Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 11531)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 11532)
@@ -8,4 +8,10 @@
 	eval $i
 done
+
+#Windows compilers: 
+if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
+	source $ISSM_TIER/externalpackages/windows/windows_environment.sh
+fi
+
 
 #CRON utilities
Index: /issm/trunk-jpl/externalpackages/windows/README
===================================================================
--- /issm/trunk-jpl/externalpackages/windows/README	(revision 11532)
+++ /issm/trunk-jpl/externalpackages/windows/README	(revision 11532)
@@ -0,0 +1,52 @@
+How to install intel compiler to work on cygwin at the command line: 
+
+This is what I got from the following post on google: 
+
+-----------------------------------------------------
+All necessary paths and environment variables are set if you put the Microsoft linker path in ICL.CFG, and open the Intel 
+compiler command line window on the Start menu. Then you can run cygwin.bat so that bash inherits the ICL paths, 
+without breaking ICL. You will sometimes get the bash warning about finding Windows style paths in the environment, 
+but those are necessary for ICL and Microsoft link. Needless to say, the Windows environment variable forgetfulness
+ point will be reached sooner with this setup.
+
+After I run cygwin.bat, and try to run icl, it says:
+
+link: invalid option -- o
+Try `ling --help' for more information.
+
+I verified that icl compiles without any problems before I run cygwin.bat
+
+What am I missing?
+
+
+
+This would indicate that you ignored my advice about icl.cfg, and so you are getting the wrong link.exe.  It should have said "link" not "ling."
+For a VC9 installation, /windows/C/Program Files/Intel/Compiler/11.1/026/bin/ia32/icl.cfg:
+-Qlocation,link,"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin"
+-Qprec-div -Qprec-sqrt -Qansi_alias
+----------------------------------------------------------
+
+
+
+
+
+So here is what you do: 
+edit /cygdrive/c/IntelInstall/Compiler/11.1/026/bin/ia32/icl.cfg
+
+add: 
+-Qlocation,link,"C:\Program Files\Microsoft Visual Studio 9.0\VC\bin"
+-Qprec-div -Qprec-sqrt -Qansi_alias
+
+
+Then run the intel compiler command window. Go to C:\Cygwin and run Cygwin.bat. 
+you are now running cygwin with the correct paths.  Type "export" at the command line, and figure out which variables have been set that relate to the intel compiler and visual studio environment. Build a file containing specific export commands and source it from your .bashrc. intel.sh is an example of such file on a Windows XP 32 build. 
+
+
+
+Compiling ISSM using Matlab compatible  compilers. 
+
+At: http://www.mathworks.com/support/compilers/R2011b/win64.html#n2 
+you will find a list of Matlab supported compilers. 
+
+
+We'll try the compile with the Microsoft Windows SDK 7.1: http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=8279
Index: /issm/trunk-jpl/externalpackages/windows/configs/intel-winXP.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/windows/configs/intel-winXP.sh	(revision 11532)
+++ /issm/trunk-jpl/externalpackages/windows/configs/intel-winXP.sh	(revision 11532)
@@ -0,0 +1,16 @@
+ export CPATH="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\include;"
+ export DEVENVDIR="C:\\MicrosoftVisualStudio 9.0\\Common7\\IDE"
+ export FPATH="C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\include;"
+ export FRAMEWORK35VERSION="v3.5"
+ export FRAMEWORKDIR="C:\\WINDOWS\\Microsoft.NET\\Framework"
+ export FRAMEWORKVERSION="v2.0.50727"
+ export INCLUDE="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\tbb\\include;C:\\IntelInstall\\Compiler\\11.1\\038\\include;C:\\MicrosoftVisualStudio 9.0\\VC\\INCLUDE;C:\\Program Files\\Microsoft SDKs\\Windows\\v6.0A\\include;"
+ export IPPROOT="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32"
+ export LIB="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\stublib;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\ia32\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\tbb\\ia32\\vc9\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\Lib\\ia32;C:\\MicrosoftVisualStudio 9.0\\VC\\LIB;C:\\Program Files\\Microsoft SDKs\\Windows\\v6.0A\\lib;"
+ export LIBPATH="C:\\WINDOWS\\Microsoft.NET\\Framework\\v3.5;C:\\WINDOWS\\Microsoft.NET\\Framework\\v2.0.50727;C:\\MicrosoftVisualStudio 9.0\\VC\\LIB;"
+ export LIBRARY_PATH="C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\lib;C:\\IntelInstall\\Compiler\\11.1\\038\\ipp\\ia32\\stublib;C:\\IntelInstall\\Compiler\\11.1\\038\\mkl\\ia32\\lib;"
+ export PATH="$PATH:/cygdrive/c/IntelInstall/Compiler/11.1/038/Bin/ia32:/cygdrive/c/MicrosoftVisualStudio 9.0/Common7/IDE:/cygdrive/c/MicrosoftVisualStudio 9.0/VC/BIN:/cygdrive/c/MicrosoftVisualStudio 9.0/Common7/Tools:/cygdrive/c/WINDOWS/Microsoft.NET/Framework/v3.5:/cygdrive/c/WINDOWS/Microsoft.NET/Framework/v2.0.50727:/cygdrive/c/MicrosoftVisualStudio 9.0/VC/VCPackages:/cygdrive/c/Program Files/Microsoft SDKs/Windows/v6.0A/bin:/cygdrive/c/WINDOWS"
+ export TBB_ARCH_PLATFORM="ia32\\vc9"
+ export VCINSTALLDIR="C:\\MicrosoftVisualStudio 9.0\\VC"
+ export VSINSTALLDIR="C:\\MicrosoftVisualStudio 9.0"
+ export WINDOWSSDKDIR="C:\\Program Files\\Microsoft SDKs\\Windows\\v6.0A\\"
Index: /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-32.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-32.sh	(revision 11532)
+++ /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-32.sh	(revision 11532)
@@ -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: /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh	(revision 11532)
+++ /issm/trunk-jpl/externalpackages/windows/configs/sdk7.1.win7-64.sh	(revision 11532)
@@ -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/trunk-jpl/externalpackages/windows/windows_environment.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/windows/windows_environment.sh	(revision 11532)
+++ /issm/trunk-jpl/externalpackages/windows/windows_environment.sh	(revision 11532)
@@ -0,0 +1,24 @@
+#This file sources all relevant scripts to setup the paths to windows compilers.
+
+#Where are the configuration files for each compiler: 
+config_dir="$ISSM_TIER/externalpackages/windows/configs"
+
+#your choise of compiler: 
+# 1: sdk 7.1 32 bits on Win7
+# 2: sdk 7.1 64 bits on Win7
+# 3: intel compiler on Win7
+# 4: intel compiler on WinXP
+
+compiler=1;
+
+#source corresponding environment variables: 
+
+if [[ "$compiler" == "1" ]]; then 
+	source $config_dir/sdk7.1.win7-32.sh
+elif [[ "$compiler" == "2" ]]; then 
+	source $config_dir/sdk7.1.win7-64.sh
+elif [[ "$compiler" == "3" ]]; then 
+	source $config_dir/intel-win7.sh
+else 
+	source $config_dir/intel-winXP.sh
+fi
