Index: ../trunk-jpl/packagers/ubuntu/README
===================================================================
--- ../trunk-jpl/packagers/ubuntu/README	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/README	(revision 18436)
@@ -1,60 +0,0 @@
-TARBALL INSTALLATION:
-
-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;"
-
-
-UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION 
--------------------------------------------------------------------------------
-				OR THE RIGHT WAY....
-DPKG/DEB INSTALLATION:
-
-To install from deb archives (*.deb), use:
-
-	> sudo dpkg --install <debarchive>
-
-That's it! But not really. Do make sure that you install petsc and metis first.
-When you first try to install issm, dpkg will tell you that you are missing
-dependencies. Just:
-
-	> sudo apt-get install -f
-
-to fix the dependencies and complete the install. When apt-get is done, you 
-should see something that says that ISSM is installed correctly on your 
-machine. That's it! For real this time.
-
-Uninstalling is simple too:
-
-	> sudo apt-get remove <issmPackageName>
-
-That'll do all the work for you. This won't delete any configuration or user
-defined environment stuff. Just swap "remove" out for "purge" and that'll
-delete everything. And apt-get might ask you to remove unneeded dependencies,
-so you should probably do that to keep your system clean.
-
-To create your own custom debian archive, see the README in issmpkg.
-
--------------------------------------------------------------------------------
-
-APT-GET INSTALLATION: (this doesnot work yet)
-
-To install from apt-get:
-
-	> sudo add-apt-repository <issm_PPA_URL>
-	> sudo apt-get install <issmPackageName>
-
-Just say yes to everything apt asks you, and you're good.
-
-UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION 
Index: ../trunk-jpl/packagers/ubuntu/issmpkg/issm_options.m4
===================================================================
--- ../trunk-jpl/packagers/ubuntu/issmpkg/issm_options.m4	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/issmpkg/issm_options.m4	(revision 18436)
@@ -1,1690 +0,0 @@
-dnl ISSM Options
-
-AC_DEFUN([ISSM_OPTIONS],[
-
-	dnl ISSM's internal options
-	dnl Debugging {{{
-	AC_ARG_ENABLE([debugging],                                        dnl feature
-		AS_HELP_STRING([--enable-debugging],[turn debug support on]),  dnl help string
-		[enable_debugging=$enableval],                                 dnl action if given
-		[enable_debugging=no])                                         dnl action if not given
-	if test "x$enable_debugging" = xyes; then
-		AC_DEFINE([_ISSM_DEBUG_],[1],[Macro to enable debugging in ISSM])
-	fi
-
-	dnl }}}
-    dnl Shared build {{{
-    AC_ARG_ENABLE([sharedlibs],                                                dnl feature
-        AS_HELP_STRING([--enable-sharedlibs], [produce libISSM.so.0]),         dnl help string
-        [enable_sharedlibs=$enableval],                                        dnl action if given
-        [enable_sharedlibs=no])                                                dnl action if not given
-    AM_CONDITIONAL([SHAREDLIBS], [test x$enable_sharedlibs = xyes])
-    dnl }}}
-    dnl Version{{{
-    AC_ARG_ENABLE([version],                                                dnl feature
-        AS_HELP_STRING([--enable-version], [produce libISSM.so.0]),         dnl help string
-        [enable_version=$enableval],                                        dnl action if given
-        [enable_version=no])                                                dnl action if not given
-    AM_CONDITIONAL([VERSION], [test x$enable_VERSION = xyes])
-    dnl }}}
-	dnl Wrappers build {{{
-	AC_ARG_WITH([wrappers],
-		AS_HELP_STRING([--with-wrappers = value],[wrappers compilation. ]),
-		[WRAPPERS_VALUE=$withval],[WRAPPERS_VALUE="yes"])
-	AC_MSG_CHECKING(for wrappers compilation)
-	AM_CONDITIONAL([WRAPPERS], [test x$WRAPPERS_VALUE = xyes])
-	AC_MSG_RESULT($WRAPPERS_VALUE) 
-	dnl }}}
-	dnl Extensions{{{
-	ISSMEXT=".exe"
-	AC_SUBST([ISSMEXT])
-	dnl }}}
-
-	dnl ISSM's externalpackages
-	dnl vendor{{{
-	AC_ARG_WITH([vendor],
-	  AS_HELP_STRING([--with-vendor = VENDOR], [vendor name, ex: intel]),
-	  [VENDOR=$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=cl
-			export CXX=cccl
-			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
-			export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
-			export AR="ar-lib lib"
-			export OS_LDFLAG="-Wl,"
-			export RANLIB=true
-			OSLIBS="-Wl,kernel32.lib -Wl,user32.lib -Wl,gdi32.lib -Wl,winspool.lib -Wl,comdlg32.lib -Wl,advapi32.lib -Wl,shell32.lib -Wl,ole32.lib -Wl,oleaut32.lib -Wl,uuid.lib -Wl,odbc32.lib -Wl,odbccp32.lib"
-		elif  test $VENDOR = intel-win7-64; then
-			export CC=cl
-			export CXX=cccl
-			export CXXFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
-			export CFLAGS="-DWIN32 -D_INTEL_WIN_ -EHsc"
-			export AR="ar-lib lib"
-			export OS_LDFLAG="-Wl,"
-			export RANLIB=true
-			OSLIBS="-Wl,kernel32.lib -Wl,user32.lib -Wl,gdi32.lib -Wl,winspool.lib -Wl,comdlg32.lib -Wl,advapi32.lib -Wl,shell32.lib -Wl,ole32.lib -Wl,oleaut32.lib -Wl,uuid.lib -Wl,odbc32.lib -Wl,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-discover; then
-			export CC=icc
-			export CXX=icpc
-			export CXXFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
-			export CFLAGS=" -O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
-		elif test $VENDOR = intel-pleiades; then
-			export CC=icc
-			export CXX=icpc
-			export CXXFLAGS=" -O3 -D_INTEL_LINUX_ "
-			export CFLAGS=" -O3 -D_INTEL_LINUX_ "
-        else
-		AC_MSG_ERROR([unknown compiler vendor!])
-		fi
-	fi
-	AC_SUBST([OSLIBS]) 
-	AC_MSG_RESULT(done)
-	dnl }}}
-	dnl matlab{{{
-
-	dnl 1. See if matlab has been provided
-	AC_ARG_WITH([matlab-dir],
-		AS_HELP_STRING([--with-matlab-dir=DIR], [matlab root directory. necessary for serial build.]),
-		[MATLAB_ROOT=$withval],[MATLAB_ROOT=""]) 
-
-	AC_MSG_CHECKING([whether matlab is enabled])
-	if test -d "$MATLAB_ROOT"; then
-		HAVE_MATLAB=yes
-	else
-		HAVE_MATLAB=no
-	fi
-	if test x$HAVE_MATLAB = xyes; then
-		AC_DEFINE([_HAVE_MATLAB_],[1],[with Matlab in ISSM src])
-	fi
-	AC_MSG_RESULT($HAVE_MATLAB)
-	AM_CONDITIONAL([MATLAB], [test x$HAVE_MATLAB = xyes])
-
-	dnl 2. Get Matlab libraries
-	if test x$HAVE_MATLAB = xyes; then
-
-		AC_MSG_CHECKING(for matlab headers and libraries in $MATLAB_ROOT)
-  		MATLABINCL="-I$MATLAB_ROOT/extern/include/"
-		
-		dnl 4. get MEXLIB MEXLINK and MEXEXT (experimental)
-      dnl OS-dependent variables and checks
-  		case "${host_os}" in
-  			*cygwin*) 
-  				if  test $VENDOR = intel-win7-32; then
-  					MEXLIB="-Wl,./../../c/libISSMCore.a -Wl,libISSMApi.a -Wl,libISSMMatlab.a -Wl,./../../c/libISSMModules.a -Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" 
-               MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -no-undefined -Wl,/export:mexFunction" 
-  				elif  test l-win7-64; then
-  					MEXLIB="-Wl,./../../c/libISSMCore.a -Wl,libISSMApi.a -Wl,libISSMMatlab.a -Wl,./../../c/libISSMModules.a -Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" 
-               MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -no-undefined -Wl,/export:mexFunction" 
-  				fi
-  				MEXEXT=`$MATLAB_ROOT/bin/mexext.bat`
-  				MEXEXT=".$MEXEXT"
-  			;;
-		   *)
-		      MEXLINK=$(mex -v 2>&1 < /dev/null | grep LDFLAGS     | sed -e "s/         LDFLAGS            = //g")
-	         MEXLIB=$( mex -v 2>&1 < /dev/null | grep CXXLIBS     | sed -e "s/         CXXLIBS            = //g")
-		      MEXEXT=$( mex -v 2>&1 < /dev/null | grep LDEXTENSION | sed -e "s/         LDEXTENSION        = //g")
-  			;;
-      esac
-	   AC_MSG_RESULT(done)
-
-		AC_SUBST([MATLABINCL])
-		AC_SUBST([MEX])
-		MATLABWRAPPEREXT=$MEXEXT
-		AC_SUBST([MATLABWRAPPEREXT])
-	   AC_SUBST([MEXLIB]) 
-		AC_SUBST([MEXLINK])
-	fi
-	dnl }}}
-	dnl triangle {{{
-	AC_ARG_WITH([triangle-dir],
-		AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory. necessary for serial build]),
-		[TRIANGLE_ROOT=$withval],
-		[TRIANGLE_ROOT=""]) 
-	AC_ARG_WITH([triangle-include-dir],
-		AS_HELP_STRING([--with-triangle-include-dir], [triangle include dir]),
-		[TRIANGLE_INCL=$withval],
-		[TRIANGLE_INCL="$TRIANGLE_ROOT"])
-	AC_ARG_WITH([triangle-lib-dir],
-		AS_HELP_STRING([--with-triangle-lib-dir], [triangle lib dir]),
-		[TRIANGLE_LIB=$withval],
-		[TRIANGLE_LIB="$TRIANGLE_ROOT"])
-	AC_MSG_CHECKING(for triangle headers and libraries)
-
-	if test -d "$TRIANGLE_ROOT"; then
-
-		dnl defaults
-		HAVE_TRIANGLE=yes
-		TRIANGLEINCL=-I$TRIANGLE_INCL
-
-		case "${host_os}" in
-				*cygwin*)
-				TRIANGLELIB="-Wl,`cygpath -m $TRIANGLE_LIB/`triangle.lib"
-				;;
-				*linux*)
-				TRIANGLELIB="-ltriangle"
-				;;
-				*darwin*)
-				TRIANGLELIB=$TRIANGLE_LIB/triangle.a
-				;;
-			esac
-
-		AC_DEFINE([_HAVE_TRIANGLE_],[1],[with Triangle in ISSM src])
-		AC_SUBST([TRIANGLEINCL])
-		AC_SUBST([TRIANGLELIB])
-
-	else
-		HAVE_TRIANGLE=no
-	fi
-	AC_MSG_RESULT($HAVE_TRIANGLE)
-	dnl }}}
-	dnl boost{{{
-	AC_ARG_WITH([boost-dir],
-	  AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]),
-	  [BOOST_ROOT=$withval],[BOOST_ROOT=""]) 
-	AC_MSG_CHECKING(for boost)
-	
-	if test -d "$BOOST_ROOT"; then
-		dnl defaults
-		HAVE_BOOST=yes
-		BOOSTINCL=-I$BOOST_ROOT/include
-		BOOSTLIB="-L$BOOST_ROOT/lib -lboost_python"
-
-		AC_DEFINE([_HAVE_BOOST_],[1],[with Boost in ISSM src])
-		AC_SUBST([BOOSTINCL])
-		AC_SUBST([BOOSTLIB])
-	else
-		HAVE_BOOST=no
-	fi
-	AM_CONDITIONAL([BOOST], [test x$HAVE_BOOST = xyes])
-	AC_MSG_RESULT($HAVE_BOOST)
-	dnl }}}
-	dnl dakota{{{
-	AC_ARG_WITH([dakota-dir],
-	  AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory. necessary for serial build]),
-	  [DAKOTA_ROOT=$withval],[DAKOTA_ROOT=""]) 
