++ __gnu_cxx::__versa_string<_CharT, _Traits, ++ _Alloc, _Base>& __str) ++ { ++ typedef basic_istream<_CharT, _Traits> __istream_type; ++ typedef typename __istream_type::ios_base __ios_base; ++ typedef __gnu_cxx::__versa_string<_CharT, _Traits, _Alloc, _Base> ++ __string_type; ++ typedef typename __istream_type::int_type __int_type; ++ typedef typename __string_type::size_type __size_type; ++ typedef ctype<_CharT> __ctype_type; ++ typedef typename __ctype_type::ctype_base __ctype_base; ++ ++ __size_type __extracted = 0; ++ typename __ios_base::iostate __err = __ios_base::goodbit; ++ typename __istream_type::sentry __cerb(__in, false); ++ if (__cerb) ++ { ++ __try ++ { ++ // Avoid reallocation for common case. ++ __str.erase(); ++ _CharT __buf[128]; ++ __size_type __len = 0; ++ const streamsize __w = __in.width(); ++ const __size_type __n = __w > 0 ? static_cast<__size_type>(__w) ++ : __str.max_size(); ++ const __ctype_type& __ct = use_facet<__ctype_type>(__in.getloc()); ++ const __int_type __eof = _Traits::eof(); ++ __int_type __c = __in.rdbuf()->sgetc(); ++ ++ while (__extracted < __n ++ && !_Traits::eq_int_type(__c, __eof) ++ && !__ct.is(__ctype_base::space, ++ _Traits::to_char_type(__c))) ++ { ++ if (__len == sizeof(__buf) / sizeof(_CharT)) ++ { ++ __str.append(__buf, sizeof(__buf) / sizeof(_CharT)); ++ __len = 0; ++ } ++ __buf[__len++] = _Traits::to_char_type(__c); ++ ++__extracted; ++ __c = __in.rdbuf()->snextc(); ++ } ++ __str.append(__buf, __len); ++ ++ if (_Traits::eq_int_type(__c, __eof)) ++ __err |= __ios_base::eofbit; ++ __in.width(0); ++ } ++ __catch(__cxxabiv1::__forced_unwind&) ++ { ++ __in._M_setstate(__ios_base::badbit); ++ __throw_exception_again; ++ } ++ __catch(...) ++ { ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 91. Description of operator>> and getline() for string<> ++ // might cause endless loop ++ __in._M_setstate(__ios_base::badbit); ++ } ++ } ++ // 211. operator>>(istream&, string&) doesn't set failbit ++ if (!__extracted) ++ __err |= __ios_base::failbit; ++ if (__err) ++ __in.setstate(__err); ++ return __in; ++ } ++ ++ template class _Base> ++ basic_istream<_CharT, _Traits>& ++ getline(basic_istream<_CharT, _Traits>& __in, ++ __gnu_cxx::__versa_string<_CharT, _Traits, _Alloc, _Base>& __str, ++ _CharT __delim) ++ { ++ typedef basic_istream<_CharT, _Traits> __istream_type; ++ typedef typename __istream_type::ios_base __ios_base; ++ typedef __gnu_cxx::__versa_string<_CharT, _Traits, _Alloc, _Base> ++ __string_type; ++ typedef typename __istream_type::int_type __int_type; ++ typedef typename __string_type::size_type __size_type; ++ ++ __size_type __extracted = 0; ++ const __size_type __n = __str.max_size(); ++ typename __ios_base::iostate __err = __ios_base::goodbit; ++ typename __istream_type::sentry __cerb(__in, true); ++ if (__cerb) ++ { ++ __try ++ { ++ // Avoid reallocation for common case. ++ __str.erase(); ++ _CharT __buf[128]; ++ __size_type __len = 0; ++ const __int_type __idelim = _Traits::to_int_type(__delim); ++ const __int_type __eof = _Traits::eof(); ++ __int_type __c = __in.rdbuf()->sgetc(); ++ ++ while (__extracted < __n ++ && !_Traits::eq_int_type(__c, __eof) ++ && !_Traits::eq_int_type(__c, __idelim)) ++ { ++ if (__len == sizeof(__buf) / sizeof(_CharT)) ++ { ++ __str.append(__buf, sizeof(__buf) / sizeof(_CharT)); ++ __len = 0; ++ } ++ __buf[__len++] = _Traits::to_char_type(__c); ++ ++__extracted; ++ __c = __in.rdbuf()->snextc(); ++ } ++ __str.append(__buf, __len); ++ ++ if (_Traits::eq_int_type(__c, __eof)) ++ __err |= __ios_base::eofbit; ++ else if (_Traits::eq_int_type(__c, __idelim)) ++ { ++ ++__extracted; ++ __in.rdbuf()->sbumpc(); ++ } ++ else ++ __err |= __ios_base::failbit; ++ } ++ __catch(__cxxabiv1::__forced_unwind&) ++ { ++ __in._M_setstate(__ios_base::badbit); ++ __throw_exception_again; ++ } ++ __catch(...) ++ { ++ // _GLIBCXX_RESOLVE_LIB_DEFECTS ++ // 91. Description of operator>> and getline() for string<> ++ // might cause endless loop ++ __in._M_setstate(__ios_base::badbit); ++ } ++ } ++ if (!__extracted) ++ __err |= __ios_base::failbit; ++ if (__err) ++ __in.setstate(__err); ++ return __in; ++ } ++ ++_GLIBCXX_END_NAMESPACE ++ ++#endif // _VSTRING_TCC +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/rope +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/rope (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/rope (revision 11967) +@@ -0,0 +1,2958 @@ ++// SGI's rope class -*- C++ -*- ++ ++// Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/* ++ * Copyright (c) 1997 ++ * Silicon Graphics Computer Systems, Inc. ++ * ++ * Permission to use, copy, modify, distribute and sell this software ++ * and its documentation for any purpose is hereby granted without fee, ++ * provided that the above copyright notice appear in all copies and ++ * that both that copyright notice and this permission notice appear ++ * in supporting documentation. Silicon Graphics makes no ++ * representations about the suitability of this software for any ++ * purpose. It is provided "as is" without express or implied warranty. ++ */ ++ ++/** @file ext/rope ++ * This file is a GNU extension to the Standard C++ Library (possibly ++ * containing extensions from the HP/SGI STL subset). ++ */ ++ ++#ifndef _ROPE ++#define _ROPE 1 ++ ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++ ++# ifdef __GC ++# define __GC_CONST const ++# else ++# define __GC_CONST // constant except for deallocation ++# endif ++ ++#include // For uninitialized_copy_n ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ namespace __detail ++ { ++ enum { _S_max_rope_depth = 45 }; ++ enum _Tag {_S_leaf, _S_concat, _S_substringfn, _S_function}; ++ } // namespace __detail ++ ++ using std::size_t; ++ using std::ptrdiff_t; ++ using std::allocator; ++ using std::_Destroy; ++ ++ // See libstdc++/36832. ++ template ++ void ++ _Destroy_const(_ForwardIterator __first, ++ _ForwardIterator __last, _Allocator __alloc) ++ { ++ for (; __first != __last; ++__first) ++ __alloc.destroy(&*__first); ++ } ++ ++ template ++ inline void ++ _Destroy_const(_ForwardIterator __first, ++ _ForwardIterator __last, allocator<_Tp>) ++ { _Destroy(__first, __last); } ++ ++ // The _S_eos function is used for those functions that ++ // convert to/from C-like strings to detect the end of the string. ++ ++ // The end-of-C-string character. ++ // This is what the draft standard says it should be. ++ template ++ inline _CharT ++ _S_eos(_CharT*) ++ { return _CharT(); } ++ ++ // Test for basic character types. ++ // For basic character types leaves having a trailing eos. ++ template ++ inline bool ++ _S_is_basic_char_type(_CharT*) ++ { return false; } ++ ++ template ++ inline bool ++ _S_is_one_byte_char_type(_CharT*) ++ { return false; } ++ ++ inline bool ++ _S_is_basic_char_type(char*) ++ { return true; } ++ ++ inline bool ++ _S_is_one_byte_char_type(char*) ++ { return true; } ++ ++ inline bool ++ _S_is_basic_char_type(wchar_t*) ++ { return true; } ++ ++ // Store an eos iff _CharT is a basic character type. ++ // Do not reference _S_eos if it isn't. ++ template ++ inline void ++ _S_cond_store_eos(_CharT&) { } ++ ++ inline void ++ _S_cond_store_eos(char& __c) ++ { __c = 0; } ++ ++ inline void ++ _S_cond_store_eos(wchar_t& __c) ++ { __c = 0; } ++ ++ // char_producers are logically functions that generate a section of ++ // a string. These can be converted to ropes. The resulting rope ++ // invokes the char_producer on demand. This allows, for example, ++ // files to be viewed as ropes without reading the entire file. ++ template ++ class char_producer ++ { ++ public: ++ virtual ~char_producer() { }; ++ ++ virtual void ++ operator()(size_t __start_pos, size_t __len, ++ _CharT* __buffer) = 0; ++ // Buffer should really be an arbitrary output iterator. ++ // That way we could flatten directly into an ostream, etc. ++ // This is thoroughly impossible, since iterator types don't ++ // have runtime descriptions. ++ }; ++ ++ // Sequence buffers: ++ // ++ // Sequence must provide an append operation that appends an ++ // array to the sequence. Sequence buffers are useful only if ++ // appending an entire array is cheaper than appending element by element. ++ // This is true for many string representations. ++ // This should perhaps inherit from ostream ++ // and be implemented correspondingly, so that they can be used ++ // for formatted. For the sake of portability, we don't do this yet. ++ // ++ // For now, sequence buffers behave as output iterators. But they also ++ // behave a little like basic_ostringstream and a ++ // little like containers. ++ ++ template ++ class sequence_buffer ++ : public std::iterator ++ { ++ public: ++ typedef typename _Sequence::value_type value_type; ++ protected: ++ _Sequence* _M_prefix; ++ value_type _M_buffer[_Buf_sz]; ++ size_t _M_buf_count; ++ public: ++ ++ void ++ flush() ++ { ++ _M_prefix->append(_M_buffer, _M_buffer + _M_buf_count); ++ _M_buf_count = 0; ++ } ++ ++ ~sequence_buffer() ++ { flush(); } ++ ++ sequence_buffer() ++ : _M_prefix(0), _M_buf_count(0) { } ++ ++ sequence_buffer(const sequence_buffer& __x) ++ { ++ _M_prefix = __x._M_prefix; ++ _M_buf_count = __x._M_buf_count; ++ std::copy(__x._M_buffer, __x._M_buffer + __x._M_buf_count, _M_buffer); ++ } ++ ++ sequence_buffer(sequence_buffer& __x) ++ { ++ __x.flush(); ++ _M_prefix = __x._M_prefix; ++ _M_buf_count = 0; ++ } ++ ++ sequence_buffer(_Sequence& __s) ++ : _M_prefix(&__s), _M_buf_count(0) { } ++ ++ sequence_buffer& ++ operator=(sequence_buffer& __x) ++ { ++ __x.flush(); ++ _M_prefix = __x._M_prefix; ++ _M_buf_count = 0; ++ return *this; ++ } ++ ++ sequence_buffer& ++ operator=(const sequence_buffer& __x) ++ { ++ _M_prefix = __x._M_prefix; ++ _M_buf_count = __x._M_buf_count; ++ std::copy(__x._M_buffer, __x._M_buffer + __x._M_buf_count, _M_buffer); ++ return *this; ++ } ++ ++ void ++ push_back(value_type __x) ++ { ++ if (_M_buf_count < _Buf_sz) ++ { ++ _M_buffer[_M_buf_count] = __x; ++ ++_M_buf_count; ++ } ++ else ++ { ++ flush(); ++ _M_buffer[0] = __x; ++ _M_buf_count = 1; ++ } ++ } ++ ++ void ++ append(value_type* __s, size_t __len) ++ { ++ if (__len + _M_buf_count <= _Buf_sz) ++ { ++ size_t __i = _M_buf_count; ++ for (size_t __j = 0; __j < __len; __i++, __j++) ++ _M_buffer[__i] = __s[__j]; ++ _M_buf_count += __len; ++ } ++ else if (0 == _M_buf_count) ++ _M_prefix->append(__s, __s + __len); ++ else ++ { ++ flush(); ++ append(__s, __len); ++ } ++ } ++ ++ sequence_buffer& ++ write(value_type* __s, size_t __len) ++ { ++ append(__s, __len); ++ return *this; ++ } ++ ++ sequence_buffer& ++ put(value_type __x) ++ { ++ push_back(__x); ++ return *this; ++ } ++ ++ sequence_buffer& ++ operator=(const value_type& __rhs) ++ { ++ push_back(__rhs); ++ return *this; ++ } ++ ++ sequence_buffer& ++ operator*() ++ { return *this; } ++ ++ sequence_buffer& ++ operator++() ++ { return *this; } ++ ++ sequence_buffer ++ operator++(int) ++ { return *this; } ++ }; ++ ++ // The following should be treated as private, at least for now. ++ template ++ class _Rope_char_consumer ++ { ++ public: ++ // If we had member templates, these should not be virtual. ++ // For now we need to use run-time parametrization where ++ // compile-time would do. Hence this should all be private ++ // for now. ++ // The symmetry with char_producer is accidental and temporary. ++ virtual ~_Rope_char_consumer() { }; ++ ++ virtual bool ++ operator()(const _CharT* __buffer, size_t __len) = 0; ++ }; ++ ++ // First a lot of forward declarations. The standard seems to require ++ // much stricter "declaration before use" than many