Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 12947)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 12948)
@@ -6,293 +6,323 @@
 fi
 
-source $ISSM_DIR/etc/environment_variables.sh
-
-#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them after exporting the variables
-#to environment.
-for i in $@
-do
-	eval $i
-done
-
-#CRON utilities
-PATH="$PATH:$ISSM_DIR/cron"
-
-#scripts
-PATH="$PATH:$ISSM_DIR/scripts"
-
-##MATLAB
-export MATLAB_DIR
-PATH="$MATLAB_DIR/bin:$PATH" #take precedence over /usr/local/bin/matlab
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/lib"
-#export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/bin/glnxa64"
-#export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/bin/glnxa64"
-
-#MPI
-export MPI_DIR
-PATH="$MPI_DIR/bin:$PATH"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MPI_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$MPI_DIR/lib"
-export MANPATH="$MANPATH:$MPI_DIR/man"
-export MPIRUN_NPROCS=24
-
-#PETSC
-export PETSC_DIR
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib/$ISSM_ARCH:$PETSC_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib/$ISSM_ARCH"
-
-#SLEPC
-export SLEPC_DIR
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SLEPC_DIR/lib/$ISSM_ARCH"
-export LD_RUN_PATH="$LD_RUN_PATH:$SLEPC_DIR/lib/$ISSM_ARCH"
-
-#Dakota
-export DAKOTA_DIR
-PATH="$PATH:$DAKOTA_DIR/bin"
-export MANPATH="$MANPATH:$MPI_DIR/man:$DAKOTA_DIR/docs/man:$DAKOTA_DIR/docs/man-ref"
-
-#Qhull
-export QHULL_DIR
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$QHULL_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$QHULL_DIR/lib"
-
-#Doxygen
-export DOXYGEN_DIR
-MANPATH="$MANPATH:$DOXYGEN_DIR/man"
-PATH="$PATH:$DOXYGEN_DIR/bin"
-
-#MTOC
-export MTOC_DIR
-PATH="$PATH:$MTOC_DIR"
-
-#TRIANGLE
-export TRIANGLE_DIR
-
-#METIS
-export METIS_DIR
-	
-#BLAS
-export BLAS_DIR
-
-#LAPACK
-export LAPACK_DIR
-
-#SCALAPACK
-export SCALAPACK_DIR
-
-#PLAPACK
-export PLAPACK_DIR
-
-#BLACS
-export BLACS_DIR
-
-#YAMS
-export YAMS_DIR
-PATH="$PATH:$YAMS_DIR"
-
-#BAMG
-export BAMG_DIR
-PATH="$PATH:$BAMG_DIR"
-
-#TEX2IM
-export TEX2IM_DIR
-PATH="$PATH:$TEX2IM_DIR"
-
-#SOWING
-export SOWING_DIR
-PATH="$PATH:$SOWING_DIR/bin"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SOWING_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$SOWING_DIR/lib"
-export MANPATH="$MANPATH:$SOWING_DIR/man"
-
-#Chaco
-export CHACO_DIR
-PATH="$PATH:$CHACO_DIR"
-
-#MeshPart
-export MESHPART_DIR
-PATH="$PATH:$MESHPART_DIR"
-
-#SCOTCH
-export SCOTCH_DIR
-PATH="$PATH:$SCOTCH_DIR"
-export MANPATH="$MANPATH:$SCOTCH_DIR/man"
-
-#AUTOCONF
-export AUTOCONF_DIR
-PATH="$AUTOCONF_DIR/bin:$PATH"
-
-#AUTOMAKE
-export AUTOMAKE_DIR
-PATH="$AUTOMAKE_DIR/bin:$PATH"
-
-export LIBTOOL_DIR
-PATH="$LIBTOOL_DIR/bin:$PATH"
-
-#BORLAND
-export BORLAND_DIR
-PATH="$PATH:$BORLAND_DIR/Bin"
-
-#INTEL
-#export INTEL_DIR
-#PATH="$PATH:$INTEL_DIR"