-	AC_MSG_CHECKING(for dakota)
-	
-	if test -d "$DAKOTA_ROOT"; then
-
-		dnl defaults
-		HAVE_DAKOTA=yes
-		AC_MSG_RESULT($HAVE_DAKOTA)
-		DAKOTAINCL=-I$DAKOTA_ROOT/include
-		AC_MSG_CHECKING(for dakota version)
-		if test -f "$DAKOTA_ROOT/../src/src/CommandLineHandler.C"; then
-			DAKOTA_VERSION=`cat $DAKOTA_ROOT/../src/src/CommandLineHandler.C | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
-		else if test -f "$DAKOTA_ROOT/../src/src/CommandLineHandler.cpp"; then
-			DAKOTA_VERSION=`cat $DAKOTA_ROOT/../src/src/CommandLineHandler.cpp | grep 'DAKOTA version' | grep 'release' | grep -v // | sed 's/.*DAKOTA version //' | sed 's/ .*//' `
-		else
-			AC_MSG_ERROR([Dakota CommandLineHandler.C or CommandLineHandler.cpp file not found to determine DAKOTA_VERSION!]);
-		fi
-		fi
-
-		AC_MSG_RESULT($DAKOTA_VERSION)
-		AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_],"$DAKOTA_VERSION",[Dakota version number])
-		DAKOTAFLAGS=""
-		case "${host_os}" in
-			*cygwin*)
-				if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
-					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver"
-				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
-					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem"
-				else
-					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
-				fi
-				fi
-			;;
-			*linux*)
-				if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
-					DAKOTALIB="-L$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"
-				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
-					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system -ldl"
-				else if test x$DAKOTA_VERSION = x5.3 || test x$DAKOTA_VERSION = x5.3.1; then
-					DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_COLINY -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_JEGA -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
-					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -lmods -lmod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack_fortran -lutilib -lcolin -linterfaces -lscolib -l3po -lpebbl -ltinyxml -lconmin -ldace -lanalyzer -lrandom -lsampling -lbose -lfsudace -lhopspack -ljega -ljega_fe -lmoga -lsoga -leutils -lutilities -lncsuopt -lcport -loptpp -lpsuade -lamplsolver -L$BOOST_ROOT/lib -lboost_signals -lboost_regex -lboost_filesystem -lboost_system "
-				else
-					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
-				fi
-				fi
-				fi
-			;;
-			*darwin*)
-				if      test x$DAKOTA_VERSION = x4.2 || test x$DAKOTA_VERSION = x4.2+; then
-					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -lfftw3 -llhs -levidence -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -lopt -lpsuade -lnewmat -lncsuopt -lgsl -lquadrature -lcoliny -lcolin -lpebbl -lutilib -l3po -lnappspack -lappspack -lconveyor -lshared -lcdd -lamplsolver" 
-					dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
-				else if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
-					DAKOTALIB="-L$DAKOTA_ROOT/lib -ldakota -lteuchos -lpecos -llhs -lsparsegrid -lsurfpack -lconmin -lddace -lfsudace -ljega -lcport -loptpp -lpsuade -lncsuopt -lcolin -linterfaces -lmomh -lscolib -lpebbl -ltinyxml -lutilib -l3po -lhopspack -lnidr -lamplsolver -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
-					dnl DAKOTALIB+= "-lgslcblas -L/usr/lib -lblas -llapack"
-				else
-					AC_MSG_ERROR([Dakota version not found or version ($DAKOTA_VERSION) not supported!]);
-				fi
-				fi
-			;;
-		esac
-		AC_DEFINE([_HAVE_DAKOTA_],[1],[with Dakota in ISSM src])
-
-		case $DAKOTA_VERSION in
-			@<:@1-9@:>@.@<:@0-9@:>@.@<:@0-9@:>@)
-				DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
-				DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\)\..*/\1/'`
-				DAKOTA_BUILD=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
-			;;
-			@<:@1-9@:>@.@<:@0-9@:>@)
-				DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
-				DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
-				DAKOTA_BUILD=0
-			;;
-			@<:@1-9@:>@.@<:@0-9@:>@+)
-				DAKOTA_MAJOR=`echo $DAKOTA_VERSION | sed -e 's/^\(@<:@0-9@:>@*\)\..*/\1/'`
-				DAKOTA_MINOR=`echo $DAKOTA_VERSION | sed -e 's/^@<:@0-9@:>@*\.\(@<:@0-9@:>@*\).*/\1/'`
-				DAKOTA_BUILD=0
-			;;
-			*)
-				AC_MSG_ERROR([Dakota version ($DAKOTA_VERSION) not supported!]);
-		   ;;
-		esac
-		AC_MSG_CHECKING(for dakota major version)
-		AC_MSG_RESULT($DAKOTA_MAJOR)
-		AC_DEFINE_UNQUOTED([_DAKOTA_MAJOR_],$DAKOTA_MAJOR,[Dakota major version number])
-		AC_MSG_CHECKING(for dakota minor version)
-		AC_MSG_RESULT($DAKOTA_MINOR)
-		AC_DEFINE_UNQUOTED([_DAKOTA_MINOR_],$DAKOTA_MINOR,[Dakota minor version number])
-		AC_MSG_CHECKING(for dakota build version)
-		AC_MSG_RESULT($DAKOTA_BUILD)
-		AC_DEFINE_UNQUOTED([_DAKOTA_BUILD_],$DAKOTA_BUILD,[Dakota build version number])
-
-		AC_SUBST([DAKOTAINCL])
-		AC_SUBST([DAKOTAFLAGS])
-		AC_SUBST([DAKOTALIB])
-
-	else
-		HAVE_DAKOTA=no
-		AC_MSG_RESULT($HAVE_DAKOTA)
-	fi
-
-	AM_CONDITIONAL([DAKOTA], [test x$HAVE_DAKOTA = xyes])
-	dnl }}}
-	dnl python{{{
-	AC_ARG_WITH([python-dir],
-		AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]),
-		[PYTHON_ROOT=$withval],
-		[PYTHON_ROOT=""]) 
-
-	AC_ARG_WITH([python-include-dir],
-		AS_HELP_STRING([--with-python-include-dir=DIR], [python include directory.]),
-		[PYTHON_INCL=$withval],
-		[PYTHON_INCL="$PYTHON_ROOT/include"]) 
-
-	AC_ARG_WITH([python-lib-dir],
-		AS_HELP_STRING([--with-python-lib-dir=DIR], [python lib directory.]),
-		[PYTHON_LIB=$withval],
-		[PYTHON_LIB="$PYTHON_ROOT/lib"]) 
-
-	AC_MSG_CHECKING(for python)
-	if test -d "$PYTHON_ROOT"; then
-		HAVE_PYTHON="yes"
-		AC_DEFINE([_HAVE_PYTHON_],[1],[with Python in ISSM src])
-	else
-		HAVE_PYTHON=no
-	fi
-	AC_MSG_RESULT($HAVE_PYTHON)
-
-	dnl get python version
-	if test x$HAVE_PYTHON = xyes; then
-		AC_MSG_CHECKING(for python version)
-		dnl Query Python for its version number.  Getting [:3] seems to be
-		dnl the best way to do this; it's what "site.py" does in the standard
-		dnl library.
-		PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]")
-		AC_MSG_RESULT($PYTHON_VERSION)
-
-		dnl recover major: 
-		PYTHON_MAJOR=${PYTHON_VERSION%.*}
-		if test x$PYTHON_MAJOR = x3; then
-			dnl are we running python 3?
-			HAVE_PYTHON3="yes"
-		else
-			HAVE_PYTHON3="no"
-		fi
-		AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major])
-
-		PYTHONINCL="-I$PYTHON_INCL"
-		PYTHONLIB="-L$PYTHON_LIB -lpython$PYTHON_VERSION"
-		PYTHONEXT=.so
-
-		case "${host_os}" in
-			*cygwin*)
-			PYTHONLINK="-shared"
-			;;
-			*linux*)
-			PYTHONLINK="-shared"
-			;;
-			*darwin*)
-			PYTHONLINK="-dynamiclib"
-			;;
-		esac
-
-		AC_SUBST([PYTHONINCL])
-		AC_SUBST([PYTHONLIB])
-		PYTHONWRAPPEREXT=$PYTHONEXT
-		AC_SUBST([PYTHONWRAPPEREXT])
-		AC_SUBST([PYTHONLINK])
-	fi
-	AM_CONDITIONAL([PYTHON], [test x$HAVE_PYTHON = xyes])
-	AM_CONDITIONAL([PYTHON3], [test x$HAVE_PYTHON3 = xyes])
-	dnl }}}
-	dnl python-numpy{{{
-	AC_ARG_WITH([python-numpy-dir],
-	  AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]),
-	  [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT=""]) 
-	AC_MSG_CHECKING(for python-numpy)
-	
-	if test -d "$PYTHON_NUMPY_ROOT"; then
-		dnl defaults
-		HAVE_PYTHON_NUMPY=yes
-		PYTHON_NUMPYINCL="-I$PYTHON_NUMPY_ROOT -I$PYTHON_NUMPY_ROOT/core/include/numpy"
-
-		AC_DEFINE([_HAVE_PYTHON_NUMPY_],[1],[with Python-Numpy in ISSM src])
-		AC_SUBST([PYTHON_NUMPYINCL])
-	else
-		HAVE_PYTHON_NUMPY=no
-	fi
-	AC_MSG_RESULT($HAVE_PYTHON_NUMPY)
-	dnl }}}
-	dnl chaco{{{
-	AC_ARG_WITH([chaco-dir],
-	  AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]),
-	  [CHACO_ROOT=$withval],[CHACO_ROOT=""]) 
-	AC_MSG_CHECKING(for chaco)
-	
-	if test -d "$CHACO_ROOT"; then
-
-		dnl defaults
-		HAVE_CHACO=yes
-		CHACOINCL=-I$CHACO_ROOT/include
-		CHACOLIB="-L$CHACO_ROOT/lib -lchacominusblas"
-
-		AC_DEFINE([_HAVE_CHACO_],[1],[with Chaco in ISSM src])
-		AC_SUBST([CHACOINCL])
-		AC_SUBST([CHACOLIB])
-
-	else
-		HAVE_CHACO=no
-	fi
-	AC_MSG_RESULT($HAVE_CHACO)
-	dnl }}}
-	dnl scotch{{{
-	AC_ARG_WITH([scotch-dir],
-	  AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]),
-	  [SCOTCH_ROOT=$withval],[SCOTCH_ROOT=""]) 
-	AC_MSG_CHECKING(for scotch)
-	
-	if test -d "$SCOTCH_ROOT"; then
-
-		dnl defaults
-		HAVE_SCOTCH=yes
-		SCOTCHINCL="-DNOFILEIO -I$SCOTCH_ROOT/include -DSCOTCH_VERSION=\\\"UNKNOWN\\\""
-		SCOTCHLIB="-L$SCOTCH_ROOT/lib -lnfioscotch -lnfioscotcherr -lnfioscotcherrexit -lscotchmetis"
-
-		AC_DEFINE([_HAVE_SCOTCH_],[1],[with Scotch in ISSM src])
-		AC_SUBST([SCOTCHINCL])
-		AC_SUBST([SCOTCHLIB])
-
-	else
-		HAVE_SCOTCH=no
-	fi
-	AC_MSG_RESULT($HAVE_SCOTCH)
-	dnl }}}
-	dnl adolc{{{
-	AC_ARG_WITH([adolc-dir],
-		AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]),
-		[ADOLC_ROOT=$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$ADOLC_ROOT/include"
-			ADOLCLIB="-L$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 adolc-version{{{
-	AC_ARG_WITH([adolc-version],
-		AS_HELP_STRING([--with-adolc-version=number], [adolc version.]),
-		[ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) 
-	AC_MSG_CHECKING(for adolc-version) 
-
-	AC_DEFINE_UNQUOTED([_ADOLC_VERSION_],$ADOLC_VERSION,[ADOLC version])
-	AC_MSG_RESULT($ADOLC_VERSION)
-	dnl }}}
-	dnl adic2{{{
-	AC_ARG_WITH([adic2-dir],
-	  AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]),
-	  [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) 
-	AC_MSG_CHECKING(for adic2)
-
-	if test "x$ADIC2_ROOT" = "xno"; then
-		HAVE_ADIC2=no
-	else
-		if test -d "$ADIC2_ROOT"; then
-
-			dnl defaults
-			HAVE_ADIC2=yes
-			ADIC2INCL="-DADIC2_DENSE -I$ADIC2_ROOT/include -I$ADIC2_ROOT/share/runtime_dense/"
-			ADIC2LIB=""
-
-			AC_DEFINE([_HAVE_ADIC2_],[1],[with adic2 in ISSM src])
-			AC_SUBST([ADIC2INCL])
-			AC_SUBST([ADIC2LIB])
-
-		else
-			echo  "Specified directory does not exist!"