of the implementations ++ // that preceded it. ++ template > ++ class rope; ++ ++ template ++ struct _Rope_RopeConcatenation; ++ ++ template ++ struct _Rope_RopeLeaf; ++ ++ template ++ struct _Rope_RopeFunction; ++ ++ template ++ struct _Rope_RopeSubstring; ++ ++ template ++ class _Rope_iterator; ++ ++ template ++ class _Rope_const_iterator; ++ ++ template ++ class _Rope_char_ref_proxy; ++ ++ template ++ class _Rope_char_ptr_proxy; ++ ++ template ++ bool ++ operator==(const _Rope_char_ptr_proxy<_CharT, _Alloc>& __x, ++ const _Rope_char_ptr_proxy<_CharT, _Alloc>& __y); ++ ++ template ++ _Rope_const_iterator<_CharT, _Alloc> ++ operator-(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ ptrdiff_t __n); ++ ++ template ++ _Rope_const_iterator<_CharT, _Alloc> ++ operator+(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ ptrdiff_t __n); ++ ++ template ++ _Rope_const_iterator<_CharT, _Alloc> ++ operator+(ptrdiff_t __n, ++ const _Rope_const_iterator<_CharT, _Alloc>& __x); ++ ++ template ++ bool ++ operator==(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y); ++ ++ template ++ bool ++ operator<(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y); ++ ++ template ++ ptrdiff_t ++ operator-(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y); ++ ++ template ++ _Rope_iterator<_CharT, _Alloc> ++ operator-(const _Rope_iterator<_CharT, _Alloc>& __x, ptrdiff_t __n); ++ ++ template ++ _Rope_iterator<_CharT, _Alloc> ++ operator+(const _Rope_iterator<_CharT, _Alloc>& __x, ptrdiff_t __n); ++ ++ template ++ _Rope_iterator<_CharT, _Alloc> ++ operator+(ptrdiff_t __n, const _Rope_iterator<_CharT, _Alloc>& __x); ++ ++ template ++ bool ++ operator==(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y); ++ ++ template ++ bool ++ operator<(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y); ++ ++ template ++ ptrdiff_t ++ operator-(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y); ++ ++ template ++ rope<_CharT, _Alloc> ++ operator+(const rope<_CharT, _Alloc>& __left, ++ const rope<_CharT, _Alloc>& __right); ++ ++ template ++ rope<_CharT, _Alloc> ++ operator+(const rope<_CharT, _Alloc>& __left, const _CharT* __right); ++ ++ template ++ rope<_CharT, _Alloc> ++ operator+(const rope<_CharT, _Alloc>& __left, _CharT __right); ++ ++ // Some helpers, so we can use power on ropes. ++ // See below for why this isn't local to the implementation. ++ ++ // This uses a nonstandard refcount convention. ++ // The result has refcount 0. ++ template ++ struct _Rope_Concat_fn ++ : public std::binary_function, rope<_CharT, _Alloc>, ++ rope<_CharT, _Alloc> > ++ { ++ rope<_CharT, _Alloc> ++ operator()(const rope<_CharT, _Alloc>& __x, ++ const rope<_CharT, _Alloc>& __y) ++ { return __x + __y; } ++ }; ++ ++ template ++ inline rope<_CharT, _Alloc> ++ identity_element(_Rope_Concat_fn<_CharT, _Alloc>) ++ { return rope<_CharT, _Alloc>(); } ++ ++ // Class _Refcount_Base provides a type, _RC_t, a data member, ++ // _M_ref_count, and member functions _M_incr and _M_decr, which perform ++ // atomic preincrement/predecrement. The constructor initializes ++ // _M_ref_count. ++ struct _Refcount_Base ++ { ++ // The type _RC_t ++ typedef size_t _RC_t; ++ ++ // The data member _M_ref_count ++ volatile _RC_t _M_ref_count; ++ ++ // Constructor ++ __gthread_mutex_t _M_ref_count_lock; ++ ++ _Refcount_Base(_RC_t __n) : _M_ref_count(__n), _M_ref_count_lock() ++ { ++#ifdef __GTHREAD_MUTEX_INIT ++ __gthread_mutex_t __tmp = __GTHREAD_MUTEX_INIT; ++ _M_ref_count_lock = __tmp; ++#elif defined(__GTHREAD_MUTEX_INIT_FUNCTION) ++ __GTHREAD_MUTEX_INIT_FUNCTION (&_M_ref_count_lock); ++#else ++#error __GTHREAD_MUTEX_INIT or __GTHREAD_MUTEX_INIT_FUNCTION should be defined by gthr.h abstraction layer, report problem to libstdc++@gcc.gnu.org. ++#endif ++ } ++ ++ void ++ _M_incr() ++ { ++ __gthread_mutex_lock(&_M_ref_count_lock); ++ ++_M_ref_count; ++ __gthread_mutex_unlock(&_M_ref_count_lock); ++ } ++ ++ _RC_t ++ _M_decr() ++ { ++ __gthread_mutex_lock(&_M_ref_count_lock); ++ volatile _RC_t __tmp = --_M_ref_count; ++ __gthread_mutex_unlock(&_M_ref_count_lock); ++ return __tmp; ++ } ++ }; ++ ++ // ++ // What follows should really be local to rope. Unfortunately, ++ // that doesn't work, since it makes it impossible to define generic ++ // equality on rope iterators. According to the draft standard, the ++ // template parameters for such an equality operator cannot be inferred ++ // from the occurrence of a member class as a parameter. ++ // (SGI compilers in fact allow this, but the __result wouldn't be ++ // portable.) ++ // Similarly, some of the static member functions are member functions ++ // only to avoid polluting the global namespace, and to circumvent ++ // restrictions on type inference for template functions. ++ // ++ ++ // ++ // The internal data structure for representing a rope. This is ++ // private to the implementation. A rope is really just a pointer ++ // to one of these. ++ // ++ // A few basic functions for manipulating this data structure ++ // are members of _RopeRep. Most of the more complex algorithms ++ // are implemented as rope members. ++ // ++ // Some of the static member functions of _RopeRep have identically ++ // named functions in rope that simply invoke the _RopeRep versions. ++ ++#define __ROPE_DEFINE_ALLOCS(__a) \ ++ __ROPE_DEFINE_ALLOC(_CharT,_Data) /* character data */ \ ++ typedef _Rope_RopeConcatenation<_CharT,__a> __C; \ ++ __ROPE_DEFINE_ALLOC(__C,_C) \ ++ typedef _Rope_RopeLeaf<_CharT,__a> __L; \ ++ __ROPE_DEFINE_ALLOC(__L,_L) \ ++ typedef _Rope_RopeFunction<_CharT,__a> __F; \ ++ __ROPE_DEFINE_ALLOC(__F,_F) \ ++ typedef _Rope_RopeSubstring<_CharT,__a> __S; \ ++ __ROPE_DEFINE_ALLOC(__S,_S) ++ ++ // Internal rope nodes potentially store a copy of the allocator ++ // instance used to allocate them. This is mostly redundant. ++ // But the alternative would be to pass allocator instances around ++ // in some form to nearly all internal functions, since any pointer ++ // assignment may result in a zero reference count and thus require ++ // deallocation. ++ ++#define __STATIC_IF_SGI_ALLOC /* not static */ ++ ++ template ++ struct _Rope_rep_base ++ : public _Alloc ++ { ++ typedef _Alloc allocator_type; ++ ++ allocator_type ++ get_allocator() const ++ { return *static_cast(this); } ++ ++ allocator_type& ++ _M_get_allocator() ++ { return *static_cast<_Alloc*>(this); } ++ ++ const allocator_type& ++ _M_get_allocator() const ++ { return *static_cast(this); } ++ ++ _Rope_rep_base(size_t __size, const allocator_type&) ++ : _M_size(__size) { } ++ ++ size_t _M_size; ++ ++# define __ROPE_DEFINE_ALLOC(_Tp, __name) \ ++ typedef typename \ ++ _Alloc::template rebind<_Tp>::other __name##Alloc; \ ++ static _Tp* __name##_allocate(size_t __n) \ ++ { return __name##Alloc().allocate(__n); } \ ++ static void __name##_deallocate(_Tp *__p, size_t __n) \ ++ { __name##Alloc().deallocate(__p, __n); } ++ __ROPE_DEFINE_ALLOCS(_Alloc) ++# undef __ROPE_DEFINE_ALLOC ++ }; ++ ++ template ++ struct _Rope_RopeRep ++ : public _Rope_rep_base<_CharT, _Alloc> ++# ifndef __GC ++ , _Refcount_Base ++# endif ++ { ++ public: ++ __detail::_Tag _M_tag:8; ++ bool _M_is_balanced:8; ++ unsigned char _M_depth; ++ __GC_CONST _CharT* _M_c_string; ++ __gthread_mutex_t _M_c_string_lock; ++ /* Flattened version of string, if needed. */ ++ /* typically 0. */ ++ /* If it's not 0, then the memory is owned */ ++ /* by this node. */ ++ /* In the case of a leaf, this may point to */ ++ /* the same memory as the data field. */ ++ typedef typename _Rope_rep_base<_CharT, _Alloc>::allocator_type ++ allocator_type; ++ ++ using _Rope_rep_base<_CharT, _Alloc>::get_allocator; ++ using _Rope_rep_base<_CharT, _Alloc>::_M_get_allocator; ++ ++ _Rope_RopeRep(__detail::_Tag __t, int __d, bool __b, size_t __size, ++ const allocator_type& __a) ++ : _Rope_rep_base<_CharT, _Alloc>(__size, __a), ++#ifndef __GC ++ _Refcount_Base(1), ++#endif ++ _M_tag(__t), _M_is_balanced(__b), _M_depth(__d), _M_c_string(0) ++#ifdef __GTHREAD_MUTEX_INIT ++ { ++ // Do not copy a POSIX/gthr mutex once in use. However, bits are bits. ++ __gthread_mutex_t __tmp = __GTHREAD_MUTEX_INIT; ++ _M_c_string_lock = __tmp; ++ } ++#else ++ { __GTHREAD_MUTEX_INIT_FUNCTION (&_M_c_string_lock); } ++#endif ++#ifdef __GC ++ void ++ _M_incr () { } ++#endif ++ static void ++ _S_free_string(__GC_CONST _CharT*, size_t __len, ++ allocator_type& __a); ++#define __STL_FREE_STRING(__s, __l, __a) _S_free_string(__s, __l, __a); ++ // Deallocate data section of a leaf. ++ // This shouldn't be a member function. ++ // But its hard to do anything else at the ++ // moment, because it's templatized w.r.t. ++ // an allocator. ++ // Does nothing if __GC is defined. ++#ifndef __GC ++ void _M_free_c_string(); ++ void _M_free_tree(); ++ // Deallocate t. Assumes t is not 0. ++ void ++ _M_unref_nonnil() ++ { ++ if (0 == _M_decr()) ++ _M_free_tree(); ++ } ++ ++ void ++ _M_ref_nonnil() ++ { _M_incr(); } ++ ++ static void ++ _S_unref(_Rope_RopeRep* __t) ++ { ++ if (0 != __t) ++ __t->_M_unref_nonnil(); ++ } ++ ++ static void ++ _S_ref(_Rope_RopeRep* __t) ++ { ++ if (0 != __t) ++ __t->_M_incr(); ++ } ++ ++ static void ++ _S_free_if_unref(_Rope_RopeRep* __t) ++ { ++ if (0 != __t && 0 == __t->_M_ref_count) ++ __t->_M_free_tree(); ++ } ++# else /* __GC */ ++ void _M_unref_nonnil() { } ++ void _M_ref_nonnil() { } ++ static void _S_unref(_Rope_RopeRep*) { } ++ static void _S_ref(_Rope_RopeRep*) { } ++ static void _S_free_if_unref(_Rope_RopeRep*) { } ++# endif ++protected: ++ _Rope_RopeRep& ++ operator=(const _Rope_RopeRep&); ++ ++ _Rope_RopeRep(const _Rope_RopeRep&); ++ }; ++ ++ template ++ struct _Rope_RopeLeaf ++ : public _Rope_RopeRep<_CharT, _Alloc> ++ { ++ public: ++ // Apparently needed by VC++ ++ // The data fields of leaves are allocated with some ++ // extra space, to accommodate future growth and for basic ++ // character types, to hold a trailing eos character. ++ enum { _S_alloc_granularity = 8 }; ++ ++ static size_t ++ _S_rounded_up_size(size_t __n) ++ { ++ size_t __size_with_eos; ++ ++ if (_S_is_basic_char_type((_CharT*)0)) ++ __size_with_eos = __n + 1; ++ else ++ __size_with_eos = __n; ++#ifdef __GC ++ return __size_with_eos; ++#else ++ // Allow slop for in-place expansion. ++ return ((__size_with_eos + size_t(_S_alloc_granularity) - 1) ++ &~ (size_t(_S_alloc_granularity) - 1)); ++#endif ++ } ++ __GC_CONST _CharT* _M_data; /* Not necessarily 0 terminated. */ ++ /* The allocated size is */ ++ /* _S_rounded_up_size(size), except */ ++ /* in the GC case, in which it */ ++ /* doesn't matter. */ ++ typedef typename _Rope_rep_base<_CharT,_Alloc>::allocator_type ++ allocator_type; ++ ++ _Rope_RopeLeaf(__GC_CONST _CharT* __d, size_t __size, ++ const allocator_type& __a) ++ : _Rope_RopeRep<_CharT, _Alloc>(__detail::_S_leaf, 0, true, ++ __size, __a), _M_data(__d) ++ { ++ if (_S_is_basic_char_type((_CharT *)0)) ++ { ++ // already eos terminated. ++ this->_M_c_string = __d; ++ } ++ } ++ // The constructor assumes that d has been allocated with ++ // the proper allocator and the properly padded size. ++ // In contrast, the destructor deallocates the data: ++#ifndef __GC ++ ~_Rope_RopeLeaf() throw() ++ { ++ if (_M_data != this->_M_c_string) ++ this->_M_free_c_string(); ++ ++ __STL_FREE_STRING(_M_data, this->_M_size, this->_M_get_allocator()); ++ } ++#endif ++protected: ++ _Rope_RopeLeaf& ++ operator=(const _Rope_RopeLeaf&); ++ ++ _Rope_RopeLeaf(const _Rope_RopeLeaf&); ++ }; ++ ++ template ++ struct _Rope_RopeConcatenation ++ : public _Rope_RopeRep<_CharT, _Alloc> ++ { ++ public: ++ _Rope_RopeRep<_CharT, _Alloc>* _M_left; ++ _Rope_RopeRep<_CharT, _Alloc>* _M_right; ++ ++ typedef typename _Rope_rep_base<_CharT, _Alloc>::allocator_type ++ allocator_type; ++ ++ _Rope_RopeConcatenation(_Rope_RopeRep<_CharT, _Alloc>* __l, ++ _Rope_RopeRep<_CharT, _Alloc>* __r, ++ const allocator_type& __a) ++ : _Rope_RopeRep<_CharT, _Alloc>(__detail::_S_concat, ++ std::max(__l->_M_depth, ++ __r->_M_depth) + 1, ++ false, ++ __l->_M_size + __r->_M_size, __a), ++ _M_left(__l), _M_right(__r) ++ { } ++#ifndef __GC ++ ~_Rope_RopeConcatenation() throw() ++ { ++ this->_M_free_c_string(); ++ _M_left->_M_unref_nonnil(); ++ _M_right->_M_unref_nonnil(); ++ } ++#endif ++protected: ++ _Rope_RopeConcatenation& ++ operator=(const _Rope_RopeConcatenation&); ++ ++ _Rope_RopeConcatenation(const _Rope_RopeConcatenation&); ++ }; ++ ++ template ++ struct _Rope_RopeFunction ++ : public _Rope_RopeRep<_CharT, _Alloc> ++ { ++ public: ++ char_producer<_CharT>* _M_fn; ++#ifndef __GC ++ bool _M_delete_when_done; // Char_producer is owned by the ++ // rope and should be explicitly ++ // deleted when the rope becomes ++ // inaccessible. ++#else ++ // In the GC case, we either register the rope for ++ // finalization, or not. Thus the field is unnecessary; ++ // the information is stored in the collector data structures. ++ // We do need a finalization procedure to be invoked by the ++ // collector. ++ static void ++ _S_fn_finalization_proc(void * __tree, void *) ++ { delete ((_Rope_RopeFunction *)__tree) -> _M_fn; } ++#endif ++ typedef typename _Rope_rep_base<_CharT, _Alloc>::allocator_type ++ allocator_type; ++ ++ _Rope_RopeFunction(char_producer<_CharT>* __f, size_t __size, ++ bool __d, const allocator_type& __a) ++ : _Rope_RopeRep<_CharT, _Alloc>(__detail::_S_function, 0, true, __size, __a) ++ , _M_fn(__f) ++#ifndef __GC ++ , _M_delete_when_done(__d) ++#endif ++ { ++#ifdef __GC ++ if (__d) ++ { ++ GC_REGISTER_FINALIZER(this, _Rope_RopeFunction:: ++ _S_fn_finalization_proc, 0, 0, 0); ++ } ++#endif ++ } ++#ifndef __GC ++ ~_Rope_RopeFunction() throw() ++ { ++ this->_M_free_c_string(); ++ if (_M_delete_when_done) ++ delete _M_fn; ++ } ++# endif ++ protected: ++ _Rope_RopeFunction& ++ operator=(const _Rope_RopeFunction&); ++ ++ _Rope_RopeFunction(const _Rope_RopeFunction&); ++ }; ++ // Substring results are usually represented using just ++ // concatenation nodes. But in the case of very long flat ropes ++ // or ropes with a functional representation that isn't practical. ++ // In that case, we represent the __result as a special case of ++ // RopeFunction, whose char_producer points back to the rope itself. ++ // In all cases except repeated substring operations and ++ // deallocation, we treat the __result as a RopeFunction. ++ template ++ struct _Rope_RopeSubstring ++ : public _Rope_RopeFunction<_CharT, _Alloc>, ++ public char_producer<_CharT> ++ { ++ public: ++ // XXX this whole class should be rewritten. ++ _Rope_RopeRep<_CharT,_Alloc>* _M_base; // not 0 ++ size_t _M_start; ++ ++ virtual void ++ operator()(size_t __start_pos, size_t __req_len, ++ _CharT* __buffer) ++ { ++ switch(_M_base->_M_tag) ++ { ++ case __detail::_S_function: ++ case __detail::_S_substringfn: ++ { ++ char_producer<_CharT>* __fn = ++ ((_Rope_RopeFunction<_CharT,_Alloc>*)_M_base)->_M_fn; ++ (*__fn)(__start_pos + _M_start, __req_len, __buffer); ++ } ++ break; ++ case __detail::_S_leaf: ++ { ++ __GC_CONST _CharT* __s = ++ ((_Rope_RopeLeaf<_CharT,_Alloc>*)_M_base)->_M_data; ++ uninitialized_copy_n(__s + __start_pos + _M_start, __req_len, ++ __buffer); ++ } ++ break; ++ default: ++ break; ++ } ++ } ++ ++ typedef typename _Rope_rep_base<_CharT, _Alloc>::allocator_type ++ allocator_type; ++ ++ _Rope_RopeSubstring(_Rope_RopeRep<_CharT, _Alloc>* __b, size_t __s, ++ size_t __l, const allocator_type& __a) ++ : _Rope_RopeFunction<_CharT, _Alloc>(this, __l, false, __a), ++ char_producer<_CharT>(), _M_base(__b), _M_start(__s) ++ { ++#ifndef __GC ++ _M_base->_M_ref_nonnil(); ++#endif ++ this->_M_tag = __detail::_S_substringfn; ++ } ++ virtual ~_Rope_RopeSubstring() throw() ++ { ++#ifndef __GC ++ _M_base->_M_unref_nonnil(); ++ // _M_free_c_string(); -- done by parent class ++#endif ++ } ++ }; ++ ++ // Self-destructing pointers to Rope_rep. ++ // These are not conventional smart pointers. Their ++ // only purpose in life is to ensure that unref is called ++ // on the pointer either at normal exit or if an exception ++ // is raised. It is the caller's responsibility to ++ // adjust reference counts when these pointers are initialized ++ // or assigned to. (This convention significantly reduces ++ // the number of potentially expensive reference count ++ // updates.) ++#ifndef __GC ++ template ++ struct _Rope_self_destruct_ptr ++ { ++ _Rope_RopeRep<_CharT, _Alloc>* _M_ptr; ++ ++ ~_Rope_self_destruct_ptr() ++ { _Rope_RopeRep<_CharT, _Alloc>::_S_unref(_M_ptr); } ++#ifdef __EXCEPTIONS ++ _Rope_self_destruct_ptr() : _M_ptr(0) { }; ++#else ++ _Rope_self_destruct_ptr() { }; ++#endif ++ _Rope_self_destruct_ptr(_Rope_RopeRep<_CharT, _Alloc>* __p) ++ : _M_ptr(__p) { } ++ ++ _Rope_RopeRep<_CharT, _Alloc>& ++ operator*() ++ { return *_M_ptr; } ++ ++ _Rope_RopeRep<_CharT, _Alloc>* ++ operator->() ++ { return _M_ptr; } ++ ++ operator _Rope_RopeRep<_CharT, _Alloc>*() ++ { return _M_ptr; } ++ ++ _Rope_self_destruct_ptr& ++ operator=(_Rope_RopeRep<_CharT, _Alloc>* __x) ++ { _M_ptr = __x; return *this; } ++ }; ++#endif ++ ++ // Dereferencing a nonconst iterator has to return something ++ // that behaves almost like a reference. It's not possible to ++ // return an actual reference since assignment requires extra ++ // work. And we would get into the same problems as with the ++ // CD2 version of basic_string. ++ template ++ class _Rope_char_ref_proxy ++ { ++ friend class rope<_CharT, _Alloc>; ++ friend class _Rope_iterator<_CharT, _Alloc>; ++ friend class _Rope_char_ptr_proxy<_CharT, _Alloc>; ++#ifdef __GC ++ typedef _Rope_RopeRep<_CharT, _Alloc>* _Self_destruct_ptr; ++#else ++ typedef _Rope_self_destruct_ptr<_CharT, _Alloc> _Self_destruct_ptr; ++#endif ++ typedef _Rope_RopeRep<_CharT, _Alloc> _RopeRep; ++ typedef rope<_CharT, _Alloc> _My_rope; ++ size_t _M_pos; ++ _CharT _M_current; ++ bool _M_current_valid; ++ _My_rope* _M_root; // The whole rope. ++ public: ++ _Rope_char_ref_proxy(_My_rope* __r, size_t __p) ++ : _M_pos(__p), _M_current(), _M_current_valid(false), _M_root(__r) { } ++ ++ _Rope_char_ref_proxy(const _Rope_char_ref_proxy& __x) ++ : _M_pos(__x._M_pos), _M_current(__x._M_current), ++ _M_current_valid(false), _M_root(__x._M_root) { } ++ ++ // Don't preserve cache if the reference can outlive the ++ // expression. We claim that's not possible without calling ++ // a copy constructor or generating reference to a proxy ++ // reference. We declare the latter to have undefined semantics. ++ _Rope_char_ref_proxy(_My_rope* __r, size_t __p, _CharT __c) ++ : _M_pos(__p), _M_current(__c), _M_current_valid(true), _M_root(__r) { } ++ ++ inline operator _CharT () const; ++ ++ _Rope_char_ref_proxy& ++ operator=(_CharT __c); ++ ++ _Rope_char_ptr_proxy<_CharT, _Alloc> operator&() const; ++ ++ _Rope_char_ref_proxy& ++ operator=(const _Rope_char_ref_proxy& __c) ++ { return operator=((_CharT)__c); } ++ }; ++ ++ template ++ inline void ++ swap(_Rope_char_ref_proxy <_CharT, __Alloc > __a, ++ _Rope_char_ref_proxy <_CharT, __Alloc > __b) ++ { ++ _CharT __tmp = __a; ++ __a = __b; ++ __b = __tmp; ++ } ++ ++ template ++ class _Rope_char_ptr_proxy ++ { ++ // XXX this class should be rewritten. ++ friend class _Rope_char_ref_proxy<_CharT, _Alloc>; ++ size_t _M_pos; ++ rope<_CharT,_Alloc>* _M_root; // The whole rope. ++ public: ++ _Rope_char_ptr_proxy(const _Rope_char_ref_proxy<_CharT,_Alloc>& __x) ++ : _M_pos(__x._M_pos), _M_root(__x._M_root) { } ++ ++ _Rope_char_ptr_proxy(const _Rope_char_ptr_proxy& __x) ++ : _M_pos(__x._M_pos), _M_root(__x._M_root) { } ++ ++ _Rope_char_ptr_proxy() { } ++ ++ _Rope_char_ptr_proxy(_CharT* __x) ++ : _M_root(0), _M_pos(0) { } ++ ++ _Rope_char_ptr_proxy& ++ operator=(const _Rope_char_ptr_proxy& __x) ++ { ++ _M_pos = __x._M_pos; ++ _M_root = __x._M_root; ++ return *this; ++ } ++ ++ template ++ friend bool ++ operator==(const _Rope_char_ptr_proxy<_CharT2, _Alloc2>& __x, ++ const _Rope_char_ptr_proxy<_CharT2, _Alloc2>& __y); ++ ++ _Rope_char_ref_proxy<_CharT, _Alloc> operator*() const ++ { return _Rope_char_ref_proxy<_CharT, _Alloc>(_M_root, _M_pos); } ++ }; ++ ++ // Rope iterators: ++ // Unlike in the C version, we cache only part of the stack ++ // for rope iterators, since they must be efficiently copyable. ++ // When we run out of cache, we have to reconstruct the iterator ++ // value. ++ // Pointers from iterators are not included in reference counts. ++ // Iterators are assumed to be thread private. Ropes can ++ // be shared. ++ ++ template ++ class _Rope_iterator_base ++ : public std::iterator ++ { ++ friend class rope<_CharT, _Alloc>; ++ public: ++ typedef _Alloc _allocator_type; // used in _Rope_rotate, VC++ workaround ++ typedef _Rope_RopeRep<_CharT, _Alloc> _RopeRep; ++ // Borland doesn't want this to be protected. ++ protected: ++ enum { _S_path_cache_len = 4 }; // Must be <= 9. ++ enum { _S_iterator_buf_len = 15 }; ++ size_t _M_current_pos; ++ _RopeRep* _M_root; // The whole rope. ++ size_t _M_leaf_pos; // Starting position for current leaf ++ __GC_CONST _CharT* _M_buf_start; ++ // Buffer possibly ++ // containing current char. ++ __GC_CONST _CharT* _M_buf_ptr; ++ // Pointer to current char in buffer. ++ // != 0 ==> buffer valid. ++ __GC_CONST _CharT* _M_buf_end; ++ // One past __last valid char in buffer. ++ // What follows is the path cache. We go out of our ++ // way to make this compact. ++ // Path_end contains the bottom section of the path from ++ // the root to the current leaf. ++ const _RopeRep* _M_path_end[_S_path_cache_len]; ++ int _M_leaf_index; // Last valid __pos in path_end; ++ // _M_path_end[0] ... _M_path_end[leaf_index-1] ++ // point to concatenation nodes. ++ unsigned char _M_path_directions; ++ // (path_directions >> __i) & 1 is 1 ++ // iff we got from _M_path_end[leaf_index - __i - 1] ++ // to _M_path_end[leaf_index - __i] by going to the ++ // __right. Assumes path_cache_len <= 9. ++ _CharT _M_tmp_buf[_S_iterator_buf_len]; ++ // Short buffer for surrounding chars. ++ // This is useful primarily for ++ // RopeFunctions. We put the buffer ++ // here to avoid locking in the ++ // multithreaded case. ++ // The cached path is generally assumed to be valid ++ // only if the buffer is valid. ++ static void _S_setbuf(_Rope_iterator_base& __x); ++ // Set buffer contents given ++ // path cache. ++ static void _S_setcache(_Rope_iterator_base& __x); ++ // Set buffer contents and ++ // path cache. ++ static void _S_setcache_for_incr(_Rope_iterator_base& __x); ++ // As above, but assumes path ++ // cache is valid for previous posn. ++ _Rope_iterator_base() { } ++ ++ _Rope_iterator_base(_RopeRep* __root, size_t __pos) ++ : _M_current_pos(__pos), _M_root(__root), _M_buf_ptr(0) { } ++ ++ void _M_incr(size_t __n); ++ void _M_decr(size_t __n); ++ public: ++ size_t ++ index() const ++ { return _M_current_pos; } ++ ++ _Rope_iterator_base(const _Rope_iterator_base& __x) ++ { ++ if (0 != __x._M_buf_ptr) ++ *this = __x; ++ else ++ { ++ _M_current_pos = __x._M_current_pos; ++ _M_root = __x._M_root; ++ _M_buf_ptr = 0; ++ } ++ } ++ }; ++ ++ template ++ class _Rope_iterator; ++ ++ template ++ class _Rope_const_iterator ++ : public _Rope_iterator_base<_CharT, _Alloc> ++ { ++ friend class rope<_CharT, _Alloc>; ++ protected: ++ typedef _Rope_RopeRep<_CharT, _Alloc> _RopeRep; ++ // The one from the base class may not be directly visible. ++ _Rope_const_iterator(const _RopeRep* __root, size_t __pos) ++ : _Rope_iterator_base<_CharT, _Alloc>(const_cast<_RopeRep*>(__root), ++ __pos) ++ // Only nonconst iterators modify root ref count ++ { } ++ public: ++ typedef _CharT reference; // Really a value. Returning a reference ++ // Would be a mess, since it would have ++ // to be included in refcount. ++ typedef const _CharT* pointer; ++ ++ public: ++ _Rope_const_iterator() { }; ++ ++ _Rope_const_iterator(const _Rope_const_iterator& __x) ++ : _Rope_iterator_base<_CharT,_Alloc>(__x) { } ++ ++ _Rope_const_iterator(const _Rope_iterator<_CharT,_Alloc>& __x); ++ ++ _Rope_const_iterator(const rope<_CharT, _Alloc>& __r, size_t __pos) ++ : _Rope_iterator_base<_CharT,_Alloc>(__r._M_tree_ptr, __pos) { } ++ ++ _Rope_const_iterator& ++ operator=(const _Rope_const_iterator& __x) ++ { ++ if (0 != __x._M_buf_ptr) ++ *(static_cast<_Rope_iterator_base<_CharT, _Alloc>*>(this)) = __x; ++ else ++ { ++ this->_M_current_pos = __x._M_current_pos; ++ this->_M_root = __x._M_root; ++ this->_M_buf_ptr = 0; ++ } ++ return(*this); ++ } ++ ++ reference ++ operator*() ++ { ++ if (0 == this->_M_buf_ptr) ++ _S_setcache(*this); ++ return *this->_M_buf_ptr; ++ } ++ ++ // Without this const version, Rope iterators do not meet the ++ // requirements of an Input Iterator. ++ reference ++ operator*() const ++ { ++ return *const_cast<_Rope_const_iterator&>(*this); ++ } ++ ++ _Rope_const_iterator& ++ operator++() ++ { ++ __GC_CONST _CharT* __next; ++ if (0 != this->_M_buf_ptr ++ && (__next = this->_M_buf_ptr + 1) < this->_M_buf_end) ++ { ++ this->_M_buf_ptr = __next; ++ ++this->_M_current_pos; ++ } ++ else ++ this->_M_incr(1); ++ return *this; ++ } ++ ++ _Rope_const_iterator& ++ operator+=(ptrdiff_t __n) ++ { ++ if (__n >= 0) ++ this->_M_incr(__n); ++ else ++ this->_M_decr(-__n); ++ return *this; ++ } ++ ++ _Rope_const_iterator& ++ operator--() ++ { ++ this->_M_decr(1); ++ return *this; ++ } ++ ++ _Rope_const_iterator& ++ operator-=(ptrdiff_t __n) ++ { ++ if (__n >= 0) ++ this->_M_decr(__n); ++ else ++ this->_M_incr(-__n); ++ return *this; ++ } ++ ++ _Rope_const_iterator ++ operator++(int) ++ { ++ size_t __old_pos = this->_M_current_pos; ++ this->_M_incr(1); ++ return _Rope_const_iterator<_CharT,_Alloc>(this->_M_root, __old_pos); ++ // This makes a subsequent dereference expensive. ++ // Perhaps we should instead copy the iterator ++ // if it has a valid cache? ++ } ++ ++ _Rope_const_iterator ++ operator--(int) ++ { ++ size_t __old_pos = this->_M_current_pos; ++ this->_M_decr(1); ++ return _Rope_const_iterator<_CharT,_Alloc>(this->_M_root, __old_pos); ++ } ++ ++ template ++ friend _Rope_const_iterator<_CharT2, _Alloc2> ++ operator-(const _Rope_const_iterator<_CharT2, _Alloc2>& __x, ++ ptrdiff_t __n); ++ ++ template ++ friend _Rope_const_iterator<_CharT2, _Alloc2> ++ operator+(const _Rope_const_iterator<_CharT2, _Alloc2>& __x, ++ ptrdiff_t __n); ++ ++ template ++ friend _Rope_const_iterator<_CharT2, _Alloc2> ++ operator+(ptrdiff_t __n, ++ const _Rope_const_iterator<_CharT2, _Alloc2>& __x); ++ ++ reference ++ operator[](size_t __n) ++ { return rope<_CharT, _Alloc>::_S_fetch(this->_M_root, ++ this->_M_current_pos + __n); } ++ ++ template ++ friend bool ++ operator==(const _Rope_const_iterator<_CharT2, _Alloc2>& __x, ++ const _Rope_const_iterator<_CharT2, _Alloc2>& __y); ++ ++ template ++ friend bool ++ operator<(const _Rope_const_iterator<_CharT2, _Alloc2>& __x, ++ const _Rope_const_iterator<_CharT2, _Alloc2>& __y); ++ ++ template ++ friend ptrdiff_t ++ operator-(const _Rope_const_iterator<_CharT2, _Alloc2>& __x, ++ const _Rope_const_iterator<_CharT2, _Alloc2>& __y); ++ }; ++ ++ template ++ class _Rope_iterator ++ : public _Rope_iterator_base<_CharT, _Alloc> ++ { ++ friend class rope<_CharT, _Alloc>; ++ protected: ++ typedef typename _Rope_iterator_base<_CharT, _Alloc>::_RopeRep _RopeRep; ++ rope<_CharT, _Alloc>* _M_root_rope; ++ ++ // root is treated as a cached version of this, and is used to ++ // detect changes to the underlying rope. ++ ++ // Root is included in the reference count. This is necessary ++ // so that we can detect changes reliably. Unfortunately, it ++ // requires careful bookkeeping for the nonGC case. ++ _Rope_iterator(rope<_CharT, _Alloc>* __r, size_t __pos) ++ : _Rope_iterator_base<_CharT, _Alloc>(__r->_M_tree_ptr, __pos), ++ _M_root_rope(__r) ++ { _RopeRep::_S_ref(this->_M_root); ++ if (!(__r -> empty())) ++ _S_setcache(*this); ++ } ++ ++ void _M_check(); ++ public: ++ typedef _Rope_char_ref_proxy<_CharT, _Alloc> reference; ++ typedef _Rope_char_ref_proxy<_CharT, _Alloc>* pointer; ++ ++ rope<_CharT, _Alloc>& ++ container() ++ { return *_M_root_rope; } ++ ++ _Rope_iterator() ++ { ++ this->_M_root = 0; // Needed for reference counting. ++ }; ++ ++ _Rope_iterator(const _Rope_iterator& __x) ++ : _Rope_iterator_base<_CharT, _Alloc>(__x) ++ { ++ _M_root_rope = __x._M_root_rope; ++ _RopeRep::_S_ref(this->_M_root); ++ } ++ ++ _Rope_iterator(rope<_CharT, _Alloc>& __r, size_t __pos); ++ ++ ~_Rope_iterator() ++ { _RopeRep::_S_unref(this->_M_root); } ++ ++ _Rope_iterator& ++ operator=(const _Rope_iterator& __x) ++ { ++ _RopeRep* __old = this->_M_root; ++ ++ _RopeRep::_S_ref(__x._M_root); ++ if (0 != __x._M_buf_ptr) ++ { ++ _M_root_rope = __x._M_root_rope; ++ *(static_cast<_Rope_iterator_base<_CharT, _Alloc>*>(this)) = __x; ++ } ++ else ++ { ++ this->_M_current_pos = __x._M_current_pos; ++ this->_M_root = __x._M_root; ++ _M_root_rope = __x._M_root_rope; ++ this->_M_buf_ptr = 0; ++ } ++ _RopeRep::_S_unref(__old); ++ return(*this); ++ } ++ ++ reference ++ operator*() ++ { ++ _M_check(); ++ if (0 == this->_M_buf_ptr) ++ return _Rope_char_ref_proxy<_CharT, _Alloc>(_M_root_rope, ++ this->_M_current_pos); ++ else ++ return _Rope_char_ref_proxy<_CharT, _Alloc>(_M_root_rope, ++ this->_M_current_pos, ++ *this->_M_buf_ptr); ++ } ++ ++ // See above comment. ++ reference ++ operator*() const ++ { ++ return *const_cast<_Rope_iterator&>(*this); ++ } ++ ++ _Rope_iterator& ++ operator++() ++ { ++ this->_M_incr(1); ++ return *this; ++ } ++ ++ _Rope_iterator& ++ operator+=(ptrdiff_t __n) ++ { ++ if (__n >= 0) ++ this->_M_incr(__n); ++ else ++ this->_M_decr(-__n); ++ return *this; ++ } ++ ++ _Rope_iterator& ++ operator--() ++ { ++ this->_M_decr(1); ++ return *this; ++ } ++ ++ _Rope_iterator& ++ operator-=(ptrdiff_t __n) ++ { ++ if (__n >= 0) ++ this->_M_decr(__n); ++ else ++ this->_M_incr(-__n); ++ return *this; ++ } ++ ++ _Rope_iterator ++ operator++(int) ++ { ++ size_t __old_pos = this->_M_current_pos; ++ this->_M_incr(1); ++ return _Rope_iterator<_CharT,_Alloc>(_M_root_rope, __old_pos); ++ } ++ ++ _Rope_iterator ++ operator--(int) ++ { ++ size_t __old_pos = this->_M_current_pos; ++ this->_M_decr(1); ++ return _Rope_iterator<_CharT,_Alloc>(_M_root_rope, __old_pos); ++ } ++ ++ reference ++ operator[](ptrdiff_t __n) ++ { return _Rope_char_ref_proxy<_CharT, _Alloc>(_M_root_rope, ++ this->_M_current_pos ++ + __n); } ++ ++ template ++ friend bool ++ operator==(const _Rope_iterator<_CharT2, _Alloc2>& __x, ++ const _Rope_iterator<_CharT2, _Alloc2>& __y); ++ ++ template ++ friend bool ++ operator<(const _Rope_iterator<_CharT2, _Alloc2>& __x, ++ const _Rope_iterator<_CharT2, _Alloc2>& __y); ++ ++ template ++ friend ptrdiff_t ++ operator-(const _Rope_iterator<_CharT2, _Alloc2>& __x, ++ const _Rope_iterator<_CharT2, _Alloc2>& __y); ++ ++ template ++ friend _Rope_iterator<_CharT2, _Alloc2> ++ operator-(const _Rope_iterator<_CharT2, _Alloc2>& __x, ptrdiff_t __n); ++ ++ template ++ friend _Rope_iterator<_CharT2, _Alloc2> ++ operator+(const _Rope_iterator<_CharT2, _Alloc2>& __x, ptrdiff_t __n); ++ ++ template ++ friend _Rope_iterator<_CharT2, _Alloc2> ++ operator+(ptrdiff_t __n, const _Rope_iterator<_CharT2, _Alloc2>& __x); ++ }; ++ ++ ++ template ++ struct _Rope_base ++ : public _Alloc ++ { ++ typedef _Alloc allocator_type; ++ ++ allocator_type ++ get_allocator() const ++ { return *static_cast(this); } ++ ++ allocator_type& ++ _M_get_allocator() ++ { return *static_cast<_Alloc*>(this); } ++ ++ const allocator_type& ++ _M_get_allocator() const ++ { return *static_cast(this); } ++ ++ typedef _Rope_RopeRep<_CharT, _Alloc> _RopeRep; ++ // The one in _Base may not be visible due to template rules. ++ ++ _Rope_base(_RopeRep* __t, const allocator_type&) ++ : _M_tree_ptr(__t) { } ++ ++ _Rope_base(const allocator_type&) { } ++ ++ // The only data member of a rope: ++ _RopeRep *_M_tree_ptr; ++ ++#define __ROPE_DEFINE_ALLOC(_Tp, __name) \ ++ typedef typename \ ++ _Alloc::template rebind<_Tp>::other __name##Alloc; \ ++ static _Tp* __name##_allocate(size_t __n) \ ++ { return __name##Alloc().allocate(__n); } \ ++ static void __name##_deallocate(_Tp *__p, size_t __n) \ ++ { __name##Alloc().deallocate(__p, __n); } ++ __ROPE_DEFINE_ALLOCS(_Alloc) ++#undef __ROPE_DEFINE_ALLOC ++ ++ protected: ++ _Rope_base& ++ operator=(const _Rope_base&); ++ ++ _Rope_base(const _Rope_base&); ++ }; ++ ++ /** ++ * This is an SGI extension. ++ * @ingroup SGIextensions ++ * @doctodo ++ */ ++ template ++ class rope : public _Rope_base<_CharT, _Alloc> ++ { ++ public: ++ typedef _CharT value_type; ++ typedef ptrdiff_t difference_type; ++ typedef size_t size_type; ++ typedef _CharT const_reference; ++ typedef const _CharT* const_pointer; ++ typedef _Rope_iterator<_CharT, _Alloc> iterator; ++ typedef _Rope_const_iterator<_CharT, _Alloc> const_iterator; ++ typedef _Rope_char_ref_proxy<_CharT, _Alloc> reference; ++ typedef _Rope_char_ptr_proxy<_CharT, _Alloc> pointer; ++ ++ friend class _Rope_iterator<_CharT, _Alloc>; ++ friend class _Rope_const_iterator<_CharT, _Alloc>; ++ friend struct _Rope_RopeRep<_CharT, _Alloc>; ++ friend class _Rope_iterator_base<_CharT, _Alloc>; ++ friend class _Rope_char_ptr_proxy<_CharT, _Alloc>; ++ friend class _Rope_char_ref_proxy<_CharT, _Alloc>; ++ friend struct _Rope_RopeSubstring<_CharT, _Alloc>; ++ ++ protected: ++ typedef _Rope_base<_CharT, _Alloc> _Base; ++ typedef typename _Base::allocator_type allocator_type; ++ using _Base::_M_tree_ptr; ++ using _Base::get_allocator; ++ using _Base::_M_get_allocator; ++ typedef __GC_CONST _CharT* _Cstrptr; ++ ++ static _CharT _S_empty_c_str[1]; ++ ++ static bool ++ _S_is0(_CharT __c) ++ { return __c == _S_eos((_CharT*)0); } ++ ++ enum { _S_copy_max = 23 }; ++ // For strings shorter than _S_copy_max, we copy to ++ // concatenate. ++ ++ typedef _Rope_RopeRep<_CharT, _Alloc> _RopeRep; ++ typedef _Rope_RopeConcatenation<_CharT, _Alloc> _RopeConcatenation; ++ typedef _Rope_RopeLeaf<_CharT, _Alloc> _RopeLeaf; ++ typedef _Rope_RopeFunction<_CharT, _Alloc> _RopeFunction; ++ typedef _Rope_RopeSubstring<_CharT, _Alloc> _RopeSubstring; ++ ++ // Retrieve a character at the indicated position. ++ static _CharT _S_fetch(_RopeRep* __r, size_type __pos); ++ ++#ifndef __GC ++ // Obtain a pointer to the character at the indicated position. ++ // The pointer can be used to change the character. ++ // If such a pointer cannot be produced, as is frequently the ++ // case, 0 is returned instead. ++ // (Returns nonzero only if all nodes in the path have a refcount ++ // of 1.) ++ static _CharT* _S_fetch_ptr(_RopeRep* __r, size_type __pos); ++#endif ++ ++ static bool ++ _S_apply_to_pieces(// should be template parameter ++ _Rope_char_consumer<_CharT>& __c, ++ const _RopeRep* __r, ++ size_t __begin, size_t __end); ++ // begin and end are assumed to be in range. ++ ++#ifndef __GC ++ static void ++ _S_unref(_RopeRep* __t) ++ { _RopeRep::_S_unref(__t); } ++ ++ static