-#source $ISSM_DIR/externalpackages/intel/intel.sh
-
-#SDK
-export SDK_DIR
-PATH="$PATH:$SDK_DIR"
-
-#SSH
-export SSH_DIR
-PATH="$PATH:$SSH_DIR"
-
-#VALGRIND
-export VALGRIND_DIR
-PATH="$PATH:$VALGRIND_DIR"
-
-#GRAPHVIZ
-export GRAPHVIZ_DIR
-PATH="$PATH:$GRAPHVIZ_DIR"
-
-#CPPCHECK
-export CPPCHECK_DIR
-PATH="$PATH:$CPPCHECK_DIR"
-
-#GDAL
-export GDAL_DIR
-PATH="$GDAL_DIR/bin:$PATH"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GDAL_DIR/lib"
-
-#MERCURIAL
-export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
-export PATH="$PATH:$MERCURIAL_DIR/"
-
-#BOOST
-export BOOSTROOT
-export BOOST_DIR
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$BOOST_DIR/lib"
-export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$BOOST_DIR/lib"
-export PATH="$PATH:$BOOST_DIR/bin"
-
-#XERCES
-export XERCESROOT 
-export XERCESCROOT
-
-#xaifBooster
-export XAIFBOOSTERROOT
-export XAIFBOOSTER_HOME
-export XAIF_DIR
-export PLATFORM
-
-#angel
-export ANGELROOT
-
-#openanalysis
-export OPENANALYSISROOT
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OPENANALYSISROOT/lib"
-
-#JAVA
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$JVM_DIR"
-
-#BBFTP
-export PATH="$PATH:$BBFTP_DIR/bin"
-
-#ADIC
-export PATH="$PATH:$ADIC_DIR/bin"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ADIC_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$ADIC_DIR/lib"
-
-#COLPACK
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$COLPACK_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$COLPACK_DIR/lib"
-
-#ECLIPSE
-export PATH="$PATH:$ECLIPSE_DIR"
-
-#FLAIM
-export FLAIM_DIR
-
-#APPSCAN
-export PATH="$PATH:$APPSCAN_DIR/install/bin"
-export PATH="$PATH:$APPSCAN_DIR/bin"
-
-#CPPCHECK
-export PATH="$PATH:$CPPCHECK_DIR/bin"
-
-#RATS
-export PATH="$PATH:$RATS_DIR/bin"
-
-#DYSON
-export PATH="$PATH:$DYSON_DIR"
-
-#CMAKE
-export PATH="$PATH:$CMAKE_DIR/bin"
-
-#SHAPELIB
-export PATH="$PATH:$SHAPELIB_DIR/exec"
-
-#CCCL
-export PATH="$PATH:$CCCL_DIR/bin"
-
-#PACKAGEMAKER
-export PATH="$PATH:$PACKAGEMAKER_DIR"
-
-#ANDROID_NDK:
-export ANDROID_NDK_DIR
-export PATH="$PATH:$ANDROID_NDK_DIR/"
-
-#ANDROID_DIR
-export ANDROID_DIR
-
-#ANDROID_SDK
-export PATH="$PATH:$ANDROID_SDK_DIR/"
-
-#ANDROID_ANT
-export PATH="$PATH:$ANDROID_ANT_DIR/"
-
-#GSL
-export PATH="$PATH:$GSL_DIR/bin"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GSL_DIR/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:$GSL_DIR/lib"
-
-#GMAKE
-export PATH="$GMAKE_DIR/bin:$PATH"
-
-#PYTHON
-export PATH="$PYTHON_DIR/bin:$PATH"
-export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python"
-export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$ISSM_DIR/externalpackages/python/install/lib:$LD_LIBRARY_PATH
-export PYTHONSTARTUP
-
-#MODELE
-export PATH="$MODELE_DIR/src/exec:$PATH"
-
-#GIT
-export PATH="$PATH:$GIT_DIR/install/bin"
-
-#NCVIEW
-export PATH="$PATH:$NCVIEW_DIR/install"
-
-#TCLX