-			exit 1
-		fi
-	fi
-	AM_CONDITIONAL([ADIC2], [test x$HAVE_ADIC2 = xyes])
-	AC_MSG_RESULT($HAVE_ADIC2)
-	dnl }}}
-	dnl gsl{{{
-	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$GSL_ROOT/include"
-		GSLLIB="-dy -L$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{{{
-	AC_ARG_WITH([rose-dir],
-	  AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]),
-	  [ROSE_ROOT=$withval],[ROSE_ROOT=""]) 
-	AC_MSG_CHECKING(for rose)
-	
-	if test -d "$ROSE_ROOT"; then
-
-		dnl defaults
-		HAVE_ROSE=yes
-		ROSEINCL="-I$ROSE_ROOT/include"
-		ROSELIB=""
-
-		AC_DEFINE([_HAVE_ROSE_],[1],[with rose in ISSM src])
-		AC_SUBST([ROSEINCL])
-		AC_SUBST([ROSELIB])
-
-	else
-		HAVE_ROSE=no
-	fi
-	AM_CONDITIONAL([ROSE], [test x$HAVE_ROSE = xyes])
-	AC_MSG_RESULT($HAVE_ROSE)
-	dnl }}}
-	dnl mpi{{{
-	AC_MSG_CHECKING(for mpi)
-	
-	AC_ARG_WITH([mpi-include],
-	  AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]),
-	  [MPI_INCLUDE=$withval],[MPI_INCLUDE=""])
-
-	AC_ARG_WITH([mpi-libdir],
-	  AS_HELP_STRING([--with-mpi-libdir=DIR],[mpi lib directory, necessary for parallel build]),
-	  [MPI_LIBDIR=$withval],[MPI_LIBDIR=""])
-
-	AC_ARG_WITH([mpi-libflags],
-	  AS_HELP_STRING([--with-mpi-libflags=LIBS],[mpi libraries to be used, necessary for parallel build]),
-	  [MPI_LIBFLAGS=$withval],[MPI_LIBFLAGS=""])
-
-	
-	if test -z "$MPI_INCLUDE" ; then
-		HAVE_MPI=no
-	else
-		HAVE_MPI=yes
-
-		dnl Processing for windows
-		if  test x$VENDOR = xintel-win7-32; then
-			MPI_LIBDIR=`cygpath -m $MPI_LIBDIR`
-			MPIINCL=`cygpath -m $MPI_INCLUDE`
-		elif test x$VENDOR = xintel-win7-64; then
-			MPI_LIBDIR=`cygpath -m $MPI_LIBDIR`
-			MPI_INCLUDE=`cygpath -m $MPI_INCLUDE`
-		fi
-
-		if test -z "$MPI_LIBDIR"; then
-			MPIINCL=-I"$MPI_INCLUDE"
-			MPILIB="$MPI_LIBFLAGS"
-		else
-			MPIINCL=-I"$MPI_INCLUDE"
-			MPILIB="-L$MPI_LIBDIR $MPI_LIBFLAGS"
-		fi
-		AC_DEFINE([_HAVE_MPI_],[1],[with Mpi in ISSM src])
-		AC_DEFINE([HAVE_MPI],[1],[Mpi Flag for Dakota (DO NOT REMOVE)])
-		AC_SUBST([MPIINCL])
-		AC_SUBST([MPILIB])
-	fi
-
-	AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes])
-	AC_MSG_RESULT($HAVE_MPI)
-	dnl }}}
-	dnl petsc{{{
-	AC_ARG_WITH([petsc-dir],
-	  AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]),
-	  [PETSC_ROOT=$withval],[PETSC_ROOT=""])
-		
-	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)
-
-		PETSC_VERSION_DATE_HG=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_DATE_HG" | sed 's/#define PETSC_VERSION_DATE_HG//' | sed 's/ //g' | sed -e 's/\"//g' `
-		PETSC_RELEASE=`cat $PETSC_ROOT/include/petscversion.h | grep "#define PETSC_VERSION_RELEASE" | sed 's/#define PETSC_VERSION_RELEASE//' | sed 's/ //g'`
-
-		AC_MSG_CHECKING(whether petsc is the development version)
-		dnl if test x$PETSC_VERSION_DATE_HG = xunknown; then
-		if test "$PETSC_RELEASE" = "0"; then
-		   AC_DEFINE([_HAVE_PETSCDEV_],[1],[with PETSc-dev])
-			AC_MSG_RESULT(yes)
-		else
-			AC_MSG_RESULT(no)
-		fi
-	fi
-	
-	AC_ARG_WITH([petsc-arch],
-	  AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch , necessary for parallel build]),
-	  [PETSC_ARCH=$withval],[PETSC_ARCH=""])
-
-	AC_MSG_CHECKING(for petsc headers and libraries in $PETSC_ROOT for architecture $PETSC_ARCH)
-	
-	dnl To ge PETSc's libraries:
-	dnl cd externalpackages/petsc/src
-	dnl make getlinklibs
-	if test -d "$PETSC_ROOT"; then
-
-	 PETSCINCL=" -I$PETSC_ROOT/include"
-	 dnl Add other location (not needed anymore since at least PETSc 3.0)
-	 if test "x$PETSC_ARCH" != "x" && test -d "$PETSC_ROOT/$PETSC_ARCH/include"; then
-	  PETSCINCL+=" $PETSC_ROOT/$PETSC_ARCH/include"
-	 fi
-	 if test "x$PETSC_ARCH" != "x" && test -d "$PETSC_ROOT/include/$PETSC_ARCH"; then
-	  PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH"
-	 fi
-	
-	 case "${host_os}" in
-			*cygwin*)
-			if test $PETSC_MAJOR -lt 3 ; then
-				PETSCLIB=-Wl,/LIBPATH:`cygpath -w $PETSC_ROOT/lib`  -Wl,libpetscksp.lib  -Wl,libpetscdm.lib  -Wl,libpetscmat.lib  -Wl,libpetscvec.lib  -Wl,libpetscsnes.lib  -Wl,libpetscts.lib  -Wl,libmpiuni.lib  -Wl,libpetsc.lib
-			else
-				PETSCLIB="-L$PETSC_ROOT/lib  -Wl,libpetsc.lib"
-				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+="  -Wl,libmetis.lib"; fi
-			fi
-			;;
-			*linux*)
-			if test $PETSC_MAJOR -lt 3 ; then
-				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lmpiuni -lpetsc"
-			else
-				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc -ldl"
-				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi
-			fi
-			;;
-			*darwin*)
-			if test $PETSC_MAJOR -lt 3 ; then
-				PETSCLIB="-L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsnes -lpetscts -lpetsc"
-			else
-				PETSCLIB="-L$PETSC_ROOT/lib -lpetsc"
-				if test $PETSC_MAJOR -gt 3 || test $PETSC_MINOR -ge 3; then PETSCLIB+=" -lmetis"; fi
-			fi
-			;;
-		esac
-		AC_DEFINE([_HAVE_PETSC_],[1],[with PETSc in ISSM src])
-		AC_SUBST([PETSCINCL])
-		AC_SUBST([PETSCLIB])
-		HAVE_PETSC=yes
-	else
-		HAVE_PETSC=no
-	fi
-	
-	AM_CONDITIONAL([PETSC], [test x$HAVE_PETSC = xyes])
-	AC_MSG_RESULT($HAVE_PETSC)
-	dnl }}}
-	dnl metis{{{
-	if test "$HAVE_PETSC" = "yes" && test "x$PETSC_MAJOR" = "x3" && test $PETSC_MINOR -ge 3; then
-
-		dnl in petsc >=3.3, metis is provided
-		HAVE_METIS="yes"
-		AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number])
-		AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src])
-	else
-		AC_ARG_WITH([metis-dir],
-		  AS_HELP_STRING([--with-metis-dir=DIR],[metis root directory. necessary for serial build]),
-		  [METIS_ROOT=$withval],[METIS_ROOT=""])
-
-		AC_MSG_CHECKING(for metis headers and libraries in $METIS_ROOT)
-
-		if test -d "$METIS_ROOT"; then
-
-			dnl first figure out version of metis: does the VERSION file exist?
-			if test -e "$METIS_ROOT/VERSION"; then
-				METIS_VERSION=4
-			else
-				METIS_VERSION=5
-			fi
-
-			dnl defaults
-			HAVE_METIS=yes
-
-			if test "$METIS_VERSION" = "4" ; then
-					
-				METISINCL=-I"$METIS_ROOT/Lib" 
-				case "${host_os}" in
-					*cygwin*)
-					METISLIB="-L$METIS_ROOT -Wl,libmetis.lib"
-					;;
-					*linux*)
-					METISLIB=-L"$METIS_ROOT/ -lmetis"
-					;;
-					*darwin*)
-					METISLIB=-L"$METIS_ROOT/ -lmetis"
-					;;
-				esac
-
-					AC_DEFINE([_METIS_VERSION_],[4],[ Metis version number])
-			fi
-			if test "$METIS_VERSION" = "5" ; then
-		
-				case "${host_os}" in
-					*cygwin*)
-					METISLIB="-L$METIS_ROOT libmetis.lib"
-					;;
-					*linux*)
-					METISLIB=-L"$METIS_ROOT/lib -lmetis"
-					;;
-					*darwin*)
-					METISLIB=-L"$METIS_ROOT/lib -lmetis"
-					;;
-				esac
-
-				METISINCL=-I"$METIS_ROOT/include" 
-				AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number])
-			fi
-
-			AC_DEFINE([_HAVE_METIS_],[1],[with Metis in ISSM src])
-			AC_SUBST([METISINCL])
-			AC_SUBST([METISLIB])
-		else
-			HAVE_METIS=no
-		fi
-		AC_MSG_RESULT($HAVE_METIS)
-	fi
-	AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes])
-	dnl }}}
-	dnl tao{{{
-	AC_ARG_WITH([tao-dir],
-		AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]),
-		[TAO_ROOT=$withval],[TAO_ROOT=""]) 
-	AC_MSG_CHECKING(for tao)
-
-	if test -d "$TAO_ROOT"; then
-
-	  HAVE_TAO=yes
-	  TAOINCL="-I$TAO_ROOT/ -I$TAO_ROOT/include -I$TAO_ROOT/bmake/ "
-	  TAOLIB="-L$TAO_ROOT/lib -ltao -lpetsc"
-
-	  AC_DEFINE([_HAVE_TAO_],[1],[with Tao in ISSM src])
-	  AC_SUBST([TAOINCL])
-	  AC_SUBST([TAOLIB])
-	else
-		HAVE_TAO=no
-	fi
-	AC_MSG_RESULT($HAVE_TAO)
-	dnl }}}
-	dnl slepc{{{
-	AC_ARG_WITH([slepc-dir],
-	  AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]),
-	  [SLEPC_ROOT=$withval],[SLEPC_ROOT=""])
-			  
-	AC_MSG_CHECKING(for slepc headers and libraries in $SLEPC_ROOT)
-	if test -d "$SLEPC_ROOT"; then
-		HAVE_SLEPC=yes
-		SLEPCINCL=-I"$SLEPC_ROOT/include"
-		SLEPCLIB=-L"$SLEPC_ROOT/lib/ -lslepc"
-
-		AC_DEFINE([_HAVE_SLEPC_],[1],[with Slepc in ISSM src])
-		AC_SUBST([SLEPCINCL])
-		AC_SUBST([SLEPCLIB])
-	else
-		HAVE_SLEPC=no
-	fi
-	AC_MSG_RESULT($HAVE_SLEPC)
-	dnl }}}
-	dnl shapelib{{{
-	AC_ARG_WITH([shapelib-dir],
-	  AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]),
-	  [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT=""])
-			  
-	AC_MSG_CHECKING(for shapelib headers and libraries in $SHAPELIB_ROOT)
-	if test -d "$SHAPELIB_ROOT"; then
-
-		dnl defaults
-		HAVE_SHAPELIB=yes
-		SHAPELIBINCL=-I"$SHAPELIB_ROOT/include"
-		SHAPELIBLIB=-L"$SHAPELIB_ROOT/lib/ -lshape"
-
-		AC_DEFINE([_HAVE_SHAPELIB_],[1],[with Shapelib in ISSM src])
-		AC_SUBST([SHAPELIBINCL])
-		AC_SUBST([SHAPELIBLIB])
-	else
-		HAVE_SHAPELIB=no
-	fi
-	AC_MSG_RESULT($HAVE_SHAPELIB)
-	dnl }}}
-	dnl scalapack{{{
-	AC_ARG_WITH([scalapack-dir],
-	  AS_HELP_STRING([--with-scalapack-dir=DIR],[scalapack root directory]),
-	  [SCALAPACK_ROOT=$withval],[SCALAPACK_ROOT=""])
-			  
-	AC_MSG_CHECKING(for scalapack headers and libraries in $SCALAPACK_ROOT)
-	if test -d "$SCALAPACK_ROOT"; then
-
-		dnl defaults
-		HAVE_SCALAPACK=yes
-		if test x$VENDOR = xintel-discover; then
-		 SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lmkl_scalapack_lp64"
-		else
-		 SCALAPACKLIB=-L"$SCALAPACK_ROOT/ -lscalapack"
-		fi
-
-		AC_DEFINE([_HAVE_SCALAPACK_],[1],[with Scalapack in ISSM src])
-		AC_SUBST([SCALAPACKLIB])
-	else
-		HAVE_SCALAPACK=no
-	fi
-	AC_MSG_RESULT($HAVE_SCALAPACK)
-	dnl }}}
-	dnl blas{{{
-	AC_ARG_WITH([blas-lapack-dir],
-	  AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]),
-	  [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT=""])
-			  
-	AC_MSG_CHECKING(for blas and lapack headers and libraries in $BLASLAPACK_ROOT)
-	if test -d "$BLASLAPACK_ROOT"; then
-
-		dnl defaults
-		HAVE_BLASLAPACK=yes
-		BLASLAPACKINCL=""
-	
-		if test x$VENDOR = xintel-discover; then
-		 BLASLAPACKLIB=-L"$BLASLAPACK_ROOT -lmkl_lapack -lmkl -lguide -lpthread"
-		else
-		dnl: branch on whether we are running on windows or linux.