void ++ _S_ref(_RopeRep* __t) ++ { _RopeRep::_S_ref(__t); } ++ ++#else /* __GC */ ++ static void _S_unref(_RopeRep*) { } ++ static void _S_ref(_RopeRep*) { } ++#endif ++ ++#ifdef __GC ++ typedef _Rope_RopeRep<_CharT, _Alloc>* _Self_destruct_ptr; ++#else ++ typedef _Rope_self_destruct_ptr<_CharT, _Alloc> _Self_destruct_ptr; ++#endif ++ ++ // _Result is counted in refcount. ++ static _RopeRep* _S_substring(_RopeRep* __base, ++ size_t __start, size_t __endp1); ++ ++ static _RopeRep* _S_concat_char_iter(_RopeRep* __r, ++ const _CharT* __iter, size_t __slen); ++ // Concatenate rope and char ptr, copying __s. ++ // Should really take an arbitrary iterator. ++ // Result is counted in refcount. ++ static _RopeRep* _S_destr_concat_char_iter(_RopeRep* __r, ++ const _CharT* __iter, ++ size_t __slen) ++ // As above, but one reference to __r is about to be ++ // destroyed. Thus the pieces may be recycled if all ++ // relevant reference counts are 1. ++#ifdef __GC ++ // We can't really do anything since refcounts are unavailable. ++ { return _S_concat_char_iter(__r, __iter, __slen); } ++#else ++ ; ++#endif ++ ++ static _RopeRep* _S_concat(_RopeRep* __left, _RopeRep* __right); ++ // General concatenation on _RopeRep. _Result ++ // has refcount of 1. Adjusts argument refcounts. ++ ++ public: ++ void ++ apply_to_pieces(size_t __begin, size_t __end, ++ _Rope_char_consumer<_CharT>& __c) const ++ { _S_apply_to_pieces(__c, this->_M_tree_ptr, __begin, __end); } ++ ++ protected: ++ ++ static size_t ++ _S_rounded_up_size(size_t __n) ++ { return _RopeLeaf::_S_rounded_up_size(__n); } ++ ++ static size_t ++ _S_allocated_capacity(size_t __n) ++ { ++ if (_S_is_basic_char_type((_CharT*)0)) ++ return _S_rounded_up_size(__n) - 1; ++ else ++ return _S_rounded_up_size(__n); ++ ++ } ++ ++ // Allocate and construct a RopeLeaf using the supplied allocator ++ // Takes ownership of s instead of copying. ++ static _RopeLeaf* ++ _S_new_RopeLeaf(__GC_CONST _CharT *__s, ++ size_t __size, allocator_type& __a) ++ { ++ _RopeLeaf* __space = typename _Base::_LAlloc(__a).allocate(1); ++ return new(__space) _RopeLeaf(__s, __size, __a); ++ } ++ ++ static _RopeConcatenation* ++ _S_new_RopeConcatenation(_RopeRep* __left, _RopeRep* __right, ++ allocator_type& __a) ++ { ++ _RopeConcatenation* __space = typename _Base::_CAlloc(__a).allocate(1); ++ return new(__space) _RopeConcatenation(__left, __right, __a); ++ } ++ ++ static _RopeFunction* ++ _S_new_RopeFunction(char_producer<_CharT>* __f, ++ size_t __size, bool __d, allocator_type& __a) ++ { ++ _RopeFunction* __space = typename _Base::_FAlloc(__a).allocate(1); ++ return new(__space) _RopeFunction(__f, __size, __d, __a); ++ } ++ ++ static _RopeSubstring* ++ _S_new_RopeSubstring(_Rope_RopeRep<_CharT,_Alloc>* __b, size_t __s, ++ size_t __l, allocator_type& __a) ++ { ++ _RopeSubstring* __space = typename _Base::_SAlloc(__a).allocate(1); ++ return new(__space) _RopeSubstring(__b, __s, __l, __a); ++ } ++ ++ static _RopeLeaf* ++ _S_RopeLeaf_from_unowned_char_ptr(const _CharT *__s, ++ size_t __size, allocator_type& __a) ++#define __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __size, __a) \ ++ _S_RopeLeaf_from_unowned_char_ptr(__s, __size, __a) ++ { ++ if (0 == __size) ++ return 0; ++ _CharT* __buf = __a.allocate(_S_rounded_up_size(__size)); ++ ++ __uninitialized_copy_n_a(__s, __size, __buf, __a); ++ _S_cond_store_eos(__buf[__size]); ++ __try ++ { return _S_new_RopeLeaf(__buf, __size, __a); } ++ __catch(...) ++ { ++ _RopeRep::__STL_FREE_STRING(__buf, __size, __a); ++ __throw_exception_again; ++ } ++ } ++ ++ // Concatenation of nonempty strings. ++ // Always builds a concatenation node. ++ // Rebalances if the result is too deep. ++ // Result has refcount 1. ++ // Does not increment left and right ref counts even though ++ // they are referenced. ++ static _RopeRep* ++ _S_tree_concat(_RopeRep* __left, _RopeRep* __right); ++ ++ // Concatenation helper functions ++ static _RopeLeaf* ++ _S_leaf_concat_char_iter(_RopeLeaf* __r, ++ const _CharT* __iter, size_t __slen); ++ // Concatenate by copying leaf. ++ // should take an arbitrary iterator ++ // result has refcount 1. ++#ifndef __GC ++ static _RopeLeaf* ++ _S_destr_leaf_concat_char_iter(_RopeLeaf* __r, ++ const _CharT* __iter, size_t __slen); ++ // A version that potentially clobbers __r if __r->_M_ref_count == 1. ++#endif ++ ++ private: ++ ++ static size_t _S_char_ptr_len(const _CharT* __s); ++ // slightly generalized strlen ++ ++ rope(_RopeRep* __t, const allocator_type& __a = allocator_type()) ++ : _Base(__t, __a) { } ++ ++ ++ // Copy __r to the _CharT buffer. ++ // Returns __buffer + __r->_M_size. ++ // Assumes that buffer is uninitialized. ++ static _CharT* _S_flatten(_RopeRep* __r, _CharT* __buffer); ++ ++ // Again, with explicit starting position and length. ++ // Assumes that buffer is uninitialized. ++ static _CharT* _S_flatten(_RopeRep* __r, ++ size_t __start, size_t __len, ++ _CharT* __buffer); ++ ++ static const unsigned long ++ _S_min_len[__detail::_S_max_rope_depth + 1]; ++ ++ static bool ++ _S_is_balanced(_RopeRep* __r) ++ { return (__r->_M_size >= _S_min_len[__r->_M_depth]); } ++ ++ static bool ++ _S_is_almost_balanced(_RopeRep* __r) ++ { return (__r->_M_depth == 0 ++ || __r->_M_size >= _S_min_len[__r->_M_depth - 1]); } ++ ++ static bool ++ _S_is_roughly_balanced(_RopeRep* __r) ++ { return (__r->_M_depth <= 1 ++ || __r->_M_size >= _S_min_len[__r->_M_depth - 2]); } ++ ++ // Assumes the result is not empty. ++ static _RopeRep* ++ _S_concat_and_set_balanced(_RopeRep* __left, _RopeRep* __right) ++ { ++ _RopeRep* __result = _S_concat(__left, __right); ++ if (_S_is_balanced(__result)) ++ __result->_M_is_balanced = true; ++ return __result; ++ } ++ ++ // The basic rebalancing operation. Logically copies the ++ // rope. The result has refcount of 1. The client will ++ // usually decrement the reference count of __r. ++ // The result is within height 2 of balanced by the above ++ // definition. ++ static _RopeRep* _S_balance(_RopeRep* __r); ++ ++ // Add all unbalanced subtrees to the forest of balanced trees. ++ // Used only by balance. ++ static void _S_add_to_forest(_RopeRep*__r, _RopeRep** __forest); ++ ++ // Add __r to forest, assuming __r is already balanced. ++ static void _S_add_leaf_to_forest(_RopeRep* __r, _RopeRep** __forest); ++ ++ // Print to stdout, exposing structure ++ static void _S_dump(_RopeRep* __r, int __indent = 0); ++ ++ // Return -1, 0, or 1 if __x < __y, __x == __y, or __x > __y resp. ++ static int _S_compare(const _RopeRep* __x, const _RopeRep* __y); ++ ++ public: ++ bool ++ empty() const ++ { return 0 == this->_M_tree_ptr; } ++ ++ // Comparison member function. This is public only for those ++ // clients that need a ternary comparison. Others ++ // should use the comparison operators below. ++ int ++ compare(const rope& __y) const ++ { return _S_compare(this->_M_tree_ptr, __y._M_tree_ptr); } ++ ++ rope(const _CharT* __s, const allocator_type& __a = allocator_type()) ++ : _Base(__a) ++ { ++ this->_M_tree_ptr = ++ __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, _S_char_ptr_len(__s), ++ _M_get_allocator()); ++ } ++ ++ rope(const _CharT* __s, size_t __len, ++ const allocator_type& __a = allocator_type()) ++ : _Base(__a) ++ { ++ this->_M_tree_ptr = ++ __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __len, _M_get_allocator()); ++ } ++ ++ // Should perhaps be templatized with respect to the iterator type ++ // and use Sequence_buffer. (It should perhaps use sequence_buffer ++ // even now.) ++ rope(const _CharT* __s, const _CharT* __e, ++ const allocator_type& __a = allocator_type()) ++ : _Base(__a) ++ { ++ this->_M_tree_ptr = ++ __STL_ROPE_FROM_UNOWNED_CHAR_PTR(__s, __e - __s, _M_get_allocator()); ++ } ++ ++ rope(const const_iterator& __s, const const_iterator& __e, ++ const allocator_type& __a = allocator_type()) ++ : _Base(_S_substring(__s._M_root, __s._M_current_pos, ++ __e._M_current_pos), __a) ++ { } ++ ++ rope(const iterator& __s, const iterator& __e, ++ const allocator_type& __a = allocator_type()) ++ : _Base(_S_substring(__s._M_root, __s._M_current_pos, ++ __e._M_current_pos), __a) ++ { } ++ ++ rope(_CharT __c, const allocator_type& __a = allocator_type()) ++ : _Base(__a) ++ { ++ _CharT* __buf = this->_Data_allocate(_S_rounded_up_size(1)); ++ ++ _M_get_allocator().construct(__buf, __c); ++ __try ++ { ++ this->_M_tree_ptr = _S_new_RopeLeaf(__buf, 1, ++ _M_get_allocator()); ++ } ++ __catch(...) ++ { ++ _RopeRep::__STL_FREE_STRING(__buf, 1, _M_get_allocator()); ++ __throw_exception_again; ++ } ++ } ++ ++ rope(size_t __n, _CharT __c, ++ const allocator_type& __a = allocator_type()); ++ ++ rope(const allocator_type& __a = allocator_type()) ++ : _Base(0, __a) { } ++ ++ // Construct a rope from a function that can compute its members ++ rope(char_producer<_CharT> *__fn, size_t __len, bool __delete_fn, ++ const allocator_type& __a = allocator_type()) ++ : _Base(__a) ++ { ++ this->_M_tree_ptr = (0 == __len) ? ++ 0 : _S_new_RopeFunction(__fn, __len, __delete_fn, __a); ++ } ++ ++ rope(const rope& __x, const allocator_type& __a = allocator_type()) ++ : _Base(__x._M_tree_ptr, __a) ++ { _S_ref(this->_M_tree_ptr); } ++ ++ ~rope() throw() ++ { _S_unref(this->_M_tree_ptr); } ++ ++ rope& ++ operator=(const rope& __x) ++ { ++ _RopeRep* __old = this->_M_tree_ptr; ++ this->_M_tree_ptr = __x._M_tree_ptr; ++ _S_ref(this->_M_tree_ptr); ++ _S_unref(__old); ++ return *this; ++ } ++ ++ void ++ clear() ++ { ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = 0; ++ } ++ ++ void ++ push_back(_CharT __x) ++ { ++ _RopeRep* __old = this->_M_tree_ptr; ++ this->_M_tree_ptr ++ = _S_destr_concat_char_iter(this->_M_tree_ptr, &__x, 1); ++ _S_unref(__old); ++ } ++ ++ void ++ pop_back() ++ { ++ _RopeRep* __old = this->_M_tree_ptr; ++ this->_M_tree_ptr = _S_substring(this->_M_tree_ptr, ++ 0, this->_M_tree_ptr->_M_size - 1); ++ _S_unref(__old); ++ } ++ ++ _CharT ++ back() const ++ { return _S_fetch(this->_M_tree_ptr, this->_M_tree_ptr->_M_size - 1); } ++ ++ void ++ push_front(_CharT __x) ++ { ++ _RopeRep* __old = this->_M_tree_ptr; ++ _RopeRep* __left = ++ __STL_ROPE_FROM_UNOWNED_CHAR_PTR(&__x, 1, _M_get_allocator()); ++ __try ++ { ++ this->_M_tree_ptr = _S_concat(__left, this->_M_tree_ptr); ++ _S_unref(__old); ++ _S_unref(__left); ++ } ++ __catch(...) ++ { ++ _S_unref(__left); ++ __throw_exception_again; ++ } ++ } ++ ++ void ++ pop_front() ++ { ++ _RopeRep* __old = this->_M_tree_ptr; ++ this->_M_tree_ptr ++ = _S_substring(this->_M_tree_ptr, 1, this->_M_tree_ptr->_M_size); ++ _S_unref(__old); ++ } ++ ++ _CharT ++ front() const ++ { return _S_fetch(this->_M_tree_ptr, 0); } ++ ++ void ++ balance() ++ { ++ _RopeRep* __old = this->_M_tree_ptr; ++ this->_M_tree_ptr = _S_balance(this->_M_tree_ptr); ++ _S_unref(__old); ++ } ++ ++ void ++ copy(_CharT* __buffer) const ++ { ++ _Destroy_const(__buffer, __buffer + size(), _M_get_allocator()); ++ _S_flatten(this->_M_tree_ptr, __buffer); ++ } ++ ++ // This is the copy function from the standard, but ++ // with the arguments reordered to make it consistent with the ++ // rest of the interface. ++ // Note that this guaranteed not to compile if the draft standard ++ // order is assumed. ++ size_type ++ copy(size_type __pos, size_type __n, _CharT* __buffer) const ++ { ++ size_t __size = size(); ++ size_t __len = (__pos + __n > __size? __size - __pos : __n); ++ ++ _Destroy_const(__buffer, __buffer + __len, _M_get_allocator()); ++ _S_flatten(this->_M_tree_ptr, __pos, __len, __buffer); ++ return __len; ++ } ++ ++ // Print to stdout, exposing structure. May be useful for ++ // performance debugging. ++ void ++ dump() ++ { _S_dump(this->_M_tree_ptr); } ++ ++ // Convert to 0 terminated string in new allocated memory. ++ // Embedded 0s in the input do not terminate the copy. ++ const _CharT* c_str() const; ++ ++ // As above, but also use the flattened representation as ++ // the new rope representation. ++ const _CharT* replace_with_c_str(); ++ ++ // Reclaim memory for the c_str generated flattened string. ++ // Intentionally undocumented, since it's hard to say when this ++ // is safe for multiple threads. ++ void ++ delete_c_str () ++ { ++ if (0 == this->_M_tree_ptr) ++ return; ++ if (__detail::_S_leaf == this->_M_tree_ptr->_M_tag && ++ ((_RopeLeaf*)this->_M_tree_ptr)->_M_data == ++ this->_M_tree_ptr->_M_c_string) ++ { ++ // Representation shared ++ return; ++ } ++#ifndef __GC ++ this->_M_tree_ptr->_M_free_c_string(); ++#endif ++ this->_M_tree_ptr->_M_c_string = 0; ++ } ++ ++ _CharT ++ operator[] (size_type __pos) const ++ { return _S_fetch(this->_M_tree_ptr, __pos); } ++ ++ _CharT ++ at(size_type __pos) const ++ { ++ // if (__pos >= size()) throw out_of_range; // XXX ++ return (*this)[__pos]; ++ } ++ ++ const_iterator ++ begin() const ++ { return(const_iterator(this->_M_tree_ptr, 0)); } ++ ++ // An easy way to get a const iterator from a non-const container. ++ const_iterator ++ const_begin() const ++ { return(const_iterator(this->_M_tree_ptr, 0)); } ++ ++ const_iterator ++ end() const ++ { return(const_iterator(this->_M_tree_ptr, size())); } ++ ++ const_iterator ++ const_end() const ++ { return(const_iterator(this->_M_tree_ptr, size())); } ++ ++ size_type ++ size() const ++ { return(0 == this->_M_tree_ptr? 0 : this->_M_tree_ptr->_M_size); } ++ ++ size_type ++ length() const ++ { return size(); } ++ ++ size_type ++ max_size() const ++ { ++ return _S_min_len[int(__detail::_S_max_rope_depth) - 1] - 1; ++ // Guarantees that the result can be sufficiently ++ // balanced. Longer ropes will probably still work, ++ // but it's harder to make guarantees. ++ } ++ ++ typedef std::reverse_iterator const_reverse_iterator; ++ ++ const_reverse_iterator ++ rbegin() const ++ { return const_reverse_iterator(end()); } ++ ++ const_reverse_iterator ++ const_rbegin() const ++ { return const_reverse_iterator(end()); } ++ ++ const_reverse_iterator ++ rend() const ++ { return const_reverse_iterator(begin()); } ++ ++ const_reverse_iterator ++ const_rend() const ++ { return const_reverse_iterator(begin()); } ++ ++ template ++ friend rope<_CharT2, _Alloc2> ++ operator+(const rope<_CharT2, _Alloc2>& __left, ++ const rope<_CharT2, _Alloc2>& __right); ++ ++ template ++ friend rope<_CharT2, _Alloc2> ++ operator+(const rope<_CharT2, _Alloc2>& __left, const _CharT2* __right); ++ ++ template ++ friend rope<_CharT2, _Alloc2> ++ operator+(const rope<_CharT2, _Alloc2>& __left, _CharT2 __right); ++ ++ // The symmetric cases are intentionally omitted, since they're ++ // presumed to be less common, and we don't handle them as well. ++ ++ // The following should really be templatized. The first ++ // argument should be an input iterator or forward iterator with ++ // value_type _CharT. ++ rope& ++ append(const _CharT* __iter, size_t __n) ++ { ++ _RopeRep* __result = ++ _S_destr_concat_char_iter(this->_M_tree_ptr, __iter, __n); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ return *this; ++ } ++ ++ rope& ++ append(const _CharT* __c_string) ++ { ++ size_t __len = _S_char_ptr_len(__c_string); ++ append(__c_string, __len); ++ return(*this); ++ } ++ ++ rope& ++ append(const _CharT* __s, const _CharT* __e) ++ { ++ _RopeRep* __result = ++ _S_destr_concat_char_iter(this->_M_tree_ptr, __s, __e - __s); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ return *this; ++ } ++ ++ rope& ++ append(const_iterator __s, const_iterator __e) ++ { ++ _Self_destruct_ptr __appendee(_S_substring(__s._M_root, ++ __s._M_current_pos, ++ __e._M_current_pos)); ++ _RopeRep* __result = _S_concat(this->_M_tree_ptr, ++ (_RopeRep*)__appendee); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ return *this; ++ } ++ ++ rope& ++ append(_CharT __c) ++ { ++ _RopeRep* __result = ++ _S_destr_concat_char_iter(this->_M_tree_ptr, &__c, 1); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ return *this; ++ } ++ ++ rope& ++ append() ++ { return append(_CharT()); } // XXX why? ++ ++ rope& ++ append(const rope& __y) ++ { ++ _RopeRep* __result = _S_concat(this->_M_tree_ptr, __y._M_tree_ptr); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ return *this; ++ } ++ ++ rope& ++ append(size_t __n, _CharT __c) ++ { ++ rope<_CharT,_Alloc> __last(__n, __c); ++ return append(__last); ++ } ++ ++ void ++ swap(rope& __b) ++ { ++ _RopeRep* __tmp = this->_M_tree_ptr; ++ this->_M_tree_ptr = __b._M_tree_ptr; ++ __b._M_tree_ptr = __tmp; ++ } ++ ++ protected: ++ // Result is included in refcount. ++ static _RopeRep* ++ replace(_RopeRep* __old, size_t __pos1, ++ size_t __pos2, _RopeRep* __r) ++ { ++ if (0 == __old) ++ { ++ _S_ref(__r); ++ return __r; ++ } ++ _Self_destruct_ptr __left(_S_substring(__old, 0, __pos1)); ++ _Self_destruct_ptr __right(_S_substring(__old, __pos2, __old->_M_size)); ++ _RopeRep* __result; ++ ++ if (0 == __r) ++ __result = _S_concat(__left, __right); ++ else ++ { ++ _Self_destruct_ptr __left_result(_S_concat(__left, __r)); ++ __result = _S_concat(__left_result, __right); ++ } ++ return __result; ++ } ++ ++ public: ++ void ++ insert(size_t __p, const rope& __r) ++ { ++ _RopeRep* __result = ++ replace(this->_M_tree_ptr, __p, __p, __r._M_tree_ptr); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ } ++ ++ void ++ insert(size_t __p, size_t __n, _CharT __c) ++ { ++ rope<_CharT,_Alloc> __r(__n,__c); ++ insert(__p, __r); ++ } ++ ++ void ++ insert(size_t __p, const _CharT* __i, size_t __n) ++ { ++ _Self_destruct_ptr __left(_S_substring(this->_M_tree_ptr, 0, __p)); ++ _Self_destruct_ptr __right(_S_substring(this->_M_tree_ptr, ++ __p, size())); ++ _Self_destruct_ptr __left_result(_S_concat_char_iter(__left, __i, __n)); ++ // _S_ destr_concat_char_iter should be safe here. ++ // But as it stands it's probably not a win, since __left ++ // is likely to have additional references. ++ _RopeRep* __result = _S_concat(__left_result, __right); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ } ++ ++ void ++ insert(size_t __p, const _CharT* __c_string) ++ { insert(__p, __c_string, _S_char_ptr_len(__c_string)); } ++ ++ void ++ insert(size_t __p, _CharT __c) ++ { insert(__p, &__c, 1); } ++ ++ void ++ insert(size_t __p) ++ { ++ _CharT __c = _CharT(); ++ insert(__p, &__c, 1); ++ } ++ ++ void ++ insert(size_t __p, const _CharT* __i, const _CharT* __j) ++ { ++ rope __r(__i, __j); ++ insert(__p, __r); ++ } ++ ++ void ++ insert(size_t __p, const const_iterator& __i, ++ const const_iterator& __j) ++ { ++ rope __r(__i, __j); ++ insert(__p, __r); ++ } ++ ++ void ++ insert(size_t __p, const iterator& __i, ++ const iterator& __j) ++ { ++ rope __r(__i, __j); ++ insert(__p, __r); ++ } ++ ++ // (position, length) versions of replace operations: ++ ++ void ++ replace(size_t __p, size_t __n, const rope& __r) ++ { ++ _RopeRep* __result = ++ replace(this->_M_tree_ptr, __p, __p + __n, __r._M_tree_ptr); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ } ++ ++ void ++ replace(size_t __p, size_t __n, ++ const _CharT* __i, size_t __i_len) ++ { ++ rope __r(__i, __i_len); ++ replace(__p, __n, __r); ++ } ++ ++ void ++ replace(size_t __p, size_t __n, _CharT __c) ++ { ++ rope __r(__c); ++ replace(__p, __n, __r); ++ } ++ ++ void ++ replace(size_t __p, size_t __n, const _CharT* __c_string) ++ { ++ rope __r(__c_string); ++ replace(__p, __n, __r); ++ } ++ ++ void ++ replace(size_t __p, size_t __n, ++ const _CharT* __i, const _CharT* __j) ++ { ++ rope __r(__i, __j); ++ replace(__p, __n, __r); ++ } ++ ++ void ++ replace(size_t __p, size_t __n, ++ const const_iterator& __i, const const_iterator& __j) ++ { ++ rope __r(__i, __j); ++ replace(__p, __n, __r); ++ } ++ ++ void ++ replace(size_t __p, size_t __n, ++ const iterator& __i, const iterator& __j) ++ { ++ rope __r(__i, __j); ++ replace(__p, __n, __r); ++ } ++ ++ // Single character variants: ++ void ++ replace(size_t __p, _CharT __c) ++ { ++ iterator __i(this, __p); ++ *__i = __c; ++ } ++ ++ void ++ replace(size_t __p, const rope& __r) ++ { replace(__p, 1, __r); } ++ ++ void ++ replace(size_t __p, const _CharT* __i, size_t __i_len) ++ { replace(__p, 1, __i, __i_len); } ++ ++ void ++ replace(size_t __p, const _CharT* __c_string) ++ { replace(__p, 1, __c_string); } ++ ++ void ++ replace(size_t __p, const _CharT* __i, const _CharT* __j) ++ { replace(__p, 1, __i, __j); } ++ ++ void ++ replace(size_t __p, const const_iterator& __i, ++ const const_iterator& __j) ++ { replace(__p, 1, __i, __j); } ++ ++ void ++ replace(size_t __p, const iterator& __i, ++ const iterator& __j) ++ { replace(__p, 1, __i, __j); } ++ ++ // Erase, (position, size) variant. ++ void ++ erase(size_t __p, size_t __n) ++ { ++ _RopeRep* __result = replace(this->_M_tree_ptr, __p, ++ __p + __n, 0); ++ _S_unref(this->_M_tree_ptr); ++ this->_M_tree_ptr = __result; ++ } ++ ++ // Erase, single character ++ void ++ erase(size_t __p) ++ { erase(__p, __p + 1); } ++ ++ // Insert, iterator variants. ++ iterator ++ insert(const iterator& __p, const rope& __r) ++ { ++ insert(__p.index(), __r); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p, size_t __n, _CharT __c) ++ { ++ insert(__p.index(), __n, __c); ++ return __p; ++ } ++ ++ iterator insert(const iterator& __p, _CharT __c) ++ { ++ insert(__p.index(), __c); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p ) ++ { ++ insert(__p.index()); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p, const _CharT* c_string) ++ { ++ insert(__p.index(), c_string); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p, const _CharT* __i, size_t __n) ++ { ++ insert(__p.index(), __i, __n); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p, const _CharT* __i, ++ const _CharT* __j) ++ { ++ insert(__p.index(), __i, __j); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p, ++ const const_iterator& __i, const const_iterator& __j) ++ { ++ insert(__p.index(), __i, __j); ++ return __p; ++ } ++ ++ iterator ++ insert(const iterator& __p, ++ const iterator& __i, const iterator& __j) ++ { ++ insert(__p.index(), __i, __j); ++ return __p; ++ } ++ ++ // Replace, range variants. ++ void ++ replace(const iterator& __p, const iterator& __q, const rope& __r) ++ { replace(__p.index(), __q.index() - __p.index(), __r); } ++ ++ void ++ replace(const iterator& __p, const iterator& __q, _CharT __c) ++ { replace(__p.index(), __q.index() - __p.index(), __c); } ++ ++ void ++ replace(const iterator& __p, const iterator& __q, ++ const _CharT* __c_string) ++ { replace(__p.index(), __q.index() - __p.index(), __c_string); } ++ ++ void ++ replace(const iterator& __p, const iterator& __q, ++ const _CharT* __i, size_t __n) ++ { replace(__p.index(), __q.index() - __p.index(), __i, __n); } ++ ++ void ++ replace(const iterator& __p, const iterator& __q, ++ const _CharT* __i, const _CharT* __j) ++ { replace(__p.index(), __q.index() - __p.index(), __i, __j); } ++ ++ void ++ replace(const iterator& __p, const iterator& __q, ++ const const_iterator& __i, const const_iterator& __j) ++ { replace(__p.index(), __q.index() - __p.index(), __i, __j); } ++ ++ void ++ replace(const iterator& __p, const iterator& __q, ++ const iterator& __i, const iterator& __j) ++ { replace(__p.index(), __q.index() - __p.index(), __i, __j); } ++ ++ // Replace, iterator variants. ++ void ++ replace(const iterator& __p, const