-		case "${host_os}" in
-			*cygwin*)
-			BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib  -Wl,libf2clapack.lib"
-			;;
-			*linux*)
-			BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " 
-			;;
-			*darwin*)
-			BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " 
-			;;
-		esac
-		fi
-
-		AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src])
-		AC_SUBST([BLASLAPACKLIB])
-		AC_SUBST([BLASLAPACKINCL])
-	else
-		HAVE_BLASLAPACK=no
-	fi
-	AC_MSG_RESULT($HAVE_BLASLAPACK)
-	dnl }}}
-	dnl mkl{{{
-	AC_ARG_WITH([mkl-dir],
-	  AS_HELP_STRING([--with-mkl-dir=DIR],[mkl root directory]),
-	  [MKL_ROOT=$withval],[MKL_ROOT=""])
-			  
-	AC_MSG_CHECKING(for mkl headers and libraries in $MKL_ROOT)
-	if test -d "$MKL_ROOT"; then
-
-		dnl defaults
-		HAVE_MKL=yes
-		MKLINCL=""
-		if test x$VENDOR = xintel-pleiades; then
-		 MKLLIB=-L"$MKL_ROOT -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
-		else
-		 MKLLIB=-L"$MKL_ROOT -lmkl -lmkl_lapack -lmkl_scalapack_ilp64 -lmkl_blacs_sgimpt_ilp64 -lguide -lpthread"
-		fi
-		AC_DEFINE([_HAVE_MKL_],[1],[with mkl in ISSM src])
-		AC_SUBST([MKLLIB])
-		AC_SUBST([MKLINCL])
-	else
-		HAVE_MKL=no
-	fi
-	AC_MSG_RESULT($HAVE_MKL)
-	dnl }}}
-	dnl plapack{{{
-	AC_MSG_CHECKING(for plapack)
-	
-	AC_ARG_WITH([plapack-lib],
-	  AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]),
-	  [PLAPACK_LIB=$withval],[PLAPACK_LIB=""])
-	
-	AC_ARG_WITH([plapack-include],
-			  AS_HELP_STRING([--with-plapack-include = include],
-							 [plapack include ]),
-			  [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""])
-	  
-	if test -n "$PLAPACK_LIB"; then
-		if test -n "$PLAPACK_INCLUDE"; then
-		
-			dnl defaults
-			HAVE_PLAPACK=yes
-			PLAPACKINCL="$PLAPACK_INCLUDE"
-			PLAPACKLIB="$PLAPACK_LIB"
-
-			AC_DEFINE([_HAVE_PLAPACK_],[1],[with Plapack in ISSM src])
-			AC_SUBST([PLAPACKINCL])
-			AC_SUBST([PLAPACKLIB])
-		else
-			HAVE_PLAPACK=no
-		fi
-	else
-		HAVE_PLAPACK=no
-	fi
-	AC_MSG_RESULT($HAVE_PLAPACK)
-	dnl }}}
-	dnl mumps{{{
-	AC_ARG_WITH([mumps-dir],
-	  AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]),
-	  [MUMPS_ROOT=$withval],[MUMPS_ROOT=""])
-			  
-	AC_MSG_CHECKING(for mumps headers and libraries in $MUMPS_ROOT)
-	if test -d "$MUMPS_ROOT"; then
-
-		dnl defaults
-		HAVE_MUMPS=yes
-		MUMPSINCL=-I"$MUMPS_ROOT/include"
-		if test "$PETSC_MAJOR" = "2" ; then
-		MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lpord "
-		else
-		dnl MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis -lzmumps"
-		MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps  -lmumps_common -lpord -lparmetis"
-		fi
-
-		AC_DEFINE([_HAVE_MUMPS_],[1],[with Mumps in ISSM src])
-		AC_SUBST([MUMPSINCL])
-		AC_SUBST([MUMPSLIB])
-	else
-		HAVE_MUMPS=no
-	fi
-	AM_CONDITIONAL([MUMPS], [test x$HAVE_MUMPS = xyes])
-	AC_MSG_RESULT($HAVE_MUMPS)
-	dnl }}}
-	dnl blacs{{{
-	AC_ARG_WITH([blacs-dir],
-		AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]),
-			  [BLACS_ROOT=$withval],[BLACS_ROOT=""])
-			  
-	AC_MSG_CHECKING(for blacs headers and libraries in $BLACS_ROOT)
-	if test -d "$BLACS_ROOT"; then
-
-		dnl defaults
-		HAVE_BLACS=yes
-		BLACSINCL=""
-		if test x$VENDOR = xintel-discover; then
-		 BLACSLIB=-L"$BLACS_ROOT/ -lmkl_blacs_intelmpi_lp64"
-		else
-		 BLACSLIB=-L"$BLACS_ROOT/ -lblacs"
-		fi
-        
-		AC_DEFINE([_HAVE_BLACS_],[1],[with Blacs in ISSM src])
-		AC_SUBST([BLACSINCL])
-		AC_SUBST([BLACSLIB])
-	else
-		HAVE_BLACS=no
-	fi
-	AC_MSG_RESULT($HAVE_BLACS)
-	dnl }}}
-	dnl hypre{{{
-	AC_ARG_WITH([hypre-dir],
-	  AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]),
-			  [HYPRE_ROOT=$withval],[HYPRE_ROOT=""])
-			  
-	AC_MSG_CHECKING(for hypre headers and libraries in $HYPRE_ROOT)
-	if test -d "$HYPRE_ROOT"; then
-
-		dnl defaults
-		HAVE_HYPRE=yes
-		HYPREINCL=""
-		HYPRELIB=-L"$HYPRE_ROOT/lib -lHYPRE"
-        
-		AC_DEFINE([_HAVE_HYPRE_],[1],[with Blacs in ISSM src])
-		AC_SUBST([HYPREINCL])
-		AC_SUBST([HYPRELIB])
-	else
-		HAVE_HYPRE=no
-	fi
-	AC_MSG_RESULT($HAVE_HYPRE)
-	dnl }}}
-	dnl prometheus{{{
-		AC_ARG_WITH([prometheus-dir],
-					AS_HELP_STRING([--with-prometheus-dir=DIR],[prometheus root directory]),
-					[PROMETHEUS_ROOT=$withval],[PROMETHEUS_ROOT=""])
-
-		  AC_MSG_CHECKING(for prometheus headers and libraries in $PROMETHEUS_ROOT)
-		  if test -d "$PROMETHEUS_ROOT"; then
-
-			dnl defaults
-			  HAVE_PROMETHEUS=yes
-			  PROMETHEUSINCL=-I"$PROMETHEUS_ROOT/include"
-			  PROMETHEUSLIB=-L"$PROMETHEUS_ROOT/lib -lpromfei -lprometheus -lparmetis"
-
-			  AC_DEFINE([_HAVE_PROMETHEUS_],[1],[with Prometheus in ISSM src])
-			  AC_SUBST([PROMETHEUSINCL])
-			  AC_SUBST([PROMETHEUSLIB])
-		  else
-				HAVE_PROMETHEUS=no
-			fi
-			AC_MSG_RESULT($HAVE_PROMETHEUS)
-		dnl }}}
-dnl spai{{{
-	AC_ARG_WITH([spai-dir],
-				AS_HELP_STRING([--with-spai-dir=DIR],[spai root directory]),
-				[SPAI_ROOT=$withval],[SPAI_ROOT=""])
-
-	  AC_MSG_CHECKING(for spai headers and libraries in $SPAI_ROOT)
-	  if test -d "$SPAI_ROOT"; then
-
-		dnl defaults
-		  HAVE_SPAI=yes
-		  SPAIINCL=-I"$SPAI_ROOT/include"
-		  SPAILIB=-L"$SPAI_ROOT/lib -lspai"
-
-		  AC_DEFINE([_HAVE_SPAI_],[1],[with Spai in ISSM src])
-		  AC_SUBST([SPAIINCL])
-		  AC_SUBST([SPAILIB])
-	  else
-		HAVE_SPAI=no
-		  fi
-		  AC_MSG_RESULT($HAVE_SPAI)
-		  dnl }}}
-dnl superlu{{{ 
-	AC_ARG_WITH([superlu-dir],
-				AS_HELP_STRING([--with-superlu-dir=DIR],[superlu root directory]),
-				[SUPERLU_ROOT=$withval],[SUPERLU_ROOT=""])
-
-	  AC_MSG_CHECKING(for superlu headers and libraries in $SUPERLU_ROOT)
-	  if test -d "$SUPERLU_ROOT"; then
-
-		dnl defaults
-		  HAVE_SUPERLU=yes
-		  SUPERLUINCL=-I"$SUPERLU_ROOT/include"
-		  SUPERLULIB=-L"$SUPERLU_ROOT/lib -lsuperlu_4.3"
-
-		  AC_DEFINE([_HAVE_SUPERLU_],[1],[with Superlu in ISSM src])
-		  AC_SUBST([SUPERLUINCL])
-		  AC_SUBST([SUPERLULIB])
-	  else
-		HAVE_SUPERLU=no
-		  fi
-		  AC_MSG_RESULT($HAVE_SUPERLU)
-		  dnl }}}
-dnl spooles{{{ 
-	AC_ARG_WITH([spooles-dir],
-				AS_HELP_STRING([--with-spooles-dir=DIR],[spooles root directory]),
-				[SPOOLES_ROOT=$withval],[SPOOLES_ROOT=""])
-
-	  AC_MSG_CHECKING(for spooles headers and libraries in $SPOOLES_ROOT)
-	  if test -d "$SPOOLES_ROOT"; then
-
-		dnl defaults
-		  HAVE_SPOOLES=yes
-		  SPOOLESINCL=-I"$SPOOLES_ROOT/include"
-		  SPOOLESLIB=-L"$SPOOLES_ROOT/lib -lspooles"
-
-		  AC_DEFINE([_HAVE_SPOOLES_],[1],[with Spooles in ISSM src])
-		  AC_SUBST([SPOOLESINCL])
-		  AC_SUBST([SPOOLESLIB])
-	  else
-		HAVE_SPOOLES=no
-		  fi
-		  AC_MSG_RESULT($HAVE_SPOOLES)
-		  dnl }}}
-dnl pastix{{{ 
-	AC_ARG_WITH([pastix-dir],
-				AS_HELP_STRING([--with-pastix-dir=DIR],[pastix root directory]),
-				[PASTIX_ROOT=$withval],[PASTIX_ROOT=""])
-
-	  AC_MSG_CHECKING(for pastix headers and libraries in $PASTIX_ROOT)
-	  if test -d "$PASTIX_ROOT"; then
-
-		dnl defaults
-		  HAVE_PASTIX=yes
-		  PASTIXINCL=-I"$PASTIX_ROOT/include"
-		  PASTIXLIB=-L"$PASTIX_ROOT/lib -lpastix_XXbit_mpi_smp_nobubble_int32_simple_real_scotch_i686_pc_linux -lptscotch -lptscotcherr -lpastix"
-
-		  AC_DEFINE([_HAVE_PASTIX_],[1],[with Pastix in ISSM src])
-		  AC_SUBST([PASTIXINCL])
-		  AC_SUBST([PASTIXLIB])
-	  else
-		HAVE_PASTIX=no
-		  fi
-		  AC_MSG_RESULT($HAVE_PASTIX)
-		  dnl }}}
-	dnl ml{{{
-	AC_ARG_WITH([ml-dir],
-	  AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]),
-			  [ML_ROOT=$withval],[ML_ROOT=""])
-			  
-	AC_MSG_CHECKING(for ml headers and libraries in $ML_ROOT)
-	if test -d "$ML_ROOT"; then
-
-		dnl defaults
-		HAVE_ML=yes
-		MLINCL=-I"$ML_ROOT/include"
-		MLLIB=-L"$ML_ROOT/lib -lml"
-        
-		AC_DEFINE([_HAVE_ML_],[1],[with Blacs in ISSM src])
-		AC_SUBST([MLINCL])
-		AC_SUBST([MLLIB])
-	else
-		HAVE_ML=no
-	fi
-	AC_MSG_RESULT($HAVE_ML)
-	dnl }}}
-	dnl umfpack{{{