rope& __r) ++ { replace(__p.index(), __r); } ++ ++ void ++ replace(const iterator& __p, _CharT __c) ++ { replace(__p.index(), __c); } ++ ++ void ++ replace(const iterator& __p, const _CharT* __c_string) ++ { replace(__p.index(), __c_string); } ++ ++ void ++ replace(const iterator& __p, const _CharT* __i, size_t __n) ++ { replace(__p.index(), __i, __n); } ++ ++ void ++ replace(const iterator& __p, const _CharT* __i, const _CharT* __j) ++ { replace(__p.index(), __i, __j); } ++ ++ void ++ replace(const iterator& __p, const_iterator __i, const_iterator __j) ++ { replace(__p.index(), __i, __j); } ++ ++ void ++ replace(const iterator& __p, iterator __i, iterator __j) ++ { replace(__p.index(), __i, __j); } ++ ++ // Iterator and range variants of erase ++ iterator ++ erase(const iterator& __p, const iterator& __q) ++ { ++ size_t __p_index = __p.index(); ++ erase(__p_index, __q.index() - __p_index); ++ return iterator(this, __p_index); ++ } ++ ++ iterator ++ erase(const iterator& __p) ++ { ++ size_t __p_index = __p.index(); ++ erase(__p_index, 1); ++ return iterator(this, __p_index); ++ } ++ ++ rope ++ substr(size_t __start, size_t __len = 1) const ++ { ++ return rope<_CharT, _Alloc>(_S_substring(this->_M_tree_ptr, ++ __start, ++ __start + __len)); ++ } ++ ++ rope ++ substr(iterator __start, iterator __end) const ++ { ++ return rope<_CharT, _Alloc>(_S_substring(this->_M_tree_ptr, ++ __start.index(), ++ __end.index())); ++ } ++ ++ rope ++ substr(iterator __start) const ++ { ++ size_t __pos = __start.index(); ++ return rope<_CharT, _Alloc>(_S_substring(this->_M_tree_ptr, ++ __pos, __pos + 1)); ++ } ++ ++ rope ++ substr(const_iterator __start, const_iterator __end) const ++ { ++ // This might eventually take advantage of the cache in the ++ // iterator. ++ return rope<_CharT, _Alloc>(_S_substring(this->_M_tree_ptr, ++ __start.index(), ++ __end.index())); ++ } ++ ++ rope<_CharT, _Alloc> ++ substr(const_iterator __start) ++ { ++ size_t __pos = __start.index(); ++ return rope<_CharT, _Alloc>(_S_substring(this->_M_tree_ptr, ++ __pos, __pos + 1)); ++ } ++ ++ static const size_type npos; ++ ++ size_type find(_CharT __c, size_type __pos = 0) const; ++ ++ size_type ++ find(const _CharT* __s, size_type __pos = 0) const ++ { ++ size_type __result_pos; ++ const_iterator __result = ++ std::search(const_begin() + __pos, const_end(), ++ __s, __s + _S_char_ptr_len(__s)); ++ __result_pos = __result.index(); ++#ifndef __STL_OLD_ROPE_SEMANTICS ++ if (__result_pos == size()) ++ __result_pos = npos; ++#endif ++ return __result_pos; ++ } ++ ++ iterator ++ mutable_begin() ++ { return(iterator(this, 0)); } ++ ++ iterator ++ mutable_end() ++ { return(iterator(this, size())); } ++ ++ typedef std::reverse_iterator reverse_iterator; ++ ++ reverse_iterator ++ mutable_rbegin() ++ { return reverse_iterator(mutable_end()); } ++ ++ reverse_iterator ++ mutable_rend() ++ { return reverse_iterator(mutable_begin()); } ++ ++ reference ++ mutable_reference_at(size_type __pos) ++ { return reference(this, __pos); } ++ ++#ifdef __STD_STUFF ++ reference ++ operator[] (size_type __pos) ++ { return _char_ref_proxy(this, __pos); } ++ ++ reference ++ at(size_type __pos) ++ { ++ // if (__pos >= size()) throw out_of_range; // XXX ++ return (*this)[__pos]; ++ } ++ ++ void resize(size_type __n, _CharT __c) { } ++ void resize(size_type __n) { } ++ void reserve(size_type __res_arg = 0) { } ++ ++ size_type ++ capacity() const ++ { return max_size(); } ++ ++ // Stuff below this line is dangerous because it's error prone. ++ // I would really like to get rid of it. ++ // copy function with funny arg ordering. ++ size_type ++ copy(_CharT* __buffer, size_type __n, ++ size_type __pos = 0) const ++ { return copy(__pos, __n, __buffer); } ++ ++ iterator ++ end() ++ { return mutable_end(); } ++ ++ iterator ++ begin() ++ { return mutable_begin(); } ++ ++ reverse_iterator ++ rend() ++ { return mutable_rend(); } ++ ++ reverse_iterator ++ rbegin() ++ { return mutable_rbegin(); } ++ ++#else ++ const_iterator ++ end() ++ { return const_end(); } ++ ++ const_iterator ++ begin() ++ { return const_begin(); } ++ ++ const_reverse_iterator ++ rend() ++ { return const_rend(); } ++ ++ const_reverse_iterator ++ rbegin() ++ { return const_rbegin(); } ++ ++#endif ++ }; ++ ++ template ++ const typename rope<_CharT, _Alloc>::size_type ++ rope<_CharT, _Alloc>::npos = (size_type)(-1); ++ ++ template ++ inline bool operator==(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return (__x._M_current_pos == __y._M_current_pos ++ && __x._M_root == __y._M_root); } ++ ++ template ++ inline bool operator<(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return (__x._M_current_pos < __y._M_current_pos); } ++ ++ template ++ inline bool operator!=(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return !(__x == __y); } ++ ++ template ++ inline bool operator>(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return __y < __x; } ++ ++ template ++ inline bool ++ operator<=(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return !(__y < __x); } ++ ++ template ++ inline bool ++ operator>=(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return !(__x < __y); } ++ ++ template ++ inline ptrdiff_t ++ operator-(const _Rope_const_iterator<_CharT, _Alloc>& __x, ++ const _Rope_const_iterator<_CharT, _Alloc>& __y) ++ { return (ptrdiff_t)__x._M_current_pos - (ptrdiff_t)__y._M_current_pos; } ++ ++ template ++ inline _Rope_const_iterator<_CharT, _Alloc> ++ operator-(const _Rope_const_iterator<_CharT, _Alloc>& __x, ptrdiff_t __n) ++ { return _Rope_const_iterator<_CharT, _Alloc>(__x._M_root, ++ __x._M_current_pos - __n); } ++ ++ template ++ inline _Rope_const_iterator<_CharT, _Alloc> ++ operator+(const _Rope_const_iterator<_CharT, _Alloc>& __x, ptrdiff_t __n) ++ { return _Rope_const_iterator<_CharT, _Alloc>(__x._M_root, ++ __x._M_current_pos + __n); } ++ ++ template ++ inline _Rope_const_iterator<_CharT, _Alloc> ++ operator+(ptrdiff_t __n, const _Rope_const_iterator<_CharT, _Alloc>& __x) ++ { return _Rope_const_iterator<_CharT, _Alloc>(__x._M_root, ++ __x._M_current_pos + __n); } ++ ++ template ++ inline bool ++ operator==(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ {return (__x._M_current_pos == __y._M_current_pos ++ && __x._M_root_rope == __y._M_root_rope); } ++ ++ template ++ inline bool ++ operator<(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ { return (__x._M_current_pos < __y._M_current_pos); } ++ ++ template ++ inline bool ++ operator!=(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ { return !(__x == __y); } ++ ++ template ++ inline bool ++ operator>(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ { return __y < __x; } ++ ++ template ++ inline bool ++ operator<=(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ { return !(__y < __x); } ++ ++ template ++ inline bool ++ operator>=(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ { return !(__x < __y); } ++ ++ template ++ inline ptrdiff_t ++ operator-(const _Rope_iterator<_CharT, _Alloc>& __x, ++ const _Rope_iterator<_CharT, _Alloc>& __y) ++ { return ((ptrdiff_t)__x._M_current_pos ++ - (ptrdiff_t)__y._M_current_pos); } ++ ++ template ++ inline _Rope_iterator<_CharT, _Alloc> ++ operator-(const _Rope_iterator<_CharT, _Alloc>& __x, ++ ptrdiff_t __n) ++ { return _Rope_iterator<_CharT, _Alloc>(__x._M_root_rope, ++ __x._M_current_pos - __n); } ++ ++ template ++ inline _Rope_iterator<_CharT, _Alloc> ++ operator+(const _Rope_iterator<_CharT, _Alloc>& __x, ptrdiff_t __n) ++ { return _Rope_iterator<_CharT, _Alloc>(__x._M_root_rope, ++ __x._M_current_pos + __n); } ++ ++ template ++ inline _Rope_iterator<_CharT, _Alloc> ++ operator+(ptrdiff_t __n, const _Rope_iterator<_CharT, _Alloc>& __x) ++ { return _Rope_iterator<_CharT, _Alloc>(__x._M_root_rope, ++ __x._M_current_pos + __n); } ++ ++ template ++ inline rope<_CharT, _Alloc> ++ operator+(const rope<_CharT, _Alloc>& __left, ++ const rope<_CharT, _Alloc>& __right) ++ { ++ // Inlining this should make it possible to keep __left and ++ // __right in registers. ++ typedef rope<_CharT, _Alloc> rope_type; ++ return rope_type(rope_type::_S_concat(__left._M_tree_ptr, ++ __right._M_tree_ptr)); ++ } ++ ++ template ++ inline rope<_CharT, _Alloc>& ++ operator+=(rope<_CharT, _Alloc>& __left, ++ const rope<_CharT, _Alloc>& __right) ++ { ++ __left.append(__right); ++ return __left; ++ } ++ ++ template ++ inline rope<_CharT, _Alloc> ++ operator+(const rope<_CharT, _Alloc>& __left, ++ const _CharT* __right) ++ { ++ typedef rope<_CharT, _Alloc> rope_type; ++ size_t __rlen = rope_type::_S_char_ptr_len(__right); ++ return rope_type(rope_type::_S_concat_char_iter(__left._M_tree_ptr, ++ __right, __rlen)); ++ } ++ ++ template ++ inline rope<_CharT, _Alloc>& ++ operator+=(rope<_CharT, _Alloc>& __left, ++ const _CharT* __right) ++ { ++ __left.append(__right); ++ return __left; ++ } ++ ++ template ++ inline rope<_CharT, _Alloc> ++ operator+(const rope<_CharT, _Alloc>& __left, _CharT __right) ++ { ++ typedef rope<_CharT, _Alloc> rope_type; ++ return rope_type(rope_type::_S_concat_char_iter(__left._M_tree_ptr, ++ &__right, 1)); ++ } ++ ++ template ++ inline rope<_CharT, _Alloc>& ++ operator+=(rope<_CharT, _Alloc>& __left, _CharT __right) ++ { ++ __left.append(__right); ++ return __left; ++ } ++ ++ template ++ bool ++ operator<(const rope<_CharT, _Alloc>& __left, ++ const rope<_CharT, _Alloc>& __right) ++ { return __left.compare(__right) < 0; } ++ ++ template ++ bool ++ operator==(const rope<_CharT, _Alloc>& __left, ++ const rope<_CharT, _Alloc>& __right) ++ { return __left.compare(__right) == 0; } ++ ++ template ++ inline bool ++ operator==(const _Rope_char_ptr_proxy<_CharT, _Alloc>& __x, ++ const _Rope_char_ptr_proxy<_CharT, _Alloc>& __y) ++ { return (__x._M_pos == __y._M_pos && __x._M_root == __y._M_root); } ++ ++ template ++ inline bool ++ operator!=(const rope<_CharT, _Alloc>& __x, ++ const rope<_CharT, _Alloc>& __y) ++ { return !(__x == __y); } ++ ++ template ++ inline bool ++ operator>(const rope<_CharT, _Alloc>& __x, ++ const rope<_CharT, _Alloc>& __y) ++ { return __y < __x; } ++ ++ template ++ inline bool ++ operator<=(const rope<_CharT, _Alloc>& __x, ++ const rope<_CharT, _Alloc>& __y) ++ { return !(__y < __x); } ++ ++ template ++ inline bool ++ operator>=(const rope<_CharT, _Alloc>& __x, ++ const rope<_CharT, _Alloc>& __y) ++ { return !(__x < __y); } ++ ++ template ++ inline bool ++ operator!=(const _Rope_char_ptr_proxy<_CharT, _Alloc>& __x, ++ const _Rope_char_ptr_proxy<_CharT, _Alloc>& __y) ++ { return !