-		AC_ARG_WITH([umfpack-dir],
-		  AS_HELP_STRING([--with-umfpack-dir=DIR],[UMFPACK root directory]),
-					[UMFPACK_ROOT=$withval],[UMFPACK_ROOT=""])
-
-		AC_MSG_CHECKING(for UMFPACK headers and libraries in $UMFPACK_ROOT)
-		if test -d "$UMFPACK_ROOT"; then
-
-			dnl defaults
-			HAVE_UMFPACK=yes
-			UMFPACKINCL=""
-			UMFPACKLIB=-L"$UMFPACK_ROOT/lib -lumfpack -lumfpack.5.5.1"
-
-			AC_DEFINE([_HAVE_UMFPACK_],[1],[with UMFPACK in ISSM src])
-			AC_SUBST([UMFPACKINCL])
-			AC_SUBST([UMFPACKLIB])
-		else
-			HAVE_UMFPACK=no
-		fi
-		AC_MSG_RESULT($HAVE_UMFPACK)
-	dnl }}}
-dnl math{{{
-	AC_MSG_CHECKING(for math library)
-	AC_ARG_WITH([math-lib],
-	  AS_HELP_STRING([--with-math-lib = otions],[math options, for ex: "/usr/lib/libm.a]),
-	  [MATH_LIB=$withval],[MATH_LIB=""])
-
-	dnl check that --with-math-lib may have been provided
-	if test -n "$MATH_LIB" ; then
-		HAVE_MATH=yes
-		MATHLIB="$MATH_LIB"
-
-		AC_DEFINE([_HAVE_MATH_],[1],[with MATH in ISSM src])
-		AC_SUBST([MATHLIB])
-	fi
-	AC_MSG_RESULT(done)
-	dnl }}}
-	dnl fortran{{{
-	AC_ARG_WITH([fortran],
-		AS_HELP_STRING([--with-fortran = YES], [do we compile fortran code (default is yes)]),
-		[FORTRAN=$withval],[FORTRAN=yes]) 
-	AC_MSG_CHECKING(for fortran compilation)
-	if test "x$FORTRAN" = "xyes"; then
-		dnl defaults
-		HAVE_FORTRAN=yes
-
-		AC_DEFINE([_HAVE_FORTRAN_],[1],[with fortran capability])
-	else
-		HAVE_FORTRAN=no
-	fi
-	AM_CONDITIONAL([FORTRAN], [test x$FORTRAN = xyes])
-	AC_MSG_RESULT($FORTRAN)
-
-	if test "x$FORTRAN" = "xyes"; then
-		dnl fortran library  option
-		AC_MSG_CHECKING(for fortran library)
-		AC_ARG_WITH([fortran-lib],
-		  AS_HELP_STRING([--with-fortran-lib = options],[fortran options, for ex: "/usr/lib/gfortran.a]),
-			[FORTRAN_LIB=$withval],[FORTRAN_LIB=""])
-
-		dnl check that --with-fortran-lib may have been provided
-		if test -n "$FORTRAN_LIB" ; then
-			dnl check that library provided EXISTS!
-		   FORTRAN_DIR=$(echo $FORTRAN_LIB | sed -e "s/-L//g" | awk '{print $[1]}')
-			if test -d "$FORTRAN_DIR" || test -f "$FORTRAN_DIR"; then
-				FORTRANLIB="$FORTRAN_LIB"
-				AC_DEFINE([_HAVE_FORTRAN_],[1],[with FORTRAN in ISSM src])
-				AC_SUBST([FORTRANLIB])
-			else
-			 if test "x$HAVE_MPI" = "xyes"; then
-				FORTRANLIB=$(mpif77 -print-file-name="libgfortran.a")
-				if test -f "$FORTRANLIB"; then
-					 AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist, MPI suggests the following library: $FORTRANLIB]);
-				fi
-			 fi
-				AC_MSG_ERROR([fortran library provided ($FORTRAN_LIB) does not exist!]);
-			fi
-		fi
-		AC_MSG_RESULT(done)
-	fi
-	dnl }}}
-	dnl graphics{{{
-	AC_MSG_CHECKING(for graphics library)
-	AC_ARG_WITH([graphics-lib],
-	  AS_HELP_STRING([--with-graphics-lib = options],[graphics options, for ex: "/usr/X11/lib/libX11.a]),
-	  [GRAPHICS_LIB=$withval],[GRAPHICS_LIB=""])
-
-	dnl check that --with-graphics-lib may have been provided
-	
-	if test -n "$GRAPHICS_LIB" ; then
-		dnl check that library provided EXISTS!
-		GRAPHICS_DIR=$(echo $GRAPHICS_LIB | sed -e "s/-L//g" | awk '{print $[1]}')
-		if test -d "$GRAPHICS_DIR" || test -f "$GRAPHICS_DIR"; then
-			HAVE_GRAPHICS=yes
-			GRAPHICSLIB="$GRAPHICS_LIB"
-			AC_DEFINE([_HAVE_GRAPHICS_],[1],[with GRAPHICS in ISSM src])
-			AC_SUBST([GRAPHICSLIB])
-		else
-			if test -f "$PETSC_ROOT/conf/petscvariables"; then
-				GRAPHICSLIB=$(cat $PETSC_ROOT/conf/petscvariables | grep X_LIB)
-				AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB) does not exist, PETSc suggests the following library: $GRAPHICSLIB]);
-			fi
-			AC_MSG_ERROR([graphics library provided ($GRAPHICS_LIB$) does not exist!]);
-		fi
-	fi
-	AC_MSG_RESULT(done)
-	dnl }}}
-
-	dnl Capabilities
-	dnl with-kml{{{
-	AC_ARG_WITH([kml],
-		AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is yes)]),
-		[KML=$withval],[KML=yes]) 
-	AC_MSG_CHECKING(for kml capability compilation)
-
-	if test "x$KML" = "xyes"; then
-		HAVE_KML=yes
-		AC_DEFINE([_HAVE_KML_],[1],[with kml capability])
-	else
-		HAVE_KML=no
-	fi
-	AM_CONDITIONAL([KML], [test x$HAVE_KML = xyes])
-	AC_MSG_RESULT($HAVE_KML)
-	dnl }}}
-	dnl with-kriging{{{
-	AC_ARG_WITH([kriging],
-		AS_HELP_STRING([--with-kriging = YES],[compile with kriging capabilities (default is yes)]),
-		[KRIGING=$withval],[KRIGING=yes]) 
-	AC_MSG_CHECKING(for kriging capability compilation)
-
-	if test "x$KRIGING" = "xyes"; then
-		HAVE_KRIGING=yes
-		AC_DEFINE([_HAVE_KRIGING_],[1],[with kriging capability])
-	else
-		HAVE_KRIGING=no
-	fi
-	AM_CONDITIONAL([KRIGING], [test x$HAVE_KRIGING = xyes])
-	AC_MSG_RESULT($HAVE_KRIGING)
-	dnl }}}
-	dnl with-steadystate{{{
-	AC_ARG_WITH([steadystate],
-		AS_HELP_STRING([--with-steadystate = YES],[compile with steadystate capabilities (default is yes)]),
-		[STEADYSTATE=$withval],[STEADYSTATE=yes]) 
-	AC_MSG_CHECKING(for steadystate capability compilation)
-
-	if test "x$STEADYSTATE" = "xyes"; then
-
-		dnl defaults
-		HAVE_STEADYSTATE=yes
-
-		AC_DEFINE([_HAVE_STEADYSTATE_],[1],[with steadystate capability])
-	else
-		HAVE_STEADYSTATE=no
-	fi
-	AM_CONDITIONAL([STEADYSTATE], [test x$HAVE_STEADYSTATE = xyes])
-	AC_MSG_RESULT($HAVE_STEADYSTATE)
-	dnl }}}
-	dnl with-transient{{{
-	AC_ARG_WITH([transient],
-		AS_HELP_STRING([--with-transient = YES], [compile with transient capabilities (default is yes)]),
-		[TRANSIENT=$withval],[TRANSIENT=yes]) 
-	AC_MSG_CHECKING(for transient capability compilation)
-
-	if test "x$TRANSIENT" = "xyes"; then
-
-		dnl defaults
-		HAVE_TRANSIENT=yes
-
-		AC_DEFINE([_HAVE_TRANSIENT_],[1],[with transient capability])
-	else
-		HAVE_TRANSIENT=no
-	fi
-	AM_CONDITIONAL([TRANSIENT], [test x$HAVE_TRANSIENT = xyes])
-	AC_MSG_RESULT($HAVE_TRANSIENT)
-	dnl }}}
-	dnl with-thermal{{{
-	AC_ARG_WITH([thermal],
-		AS_HELP_STRING([--with-thermal = YES], [compile with thermal capabilities (default is yes)]),
-		[THERMAL=$withval],[THERMAL=yes]) 
-	AC_MSG_CHECKING(for thermal capability compilation)
-
-	if test "x$THERMAL" = "xyes"; then
-
-		dnl defaults
-		HAVE_THERMAL=yes
-
-		AC_DEFINE([_HAVE_THERMAL_],[1],[with thermal capability])
-	else
-		HAVE_THERMAL=no
-	fi
-	AM_CONDITIONAL([THERMAL], [test x$HAVE_THERMAL = xyes])
-	AC_MSG_RESULT($HAVE_THERMAL)
-	dnl }}}
-	dnl with-prognostic{{{
-	AC_ARG_WITH([prognostic],
-		AS_HELP_STRING([--with-prognostic = YES], [compile with prognostic capabilities (default is yes)]),
-		[PROGNOSTIC=$withval],[PROGNOSTIC=yes]) 
-	AC_MSG_CHECKING(for prognostic capability compilation)
-
-	if test "x$PROGNOSTIC" = "xyes"; then
-
-		dnl defaults
-		HAVE_PROGNOSTIC=yes
-
-		AC_DEFINE([_HAVE_PROGNOSTIC_],[1],[with prognostic capability])
-	else
-		HAVE_PROGNOSTIC=no
-	fi
-	AM_CONDITIONAL([PROGNOSTIC], [test x$HAVE_PROGNOSTIC = xyes])
-	AC_MSG_RESULT($HAVE_PROGNOSTIC)
-	dnl }}}
-	dnl with-control{{{
-	AC_ARG_WITH([control],
-		AS_HELP_STRING([--with-control = YES], [compile with control capabilities (default is yes)]),
-		[CONTROL=$withval],[CONTROL=yes]) 
-	AC_MSG_CHECKING(for control capability compilation)
-
-	if test "x$CONTROL" = "xyes"; then
-
-		dnl defaults
-		HAVE_CONTROL=yes
-
-		AC_DEFINE([_HAVE_CONTROL_],[1],[with control capability])
-	else
-		HAVE_CONTROL=no
-	fi
-	AM_CONDITIONAL([CONTROL], [test x$HAVE_CONTROL = xyes])
-	AC_MSG_RESULT($HAVE_CONTROL)
-	dnl }}}
-	dnl with-hydrology{{{
-	AC_ARG_WITH([hydrology],
-		AS_HELP_STRING([--with-hydrology = YES], [compile with hydrology capabilities (default is yes)]),
-		[HYDROLOGY=$withval],[HYDROLOGY=yes]) 
-	AC_MSG_CHECKING(for hydrology capability compilation)
-
-	if test "x$HYDROLOGY" = "xyes"; then
-
-		dnl defaults
-		HAVE_HYDROLOGY=yes
-
-		AC_DEFINE([_HAVE_HYDROLOGY_],[1],[with hydrology capability])
-	else
-		HAVE_HYDROLOGY=no
-	fi
-	AM_CONDITIONAL([HYDROLOGY], [test x$HAVE_HYDROLOGY = xyes])
-	AC_MSG_RESULT($HAVE_HYDROLOGY)
-	dnl }}}
-	dnl with-diagnostic{{{
-	AC_ARG_WITH([diagnostic],
-		AS_HELP_STRING([--with-diagnostic = YES], [compile with diagnostic capabilities (default is yes)]),
-		[DIAGNOSTIC=$withval],[DIAGNOSTIC=yes]) 
-	AC_MSG_CHECKING(for diagnostic capability compilation)
-
-	if test "x$DIAGNOSTIC" = "xyes"; then
-
-		dnl defaults
-		HAVE_DIAGNOSTIC=yes
-
-		AC_DEFINE([_HAVE_DIAGNOSTIC_],[1],[with diagnostic capability])
-	else
-		HAVE_DIAGNOSTIC=no
-	fi
-	AM_CONDITIONAL([DIAGNOSTIC], [test x$HAVE_DIAGNOSTIC = xyes])
-	AC_MSG_RESULT($HAVE_DIAGNOSTIC)
-	dnl }}}
-	dnl with-balanced{{{
-	AC_ARG_WITH([balanced],
-		AS_HELP_STRING([--with-balanced = YES], [compile with balanced capabilities (default is yes)]),
-		[BALANCED=$withval],[BALANCED=yes]) 
-	AC_MSG_CHECKING(for balanced capability compilation)
-
-	if test "x$BALANCED" = "xyes"; then
-
-		dnl defaults
-		HAVE_BALANCED=yes
-
-		AC_DEFINE([_HAVE_BALANCED_],[1],[with balanced capability])
-	else
-		HAVE_BALANCED=no
-	fi
-	AM_CONDITIONAL([BALANCED], [test x$HAVE_BALANCED = xyes])
-	AC_MSG_RESULT($HAVE_BALANCED)
-	dnl }}}
-	dnl with-responses{{{
-	AC_ARG_WITH([responses],
-		AS_HELP_STRING([--with-responses = YES], [compile with responses capabilities (default is yes)]),
-		[RESPONSES=$withval],[RESPONSES=yes]) 
-	AC_MSG_CHECKING(for responses capability compilation)
-
-	if test "x$RESPONSES" = "xyes"; then
-
-		dnl defaults
-		HAVE_RESPONSES=yes
-
-		AC_DEFINE([_HAVE_RESPONSES_],[1],[with responses capability])
-	else
-		HAVE_RESPONSES=no
-	fi
-	AM_CONDITIONAL([RESPONSES], [test x$HAVE_RESPONSES = xyes])
-	AC_MSG_RESULT($HAVE_RESPONSES)
-	dnl }}}
-	dnl with-slope{{{
-	AC_ARG_WITH([slope],
-		AS_HELP_STRING([--with-slope = YES], [compile with slope capabilities (default is yes)]),
-		[SLOPE=$withval],[SLOPE=yes]) 
-	AC_MSG_CHECKING(for slope capability compilation)
-
-	if test "x$SLOPE" = "xyes"; then
-
-		dnl defaults
-		HAVE_SLOPE=yes
-
-		AC_DEFINE([_HAVE_SLOPE_],[1],[with slope capability])
-	else
-		HAVE_SLOPE=no
-	fi
-	AM_CONDITIONAL([SLOPE], [test x$HAVE_SLOPE = xyes])
-	AC_MSG_RESULT($HAVE_SLOPE)
-	dnl }}}
-	dnl with-groundingline{{{
-	AC_ARG_WITH([groundingline],
-		AS_HELP_STRING([--with-groundingline = YES], [compile with groundingline capabilities (default is yes)]),
-		[GROUNDINGLINE=$withval],[GROUNDINGLINE=yes]) 
-	AC_MSG_CHECKING(for groundingline capability compilation)
-
-	if test "x$GROUNDINGLINE" = "xyes"; then
-
-		dnl defaults
-		HAVE_GROUNDINGLINE=yes
-
-		AC_DEFINE([_HAVE_GROUNDINGLINE_],[1],[with groundingline capability])
-	else
-		HAVE_GROUNDINGLINE=no
-	fi
-	AM_CONDITIONAL([GROUNDINGLINE], [test x$HAVE_GROUNDINGLINE = xyes])
-	AC_MSG_RESULT($HAVE_GROUNDINGLINE)
-	dnl }}}
-	dnl with-rifts{{{
-	AC_ARG_WITH([rifts],
-		AS_HELP_STRING([--with-rifts = YES], [compile with rifts capabilities (default is yes)]),
-		[RIFTS=$withval],[RIFTS=yes]) 
-	AC_MSG_CHECKING(for rifts capability compilation)
-
-	if test "x$RIFTS" = "xyes"; then
-
-		dnl defaults
-		HAVE_RIFTS=yes
-
-		AC_DEFINE([_HAVE_RIFTS_],[1],[with rifts capability])
-	else
-		HAVE_RIFTS=no
-	fi
-	AM_CONDITIONAL([RIFTS], [test x$HAVE_RIFTS = xyes])
-	AC_MSG_RESULT($HAVE_RIFTS)
-	dnl }}}
-	dnl math77{{{
-	AC_ARG_WITH([math77-dir],
-		AS_HELP_STRING([--with-math77-dir=DIR], [math77 root directory.]),
-		[MATH77_ROOT=$withval],[MATH77_ROOT=""]) 
-	AC_MSG_CHECKING(for math77)
-
-	if test -d "$MATH77_ROOT"; then
-
-	  HAVE_MATH77=yes
-	  MATH77LIB="-L$MATH77_ROOT/ -lmath77"
-
-	  AC_DEFINE([_HAVE_MATH77_],[1],[with math77 in ISSM src])
-	  AC_SUBST([MATH77LIB])
-	else
-		HAVE_MATH77=no
-	fi
-	AC_MSG_RESULT($HAVE_MATH77)
-	dnl }}}
-	dnl with-gia{{{
-	AC_ARG_WITH([gia],
-		AS_HELP_STRING([--with-gia = YES], [compile with gia capabilities (default is yes)]),
-		[GIA=$withval],[GIA=no]) 
-	AC_MSG_CHECKING(for gia capability compilation)
-
-	if test "x$GIA" = "xyes"; then
-	  
-	  if test "x$HAVE_MATH77" = "xno"; then
-		  HAVE_GIA=no
-		  AC_MSG_ERROR([gia requires compilation of math77 library! Reconfigure with --with-math77 option on]);
-	  else
-		dnl defaults
-		HAVE_GIA=yes
-		AC_DEFINE([_HAVE_GIA_],[1],[with gia capability])
-	  fi
-
-	else
-		HAVE_GIA=no
-	fi
-	AM_CONDITIONAL([GIA], [test x$HAVE_GIA = xyes])
-	AC_MSG_RESULT($HAVE_GIA)
-	dnl }}}
-	dnl with-ios{{{
-	AC_ARG_WITH([ios],
-		AS_HELP_STRING([--with-ios = YES], [compile with iOS capabilities (default is no, alternatives are yes)]),
-		[IOS=$withval],[IOS=no]) 
-	AC_MSG_CHECKING(for iOS compilation)
-
-	if test "x$IOS" = "xyes"; then
-		dnl defaults
-		HAVE_IOS=yes
-
-		AC_DEFINE([_HAVE_IOS_],[1],[with android capability])
-	elif test "x$IOS" = "xno"; then
-		HAVE_IOS=no
-	else
-	  AC_MSG_ERROR([--with-ios should be either no or yes])
-	fi
-	AM_CONDITIONAL([IOS], [test x$HAVE_IOS != xno])
-	AC_MSG_RESULT($HAVE_IOS)
-	dnl }}}
-	dnl with-android{{{
-	AC_ARG_WITH([android],
-		AS_HELP_STRING([--with-android = EXE], [compile with android capabilities (default is no, alternatives are exe and jni)]),
-		[ANDROID=$withval],[ANDROID=no]) 
-	AC_MSG_CHECKING(for android capability compilation)
-
-	if test "x$ANDROID" = "xjni"; then
-
-		dnl defaults
-		HAVE_ANDROID=jni
-		AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability])
-		AC_DEFINE([_HAVE_ANDROID_JNI_],[1],[with android jni])
-	elif test "x$ANDROID" = "xexe"; then
-		dnl defaults
-		HAVE_ANDROID=exe
-
-		AC_DEFINE([_HAVE_ANDROID_],[1],[with android capability])
-	elif test "x$ANDROID" = "xno"; then
-		HAVE_ANDROID=no
-	else
-	  AC_MSG_ERROR([--with-android should be either no, exe or jni])
-	fi
-	AM_CONDITIONAL([ANDROID], [test x$HAVE_ANDROID != xno])
-	AM_CONDITIONAL([ANDROIDJNI], [test x$HAVE_ANDROID = xjni])
-	AM_CONDITIONAL([ANDROIDEXE], [test x$HAVE_ANDROID = xexe])
-	AC_MSG_RESULT($HAVE_ANDROID)
-	dnl }}}
-	dnl with-android-ndk{{{
-	AC_ARG_WITH([android-ndk],
-	  AS_HELP_STRING([--with-android-ndk=DIR], [android-ndk root directory.]),
-	  [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) 
-	AC_MSG_CHECKING(with android ndk)
-	
-	if test -d "$ANDROID_NDK_ROOT"; then
-		dnl defaults
-		HAVE_ANDROID_NDK=yes
-		ANDROID_NDKINCL="-I$ANDROID_NDK_ROOT/arm-linux-android-install/sysroot/usr/include"
-
-		AC_DEFINE([_HAVE_ANDROID_NDK_],[1],[with android ndk in ISSM src])
-		AC_SUBST([ANDROID_NDKINCL])
-	else
-		HAVE_ANDROID_NDK=no
-	fi
-	AC_MSG_RESULT($HAVE_ANDROID_NDK)
-	dnl }}}
-	dnl with-3d{{{
-	AC_ARG_WITH([3d],
-		AS_HELP_STRING([--with-3d = YES], [compile with 3d capabilities (default is yes)]),
-		[THREED=$withval],[THREED=yes]) 
-	AC_MSG_CHECKING(for 3d capability compilation)
-
-	if test "x$THREED" = "xyes"; then
-
-		dnl defaults
-		HAVE_3D=yes
-
-		AC_DEFINE([_HAVE_3D_],[1],[with 3d capability])
-	else
-		HAVE_3D=no
-	fi
-	AM_CONDITIONAL([THREED], [test x$HAVE_3D = xyes])
-	AC_MSG_RESULT($HAVE_3D)
-	dnl }}}
-	dnl checks{{{
-	AC_MSG_CHECKING(consistency between all libraries)
-	
-	dnl check that if petsc is requested , mpi should be specified
-	if test "$HAVE_PETSC" = "yes" ; then
-		if test "$HAVE_MPI" = "NO";  then
-			AC_MSG_ERROR([petsc requires mpi!]);
-		fi
-	fi
-
-	dnl check that we have either python or matlab support if we compile the modules
-	if test "$MODULES_VALUE" = "yes"  && test "$HAVE_MATLAB" = "no" && test "$HAVE_PYTHON" = "no"; then
-		AC_MSG_ERROR([need at least python or matlab support to compile modules (or use --with-modules=no)]);
-	fi
-
-	dnl check that if we have MPI, we have metis
-	if test "$HAVE_METIS" = "yes"  && test "$HAVE_MPI" = "no" ; then
-	AC_MSG_ERROR([need mpi if using the metis partitioner!]);
-	fi
-
-	AC_MSG_RESULT(done)
-	dnl }}}
-
-	dnl other options
-	dnl optimization{{{
-	dnl bypass standard optimization -g -O2 ? 