(__x == __y); } ++ ++ template ++ std::basic_ostream<_CharT, _Traits>& ++ operator<<(std::basic_ostream<_CharT, _Traits>& __o, ++ const rope<_CharT, _Alloc>& __r); ++ ++ typedef rope crope; ++ typedef rope wrope; ++ ++ inline crope::reference ++ __mutable_reference_at(crope& __c, size_t __i) ++ { return __c.mutable_reference_at(__i); } ++ ++ inline wrope::reference ++ __mutable_reference_at(wrope& __c, size_t __i) ++ { return __c.mutable_reference_at(__i); } ++ ++ template ++ inline void ++ swap(rope<_CharT, _Alloc>& __x, rope<_CharT, _Alloc>& __y) ++ { __x.swap(__y); } ++ ++_GLIBCXX_END_NAMESPACE ++ ++ ++namespace std ++{ ++namespace tr1 ++{ ++ template<> ++ struct hash<__gnu_cxx::crope> ++ { ++ size_t ++ operator()(const __gnu_cxx::crope& __str) const ++ { ++ size_t __size = __str.size(); ++ if (0 == __size) ++ return 0; ++ return 13 * __str[0] + 5 * __str[__size - 1] + __size; ++ } ++ }; ++ ++ ++ template<> ++ struct hash<__gnu_cxx::wrope> ++ { ++ size_t ++ operator()(const __gnu_cxx::wrope& __str) const ++ { ++ size_t __size = __str.size(); ++ if (0 == __size) ++ return 0; ++ return 13 * __str[0] + 5 * __str[__size - 1] + __size; ++ } ++ }; ++} // namespace tr1 ++} // namespace std ++ ++# include ++ ++#endif +Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/mt_allocator.h +=================================================================== +--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/mt_allocator.h (revision 0) ++++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/android/tmp/android-14-toolchain/arm-linux-androideabi/include/c++/4.4.3/ext/mt_allocator.h (revision 11967) +@@ -0,0 +1,751 @@ ++// MT-optimized allocator -*- C++ -*- ++ ++// Copyright (C) 2003, 2004, 2005, 2006, 2007, 2008, 2009 ++// Free Software Foundation, Inc. ++// ++// This file is part of the GNU ISO C++ Library. This library is free ++// software; you can redistribute it and/or modify it under the ++// terms of the GNU General Public License as published by the ++// Free Software Foundation; either version 3, or (at your option) ++// any later version. ++ ++// This library is distributed in the hope that it will be useful, ++// but WITHOUT ANY WARRANTY; without even the implied warranty of ++// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++// GNU General Public License for more details. ++ ++// Under Section 7 of GPL version 3, you are granted additional ++// permissions described in the GCC Runtime Library Exception, version ++// 3.1, as published by the Free Software Foundation. ++ ++// You should have received a copy of the GNU General Public License and ++// a copy of the GCC Runtime Library Exception along with this program; ++// see the files COPYING3 and COPYING.RUNTIME respectively. If not, see ++// . ++ ++/** @file ext/mt_allocator.h ++ * This file is a GNU extension to the Standard C++ Library. ++ */ ++ ++#ifndef _MT_ALLOCATOR_H ++#define _MT_ALLOCATOR_H 1 ++ ++#include ++#include ++#include ++#include ++#include ++ ++_GLIBCXX_BEGIN_NAMESPACE(__gnu_cxx) ++ ++ using std::size_t; ++ using std::ptrdiff_t; ++ ++ typedef void (*__destroy_handler)(void*); ++ ++ /// Base class for pool object. ++ struct __pool_base ++ { ++ // Using short int as type for the binmap implies we are never ++ // caching blocks larger than 32768 with this allocator. ++ typedef unsigned short int _Binmap_type; ++ ++ // Variables used to configure the behavior of the allocator, ++ // assigned and explained in detail below. ++ struct _Tune ++ { ++ // Compile time constants for the default _Tune values. ++ enum { _S_align = 8 }; ++ enum { _S_max_bytes = 128 }; ++ enum { _S_min_bin = 8 }; ++ enum { _S_chunk_size = 4096 - 4 * sizeof(void*) }; ++ enum { _S_max_threads = 4096 }; ++ enum { _S_freelist_headroom = 10 }; ++ ++ // Alignment needed. ++ // NB: In any case must be >= sizeof(_Block_record), that ++ // is 4 on 32 bit machines and 8 on 64 bit machines. ++ size_t _M_align; ++ ++ // Allocation requests (after round-up to power of 2) below ++ // this value will be handled by the allocator. A raw new/ ++ // call will be used for requests larger than this value. ++ // NB: Must be much smaller than _M_chunk_size and in any ++ // case <= 32768. ++ size_t _M_max_bytes; ++ ++ // Size in bytes of the smallest bin. ++ // NB: Must be a power of 2 and >= _M_align (and of course ++ // much smaller than _M_max_bytes). ++ size_t _M_min_bin; ++ ++ // In order to avoid fragmenting and minimize the number of ++ // new() calls we always request new memory using this ++ // value. Based on previous discussions on the libstdc++ ++ // mailing list we have chosen the value below. ++ // See http://gcc.gnu.org/ml/libstdc++/2001-07/msg00077.html ++ // NB: At least one order of magnitude > _M_max_bytes. ++ size_t _M_chunk_size; ++ ++ // The maximum number of supported threads. For ++ // single-threaded operation, use one. Maximum values will ++ // vary depending on details of the underlying system. (For ++ // instance, Linux 2.4.18 reports 4070 in ++ // /proc/sys/kernel/threads-max, while Linux 2.6.6 reports ++ // 65534) ++ size_t _M_max_threads; ++ ++ // Each time a deallocation occurs in a threaded application ++ // we make sure that there are no more than ++ // _M_freelist_headroom % of used memory on the freelist. If ++ // the number of additional records is more than ++ // _M_freelist_headroom % of the freelist, we move these ++ // records back to the global pool. ++ size_t _M_freelist_headroom; ++ ++ // Set to true forces all allocations to use new(). ++ bool _M_force_new; ++ ++ explicit ++ _Tune() ++ : _M_align(_S_align), _M_max_bytes(_S_max_bytes), _M_min_bin(_S_min_bin), ++ _M_chunk_size(_S_chunk_size), _M_max_threads(_S_max_threads), ++ _M_freelist_headroom(_S_freelist_headroom), ++ _M_force_new(std::getenv("GLIBCXX_FORCE_NEW") ? true : false) ++ { } ++ ++ explicit ++ _Tune(size_t __align, size_t __maxb, size_t __minbin, size_t __chunk, ++ size_t __maxthreads, size_t __headroom, bool __force) ++ : _M_align(__align), _M_max_bytes(__maxb), _M_min_bin(__minbin), ++ _M_chunk_size(__chunk), _M_max_threads(__maxthreads), ++ _M_freelist_headroom(__headroom), _M_force_new(__force) ++ { } ++ }; ++ ++ struct _Block_address ++ { ++ void* _M_initial; ++ _Block_address* _M_next; ++ }; ++ ++ const _Tune& ++ _M_get_options() const ++ { return _M_options; } ++ ++ void ++ _M_set_options(_Tune __t) ++ { ++ if (!_M_init) ++ _M_options = __t; ++ } ++ ++ bool ++ _M_check_threshold(size_t __bytes) ++ { return __bytes > _M_options._M_max_bytes || _M_options._M_force_new; } ++ ++ size_t ++ _M_get_binmap(size_t __bytes) ++ { return _M_binmap[__bytes]; } ++ ++ size_t ++ _M_get_align() ++ { return _M_options._M_align; } ++ ++ explicit ++ __pool_base() ++ : _M_options(_Tune()), _M_binmap(NULL), _M_init(false) { } ++ ++ explicit ++ __pool_base(const _Tune& __options) ++ : _M_options(__options), _M_binmap(NULL), _M_init(false) { } ++ ++ private: ++ explicit ++ __pool_base(const __pool_base&); ++ ++ __pool_base& ++ operator=(const __pool_base&); ++ ++ protected: ++ // Configuration options. ++ _Tune _M_options; ++ ++ _Binmap_type* _M_binmap; ++ ++ // Configuration of the pool object via _M_options can happen ++ // after construction but before initialization. After ++ // initialization is complete, this variable is set to true. ++ bool _M_init; ++ }; ++ ++ ++ /** ++ * @brief Data describing the underlying memory pool, parameterized on ++ * threading support. ++ */ ++ template ++ class __pool; ++ ++ /// Specialization for single thread. ++ template<> ++ class __pool : public __pool_base ++ { ++ public: ++ union _Block_record ++ { ++ // Points to the block_record of the next free block. ++ _Block_record* _M_next; ++ }; ++ ++ struct _Bin_record ++ { ++ // An "array" of pointers to the first free block. ++ _Block_record** _M_first; ++ ++ // A list of the initial addresses of all allocated blocks. ++ _Block_address* _M_address; ++ }; ++ ++ void ++ _M_initialize_once() ++ { ++ if (__builtin_expect(_M_init == false, false)) ++ _M_initialize(); ++ } ++ ++ void ++ _M_destroy() throw(); ++ ++ char* ++ _M_reserve_block(size_t __bytes, const size_t __thread_id); ++ ++ void ++ _M_reclaim_block(char* __p, size_t __bytes); ++ ++ size_t ++ _M_get_thread_id() { return 0; } ++ ++ const _Bin_record& ++ _M_get_bin(size_t __which) ++ { return _M_bin[__which]; } ++ ++ void ++ _M_adjust_freelist(const _Bin_record&, _Block_record*, size_t) ++ { } ++ ++ explicit __pool() ++ : _M_bin(NULL), _M_bin_size(1) { } ++ ++ explicit __pool(const __pool_base::_Tune& __tune) ++ : __pool_base(__tune), _M_bin(NULL), _M_bin_size(1) { } ++ ++ private: ++ // An "array" of bin_records each of which represents a specific ++ // power of 2 size. Memory to this "array" is allocated in ++ // _M_initialize(). ++ _Bin_record* _M_bin; ++ ++ // Actual value calculated in _M_initialize(). ++ size_t _M_bin_size; ++ ++ void ++ _M_initialize(); ++ }; ++ ++#ifdef __GTHREADS ++ /// Specialization for thread enabled, via gthreads.h. ++ template<> ++ class __pool : public __pool_base ++ { ++ public: ++ // Each requesting thread is assigned an id ranging from 1 to ++ // _S_max_threads. Thread id 0 is used as a global memory pool. ++ // In order to get constant performance on the thread assignment ++ // routine, we keep a list of free ids. When a thread first ++ // requests memory we remove the first record in this list and ++ // stores the address in a __gthread_key. When initializing the ++ // __gthread_key we specify a destructor. When this destructor ++ // (i.e. the thread dies) is called, we return the thread id to ++ // the front of this list. ++ struct _Thread_record ++ { ++ // Points to next free thread id record. NULL if last record in list. ++ _Thread_record* _M_next; ++ ++ // Thread id ranging from 1 to _S_max_threads. ++ size_t _M_id; ++ }; ++ ++ union _Block_record ++ { ++ // Points to the block_record of the next free block. ++ _Block_record* _M_next; ++ ++ // The thread id of the thread which has requested this block. ++ size_t _M_thread_id; ++ }; ++ ++ struct _Bin_record ++ { ++ // An "array" of pointers to the first free block for each ++ // thread id. Memory to this "array" is allocated in ++ // _S_initialize() for _S_max_threads + global pool 0. ++ _Block_record** _M_first; ++ ++ // A list of the initial addresses of all allocated blocks. ++ _Block_address* _M_address; ++ ++ // An "array" of counters used to keep track of the amount of ++ // blocks that are on the freelist/used for each thread id. ++ // - Note that the second part of the allocated _M_used "array" ++ // actually hosts (atomic) counters of reclaimed blocks: in ++ // _M_reserve_block and in _M_reclaim_block those numbers are ++ // subtracted from the first ones to obtain the actual size ++ // of the "working set" of the given thread. ++ // - Memory to these "arrays" is allocated in _S_initialize() ++ // for _S_max_threads + global pool 0. ++ size_t* _M_free; ++ size_t* _M_used; ++ ++ // Each bin has its own mutex which is used to ensure data ++ // integrity while changing "ownership" on a block. The mutex ++ // is initialized in _S_initialize(). ++ __gthread_mutex_t* _M_mutex; ++ }; ++ ++ // XXX GLIBCXX_ABI Deprecated ++ void ++ _M_initialize(__destroy_handler); ++ ++ void ++ _M_initialize_once() ++ { ++ if (__builtin_expect(_M_init == false, false)) ++ _M_initialize(); ++ } ++ ++ void ++ _M_destroy() throw(); ++ ++ char* ++ _M_reserve_block(size_t __bytes, const size_t __thread_id); ++ ++ void ++ _M_reclaim_block(char* __p, size_t __bytes); ++ ++ const _Bin_record& ++ _M_get_bin(size_t __which) ++ { return _M_bin[__which]; } ++ ++ void ++ _M_adjust_freelist(const _Bin_record& __bin, _Block_record* __block, ++ size_t __thread_id) ++ { ++ if (__gthread_active_p()) ++ { ++ __block->_M_thread_id = __thread_id; ++ --__bin._M_free[__thread_id]; ++ ++__bin._M_used[__thread_id]; ++ } ++ } ++ ++ // XXX GLIBCXX_ABI Deprecated ++ void ++ _M_destroy_thread_key(void*); ++ ++ size_t ++ _M_get_thread_id(); ++ ++ explicit __pool() ++ : _M_bin(NULL), _M_bin_size(1), _M_thread_freelist(NULL) ++ { } ++ ++ explicit __pool(const __pool_base::_Tune& __tune) ++ : __pool_base(__tune), _M_bin(NULL), _M_bin_size(1), ++ _M_thread_freelist(NULL) ++ { } ++ ++ private: ++ // An "array" of bin_records each of which represents a specific ++ // power of 2 size. Memory to this "array" is allocated in ++ // _M_initialize(). ++ _Bin_record* _M_bin; ++ ++ // Actual value calculated in _M_initialize(). ++ size_t _M_bin_size; ++ ++ _Thread_record* _M_thread_freelist; ++ void* _M_thread_freelist_initial; ++ ++ void ++ _M_initialize(); ++ }; ++#endif ++ ++ template