-	AC_ARG_WITH([cxxoptflags],
-	  AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]),
-	  [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2"]) 
-	AC_MSG_CHECKING(for c++ optimization flags)
-	AC_SUBST([CXXOPTFLAGS])
-	AC_MSG_RESULT(done)
-
-	dnl }}}
-	dnl multithreading{{{
-	AC_ARG_WITH([numthreads],
-	  AS_HELP_STRING([--with-numthreads = NUMTHREADS_VALUE],[numthreads, default is 1. ]),
-	  [NUMTHREADS_VALUE=$withval],[NUMTHREADS_VALUE=1])
-	AC_MSG_CHECKING(for number of threads)
-	dnl defaults
-	MULTITHREADING=no
-	MULTITHREADINLIB=""
-	if test "$NUMTHREADS_VALUE" != "1"; then
-		
-		MULTITHREADINGLIB="-lpthread -lrt"
-		case "${host_os}" in
-		*cygwin*)
-		MULTITHREADINGLIB="-lpthread -lrt"
-		;;
-		*linux*)
-		MULTITHREADINGLIB="-lpthread -lrt"
-		;;
-		*darwin*)
-		MULTITHREADINGLIB="-lpthread"
-		;;
-		esac
-
-		AC_DEFINE([_MULTITHREADING_],[1],[with numthreads enabled])
-		AC_DEFINE_UNQUOTED([_NUMTHREADS_],[$NUMTHREADS_VALUE],[number of threads])
-	fi
-	AC_SUBST([MULTITHREADINGLIB])
-	AC_MSG_RESULT($NUMTHREADS_VALUE) 
-	dnl }}}
-	dnl 64bit {{{
-	AC_ARG_WITH([64bit-indices],
-	  AS_HELP_STRING([--with-64bit-indices = bool], [use 64 bit integers, default 0, ex: --with-64bit-indices=1]),
-	  [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) 
-	AC_MSG_CHECKING(for 64 bit indices)
-
-	if test "$USE_64BIT_INDICES" == "1"; then
-	AC_DEFINE([ISSM_USE_64BIT_INDICES],[1],[with 64 bits indices])
-	else
-	AC_DEFINE([ISSM_USE_64BIT_INDICES],[0],[with 64 bits indices])
-	fi
-	AC_MSG_RESULT($USE_64BIT_INDICES)
-	dnl }}}
-])
Index: ../trunk-jpl/packagers/ubuntu/issmpkg/install-3.2-linux64.sh
===================================================================
--- ../trunk-jpl/packagers/ubuntu/issmpkg/install-3.2-linux64.sh	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/issmpkg/install-3.2-linux64.sh	(revision 18436)
@@ -1,37 +0,0 @@
-#!/bin/bash
-set -eu
-
-#Some cleanup
-rm -rf install petsc-3.2-p3 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-3.2-p3.tar.gz' 'petsc-3.2-p3.tar.gz'
-
-#Untar and move petsc to install directory
-tar -zxvf  petsc-3.2-p3.tar.gz
-mv petsc-3.2-p3/* src/
-rm -rf petsc-3.2-p3
-
-#configure
-cd src
-./config/configure.py \
-	--prefix="$ISSM_DIR/externalpackages/petsc/install" \
-	--with-mpi-dir="/usr/lib/mpich2/" \
-	--with-clanguage=C++ \
-	--PETSC_ARCH=linux-gnu-amd64 \
-	--PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
-	--with-debugging=0 \
-	--with-shared-libraries=1 \
-	--download-mumps=yes \
-	--download-scalapack=yes \
-	--download-blacs=yes \
-	--download-blas=yes \
-	--download-f-blas-lapack=yes \
-	--download-plapack=yes \
-	--download-parmetis=yes \
-	--with-pic=1
-
-#Compile petsc and install it
-make
-make install
Index: ../trunk-jpl/packagers/ubuntu/issmpkg/triangle.h.patch
===================================================================
--- ../trunk-jpl/packagers/ubuntu/issmpkg/triangle.h.patch	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/issmpkg/triangle.h.patch	(revision 18436)
@@ -1,12 +0,0 @@
-250a251,257
-> /*Patch for ISSM*/
-> #ifndef REAL
-> typedef double REAL;
-> typedef void VOID;
-> #endif
-> /*End patch*/
-> 
-283c290
-< void triangulate(char *, struct triangulateio *, struct triangulateio *,
----
-> extern "C" void triangulate(char *, struct triangulateio *, struct triangulateio *,
Index: ../trunk-jpl/packagers/ubuntu/issmpkg/README
===================================================================
--- ../trunk-jpl/packagers/ubuntu/issmpkg/README	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/issmpkg/README	(revision 18436)
@@ -1,138 +0,0 @@
-UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION 
-
-PREFACE:
-	There are configuration files included in the dir where this document
-	 resides. Use them, that's why they're there. But I know, since some of
-	 you like to go against the grain, at least one of you is going to try
-	 building a package from an install that differs from mine.
-
-	If you choose to go down that dark road, then bear in mind that there
-	 are ways to do this right, and there are ways to do this wrong....
-	 Make sure that you mind where you decide to install the bin and lib.
-	 If you specify a target outside of the trunk, and don't, let's say,
-	 write the same dir somewhere else, then the package won't work. 
-
-	Make sure when putting together a dir hierarchy for a package, that you
-	 create something sime to what you specifed during compile. If you
-	 change "--bindir" then create a dir in the package that corresponds to
-	 that. The trunk doesn't necessarily have to be in the same place as it
-	 is on the build system.
-
--------------------------------------------------------------------------------
-		    Installing ISSM to create a deb package:
--------------------------------------------------------------------------------
-
-1.	Install mpich from the ubuntu repositories:
-
-		> sudo apt-get install mpich2 (or something similar)
-
-		Check to make sure that it installs the "-dev" libs
-			if not:
-			 > sudo apt-get install libmpich-dev (or something similar)
-			Otherwise you won't get "/usr/lib/mpich2"
-
-		You can use "apt-cache search" to find a package's full name
-
-2a.	Compile petsc and metis (preferred versions: 3.2 and 4.0, respectively):
-
-		Make sure that petsc's installer file is pointing to the
-		 correct mpich dir
-
-			You should use "/usr/lib/mpich2" (or something similar)
-
-		As of now, it is preferable to use the separate mpich package
-		 because the infrastructure of the mpich package under petsc
-		 is having issues with being packaged
-
-		Also make sure that you mind the target of the installation.
-			Right now /usr/share/petsc and /usr/share/metis are the
-			 best options suffixed by version numbers
-
-2b.	Install dependencies from the ubuntu repositories
-
-		Use apt-get install to install:
-			triangle-bin, libtriangle-dev, python2.7-dev, 
-			 python-scipy, python-netcdf4, netcdf-bin, python-nose, 
-			 libnetcdfc++4, hdf5-tools
-
-		REMEMBER: that this tutorial assumes you are creating the
-		 python interface
-			
-3.	Be sure to patch the system triangle.h file
-
-		> sudo patch /usr/include/triangle.h $ISSM_DIR/externalpackages/triangle/triangle.h.patch
-			the header may also be called "libtriangle.h"
-
-		Just like always, this will move the original to 
-		 "triangle.h.old" incase you need to revert
-
-4.	Compile ISSM
-
-		> autoreconf -iv && configs/config-*-packaging.sh && make && sudo -E make install
-
--------------------------------------------------------------------------------
-		          Creating an issm.deb package
--------------------------------------------------------------------------------
-	THIS ASSUMES YOU ARE USING THE CONFIG FILE SUPPLIED HERE.
-	IF YOU ARE DOING AN ALTERNATE CONFIG, MAKE SURE THE DIR
-	HIERARCHY IS PROPERLY REFLECTED BY THE BINDIR AND LIBDIR!
-
-1.	Make a directory to work from (the dir dpkg-deb will build)
-		Anywhere will do, but using a ~/tmp dir works best
-
-		> mkdir issmpkgdir
-		> cd issmpkgdir
-
-2.	Create the dir hierarchy:
-
-		> mkdir -p usr/{bin,lib,share/issm-trunk} etc/issm DEBIAN
-
-		This is will create:
-		issmpkgdir/
-		|_ usr/
-		|  |_ bin/
-		|  |_ lib/
-		|  |_ share/
-		|     |_issm-trunk/ - this is the trunk
-		|_ etc/
-		|  |_ issm/ - this is where issmrc and other conf files go
-		|_DEBIAN/ - where control files and install scripts go
-
-		As stated, if you change "--bindir" or "--libdir" in the config
-		 file, then make sure that you create matching dirs in this
-		 step, or vice-versa.
-
-3.	Copy the contents of the package over:
-
-		> sudo cp -r /usr/bin/issm usr/bin
-		> sudo cp -r /usr/lib/issm usr/lib
-		> cp -r $ISSM_DIR/* usr/share/issm-trunk
-
-		When you copy the trunk over, this your opportunity to weed out
-		 anything you don't want included in the build.
-		Again, the config file installs the bin and lib files to a dir
-		 that's separate from the rest of the bin and lib files. If you
-		 change "--bindir" or "--libdir", make sure you install them to
-		 a subdirectory of your target to keep things neat or else 
-		 you'll have to pick them out, one-by-one to complete this step.
-
-4.	Write your control file. A template is provided, that is the bare minimum to
-		 create the package 
-
-		You will NEED the following dependencies:
-		mpich2, petsc3.2-issm, metis4.0-issm, triangle-bin, libtriangle-dev, 
-		 python2.7-dev, python-scipy, python-netcdf4, netcdf-bin, python-nose, 
-		 libnetcdfc++4, hdf5-tools
-
-5.	Create any install/uninstall scripts needed (preinst, postinst, prerm, postrm)
-		There are already some templates provided for you.
-
-		Make sure you address the issue of any user created content. By
-		 default, apt-get won't remove anything that wasn't created by
-		 the installer, even if you use purge. Put this in a rm script.
-
-6.	Build the package:
-
-		> dpkg-deb --build <workingDir> <nameOfPackage>
-
-UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION - UNDER CONSTRUCTION 
Index: ../trunk-jpl/packagers/ubuntu/issmpkg/environment.sh
===================================================================
--- ../trunk-jpl/packagers/ubuntu/issmpkg/environment.sh	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/issmpkg/environment.sh	(revision 18436)
@@ -1,287 +0,0 @@
-#ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
-
-pathprepend(){ #{{{
-	if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
-		export PATH="$1:$PATH"
-	fi
-} #}}}
-pathappend(){ #{{{
-	if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
-		export PATH="$PATH:$1"
-	fi
-} #}}}
-libpathprepend(){ #{{{
-	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
-		export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH"
-	fi
-	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
-		export LD_RUN_PATH="$1:$LD_RUN_PATH"
-	fi
-} #}}}
-libpathappend(){ #{{{
-	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
-		export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1"
-	fi
-	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
-		export LD_RUN_PATH="$LD_RUN_PATH:$1"
-	fi
-} #}}}
-dylibpathprepend(){ #{{{
-	if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then
-		export DYLD_LIBRARY_PATH="$1:$DYLD_LIBRARY_PATH"
-	fi
-	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
-		export LD_RUN_PATH="$1:$LD_RUN_PATH"
-	fi
-} #}}}
-dylibpathappend(){ #{{{
-	if [ -d "$1" ] && [[ ":$DYLD_LIBRARY_PATH:" != *":$1:"* ]]; then
-		export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$1"
-	fi
-	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
-		export LD_RUN_PATH="$LD_RUN_PATH:$1"
-	fi
-} #}}}
-
-#FIXME: during installation packages are installed one by one but environment.sh was sourced
-#before so new packages are NOT in the path.
-#may resource environment.sh with:
-#if [ -z $(echo "$PATH" | grep "$MATLAB_DIR") ]; then export $PATH...; fi
-
-#Windows compilers: 
-if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
-	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
-fi
-
-#Some basic path, in case it is not included by default
-libpathappend "/usr/local/lib"
-
-#Load ISSM scripts
-pathappend "$ISSM_DIR/scripts"
-
-MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
-export MATLAB_DIR
-pathprepend   "$MATLAB_DIR/bin" #take precedence over /usr/local/bin/matlab
-libpathappend "$MATLAB_DIR/lib"
-
-#legacy mpich2 (To be removed)
-MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
-if [ -d "$MPI_DIR" ]; then
-	export MPI_DIR
-	pathprepend   "$MPI_DIR/bin"
-	libpathappend "$MPI_DIR/lib"
-fi
-
-MPI_DIR="$ISSM_DIR/externalpackages/mpich/install"
-if [ -d "$MPI_DIR" ]; then
-	export MPI_DIR
-	pathprepend   "$MPI_DIR/bin"
-	libpathappend "$MPI_DIR/lib"
-fi
-
-PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
-export PETSC_DIR
-libpathappend "$PETSC_DIR/lib"
-
-SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
-libpathappend "$SLEPC_DIR/lib"
-
-TAO_DIR="$ISSM_DIR/externalpackages/tao/install"
-libpathappend "$TAO_DIR/lib"
-
-DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
-pathappend "$DAKOTA_DIR/bin"
-libpathappend "$DAKOTA_DIR/lib"
-
-DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
-pathprepend "$DOXYGEN_DIR/bin"
-
-AUTOTOOLS_DIR="$ISSM_DIR/externalpackages/autotools/install"
-pathprepend "$AUTOTOOLS_DIR/bin"
-
-SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
-pathappend "$SDK_DIR"
-
-SSH_DIR="$ISSM_DIR/externalpackages/ssh"
-pathappend "$SSH_DIR"
-
-VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install"
-pathprepend "$VALGRIND_DIR/bin"
-
-CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
-pathappend "$CPPCHECK_DIR/bin"
-
-GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
-pathprepend "$GDAL_DIR/bin"
-libpathappend "$GDAL_DIR/lib"
-
-PROJ4_DIR="$ISSM_DIR/externalpackages/proj.4/install"
-libpathappend "$PROJ4_DIR/lib"
-
-MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
-if [ -d "$MERCURIAL_DIR" ]; then
-	export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
-	pathappend "$MERCURIAL_DIR"
-fi
-
-BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
-BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
-if [ -d "$BOOST_DIR" ]; then
-	export BOOSTROOT
-	export BOOST_DIR
-	libpathappend   "$BOOST_DIR/lib"
-	dylibpathappend "$BOOST_DIR/lib"
-	pathappend      "$BOOST_DIR/bin"
-fi
-
-XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
-XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
-if [ -d "$XERCESROOT" ]; then
-	export XERCESROOT 
-	export XERCESCROOT
-fi
-
-XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
-XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/"
-XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
-PLATFORM="x86-Linux"
-if [ -d "$XAIF_DIR" ]; then
-	export XAIFBOOSTERROOT
-	export XAIFBOOSTER_HOME
-	export XAIF_DIR
-	export PLATFORM
-fi
-
-ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
-if [ -d "$ANGELROOT" ]; then
-	export ANGELROOT
-fi
-
-OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
-if [ -d "$OPENANALYSISROOT" ]; then
-	export OPENANALYSISROOT
-	libpathappend "$OPENANALYSISROOT/lib"
-fi
-
-JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
-libpathappend "$JVM_DIR"
-
-BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
-pathappend "$BBFTP_DIR/bin"
-
-ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
-pathappend "$ADIC_DIR/bin"
-libpathappend "$ADIC_DIR/lib"
-
-COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
-libpathappend "$COLPACK_DIR/lib"
-
-ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
-pathappend "$ECLIPSE_DIR"
-
-APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan/install"
-pathappend "$APPSCAN_DIR/bin"
-
-RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
-pathappend "$RATS_DIR/bin"
-
-DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
-pathappend "$DYSON_DIR"
-
-CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
-pathprepend "$CMAKE_DIR/bin"
-
-SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
-pathappend "$SHAPELIB_DIR/exec"
-
-CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
-pathappend "$CCCL_DIR/bin"
-
-PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
-pathappend "$PACKAGEMAKER_DIR"
-
-#android-dev-dir
-export ANDROID_DIR="$ISSM_DIR/externalpackages/android"
-
-export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
-pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin"
-
-export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install"
-pathappend "$ANDROID_SDK_DIR/"
-
-GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
-libpathappend "$GSL_DIR/lib"
-
-GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
-pathprepend "$GMAKE_DIR/bin"
-
-PYTHON_DIR="/usr"
-if [ -d "$PYTHON_DIR" ]; then
-	export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/lib"
-	export PYTHONSTARTUP="$ISSM_DIR/startup.py"
-	pathprepend    "/usr"
-	libpathprepend "$ISSM_DIR/lib"
-	libpathprepend "/usr/lib/python2.7"
-fi
-
-MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install"
-pathappend "$MODELE_DIR/src/exec"
-
-GIT_DIR="$ISSM_DIR/externalpackages/git/install"
-pathprepend "$GIT_DIR/bin"
-
-NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install"
-pathappend "$NCVIEW_DIR"
-
-TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4"
-libpathappend "$TCLX_DIR"
-
-ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/install"
-pathappend "$ASPELL_DIR/bin"
-
-HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install"
-dylibpathappend "$HDF5_DIR/lib"
-libpathappend "$HDF5_DIR/lib"
-if [ -d "$HDF5_DIR" ]; then
-	export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
-	export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
-fi
-
-NETCDF_DIR="$ISSM_DIR/externalpackages/netcdf/install"
-pathappend "$NETCDF_DIR/bin"
-dylibpathappend "$NETCDF_DIR/lib"
-libpathappend "$NETCDF_DIR/lib"
-if [ -d "$NETCDF_DIR" ]; then
-	export LIBRARY_PATH="$LIBRARY_PATH:$NETCDF_DIR/lib"
-	dylibpathappend "$NETCDF_DIR/lib"
-	libpathappend "$NETCDF_DIR/lib"
-	export C_INCLUDE_PATH="$C_INCLUDE_PATH:$NETCDF_DIR/include"
-fi
-
-NETCDF_CXX_DIR="$ISSM_DIR/externalpackages/netcdf-cxx/install"
-libpathappend "$NETCDF_CXX_DIR/lib"
-
-SVN_DIR="$ISSM_DIR/externalpackages/svn/install"
-pathprepend   "$SVN_DIR/bin"
-libpathappend "$SVN_DIR/lib"
-
-APR_DIR="$ISSM_DIR/externalpackages/apr/install"
-pathappend    "$APR_DIR/bin"
-libpathappend "$APR_DIR/lib"
-
-APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install"
-pathappend   "$APR_UTIL_DIR/bin:$PATH"
-libpathappend "$APR_UTIL_DIR/lib"
-
-SQLITE_DIR="$ISSM_DIR/externalpackages/sqlite/install"
-pathappend   "$SQLITE_DIR/bin"
-libpathappend "$SQLITE_DIR/lib"
-
-YAMS_DIR="$ISSM_DIR/externalpackages/yams/install"
-pathappend   "$YAMS_DIR"
-
-SWIG_DIR="$ISSM_DIR/externalpackages/swig/install"
-pathappend   "$SWIG_DIR"
-
-#AUX-CONFIG
-pathappend   "$ISSM_DIR/aux-config"
Index: ../trunk-jpl/packagers/ubuntu/issmpkg/templates/sampleControl
===================================================================
--- ../trunk-jpl/packagers/ubuntu/issmpkg/templates/sampleControl	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/issmpkg/templates/sampleControl	(revision 18436)
@@ -1,6 +0,0 @@
-Package: issm-python
-Version: 1.1.3
-Architecture: amd64
-Depends: mpich2, petsc3.2-issm, metis4.0-issm, triangle-bin, libtriangle-dev, python2.7-dev, python-scipy, python-netcdf4, netcdf-bin, python-nose, libnetcdfc++4, hdf5-tools
-Maintainer: issm/jpl (issm@jpl.nasa.gov)
-Description: Ice Sheet System Model, ubuntu/debian package
Index: ../trunk-jpl/packagers/ubuntu/startup.m
===================================================================
--- ../trunk-jpl/packagers/ubuntu/startup.m	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/startup.m	(revision 18436)
@@ -1,40 +0,0 @@
-%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
Index: ../trunk-jpl/packagers/ubuntu/install.sh
===================================================================
--- ../trunk-jpl/packagers/ubuntu/install.sh	(revision 0)
+++ ../trunk-jpl/packagers/ubuntu/install.sh	(revision 18436)
@@ -0,0 +1,127 @@
+#!/bin/bash
+
+# ISSM_DIR and MATLAB_DIR must be set correctly.
+# {{{
+if [ "${ISSM_DIR}x" == "x" ]; then
+   echo "ISSM_DIR is not set!" >&2
+   exit 1;
+elif [ -d ${ISSM_DIR} ]; then
+   echo "ISSM_DIR: ${ISSM_DIR}"
+else
+   echo "ISSM_DIR: ${ISSM_DIR} does not exist!" >&2
+   exit 1;
+fi
+
+if [ "${MATLAB_DIR}x" == "x" ]; then
+   echo "MATLAB_DIR is not set!"
+   exit 1;
+elif [ -d ${MATLAB_DIR} ]; then
+   echo "MATLAB_DIR: ${MATLAB_DIR}"
+else
+   echo "MATLAB_DIR: ${MATLAB_DIR} does not exist!" >&2
+   exit 1;
+fi
+# }}}
+
+#List of external pakages to be installed and their installation scripts
+EXTERNALPACKAGES="autotools install.sh                
+                  cmake     install.sh                
+                  petsc     install-3.5-linux64-static.sh
+                  triangle  install-linux64.sh "
+
+# Install Externalpackages
+# {{{
+
+#Files source environment to make sure installed packages are in PATH
+source $ISSM_DIR/etc/environment.sh
+
+#number of packages: 
+NUMPACKAGES=$(($(echo $EXTERNALPACKAGES | wc -w )/2))
+
+for ((i=1;i<=$NUMPACKAGES;i++))
+do
+	NUM1=$((2*$i-1))
+	NUM2=$((2*$i))
+	PACKAGENAME=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM1-$NUM1)
+	PACKAGEINST=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM2-$NUM2)
+
+	cd $ISSM_DIR/externalpackages/$PACKAGENAME
+
+	if [[ $PACKAGEINST -nt  install ]]; then 
+		#go ahead and reinstall. 
+		echo "Triggering new install of $PACKAGENAME"
+		install_test=1
+	else
+		#ok, we want to skip, unless the package is not installed: 
+		if [ -d install ]; then 
+			#could be empty, signaling a failed previous install: 
+			if [ "$(ls -A install)" ];then
+				echo "and install directory exists, so skipping install of $PACKAGENAME"
+				install_test=0;
+			else
+				echo "and install directory exists, however, it is empty, so triggering install of $PACKAGENAME"
+				install_test=1;
+			fi
+		else
+			echo "However, install directory does not exist, so triggering install of $PACKAGENAME"
+			install_test=1;
+		fi
+	fi
+
+	if [[ $install_test == 1 ]]; then 
+		echo "======================================================";
+		echo "       Installing $PACKAGENAME                        ";
+		echo "======================================================";
+		./$PACKAGEINST |  tee compil.log
+		if [ $? -ne 0 ]; then
+			echo "======================================================";
+			echo "    ERROR: installation of $PACKAGENAME failed        ";
+			echo "======================================================";
+			#erase install directory, so that next time, we still try and compile this!
+			rm -rf install
+		fi
+		source $ISSM_DIR/etc/environment.sh
+	else
+		echo "======================================================";
+		echo "       Skipping install of $PACKAGENAME                        ";
+		echo "======================================================";
+	fi
+	cd ..
+done
+# }}}
+
+# Compile ISSM
+#{{{
+cd $ISSM_DIR
+echo "Aureconf..."
+autoreconf -if
+echo "Configuring..."
+./configure \
+	--prefix=$ISSM_DIR \
+	--disable-static \
+	--enable-standalone-executables \
+	--enable-standalone-libraries \
+	--with-matlab-dir="/Applications/MATLAB_R2011b.app/" \
+	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
+	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
+	--with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
+	--with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include  \
+	--with-mpi-libflags=" -L$ISSM_DIR/externalpackages/petsc/install/lib -lmpich -lmpl " \
+	--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.6/ -lgfortran" \
+	--enable-debugging \
+	--with-numthreads=4
+
+
+if [ $? -ne 0 ]; then echo "FAILED TO CONFIGURE!" && exit 1; fi
+
+echo "Building..."
+make -j 8
+if [ $? -ne 0 ]; then echo "FAILED TO BUILD!" && exit 1; fi
+
+echo "Installing..."
+make install 
+if [ $? -ne 0 ]; then echo "FAILED TO INSTALL!" && exit 1; fi
+#}}}

Property changes on: ../trunk-jpl/packagers/ubuntu/install.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Index: ../trunk-jpl/packagers/ubuntu/package.sh
===================================================================
--- ../trunk-jpl/packagers/ubuntu/package.sh	(revision 18435)
+++ ../trunk-jpl/packagers/ubuntu/package.sh	(revision 18436)
@@ -1,15 +1,31 @@
-#/bin/bash
+#!/bin/bash
 
-#Just tar gz the bin/ directory and test/ directory and put a startup.m file.
+echo "modify generic" 
+cd $ISSM_DIR/bin
+cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
+echo "move mpiexec to bin" 
+cp ../externalpackages/mpich/install/bin/mpiexec .
+cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy .
 
-rm -rf ISSM ISSM-Ubuntu32.tar.gz
+#Check that test101 runs
+cd $ISSM_DIR/test/NightlyRun
+rm matlab.log
+$MATLAB_DIR/bin/matlab -nojvm -nosplash -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
 
-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
+if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then
+	echo "test101 FAILED"
+	exit 1;
+else
+	echo "test101 passed"
+fi
+
+tarball_name='issm-ubuntu-static_build.tar.gz'
+
+echo "Cleanup first" 
+cd $ISSM_DIR
+rm $tarball_name
+
+echo "Creating tarball: ${tarball_name}"
+cd $ISSM_DIR
+tar -czf $tarball_name ./bin ./lib ./test ./examples
+ls -lah $tarball_name