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$TCLX_DIR"
-export LD_RUN_PATH="$LD_RUN_PATH:$TCLX_DIR"
-
-#TCL/TK
+#source $ISSM_DIR/etc/environment_variables.sh
+
+#Some basic path, in case it is not included by default
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
 export LD_RUN_PATH="$LD_RUN_PATH:/usr/local/lib"
 
+#Load ISSM scripts
+export PATH="$PATH:$ISSM_DIR/scripts"
+
+#MATLAB
+MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
+if [ -d "$MATLAB_DIR" ]; then
+	export MATLAB_DIR
+	export PATH="$MATLAB_DIR/bin:$PATH" #take precedence over /usr/local/bin/matlab
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/lib"
+	export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/lib"
+fi
+
+#MPI
+MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
+if [ -d "$MPI_DIR" ]; then
+	export PATH="$MPI_DIR/bin:$PATH"
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MPI_DIR/lib"
+	export LD_RUN_PATH="$LD_RUN_PATH:$MPI_DIR/lib"
+	export MANPATH="$MANPATH:$MPI_DIR/man"
+fi
+
+#PETSC
+PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
+if [ -d "$PETSC_DIR" ]; then
+	export PETSC_DIR
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib/$ISSM_ARCH:$PETSC_DIR/lib"
+	export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib/$ISSM_ARCH"
+fi
+
+#SLEPC
+SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
+if [ -d "$SLEPC_DIR" ]; then
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SLEPC_DIR/lib/$ISSM_ARCH"
+	export LD_RUN_PATH="$LD_RUN_PATH:$SLEPC_DIR/lib/$ISSM_ARCH"
+fi
+
+#Dakota
+DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
+if [ -d "$DAKOTA_DIR" ]; then
+	export PATH="$PATH:$DAKOTA_DIR/bin"
+	export MANPATH="$MANPATH:$MPI_DIR/man:$DAKOTA_DIR/docs/man:$DAKOTA_DIR/docs/man-ref"
+fi
+
+#Doxygen
+DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
+if [ -d "$DOXYGEN_DIR" ]; then
+	export MANPATH="$MANPATH:$DOXYGEN_DIR/man"
+	export PATH="$PATH:$DOXYGEN_DIR/bin"
+fi
+
+#AUTOCONF
+AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install"
+if [ -d "$AUTOCONF_DIR" ]; then
+	export PATH="$AUTOCONF_DIR/bin:$PATH"
+fi
+
+#AUTOMAKE
+AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install"
+if [ -d "$AUTOMAKE_DIR" ]; then
+	export PATH="$AUTOMAKE_DIR/bin:$PATH"
+fi
+
+#LIBTOOL
+LIBTOOL_DIR="$ISSM_DIR/externalpackages/libtool/install"
+if [ -d "$LIBTOOL_DIR" ]; then
+	export PATH="$LIBTOOL_DIR/bin:$PATH"
+fi
+
+#SDK
+SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
+if [ -d "$SDK_DIR" ]; then
+	export PATH="$PATH:$SDK_DIR"
+fi
+
+#SSH
+SSH_DIR="$ISSM_DIR/externalpackages/ssh"
+if [ -d "$SSH_DIR" ]; then
+	export PATH="$PATH:$SSH_DIR"
+fi
+
+#VALGRIND
+VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin"
+if [ -d "$VALGRIND_DIR" ]; then
+	export PATH="$VALGRIND_DIR:$PATH"
+fi
+
+#CPPCHECK
+CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
+if [ -d "$CPPCHECK_DIR" ]; then
+	export PATH="$PATH:$CPPCHECK_DIR/bin"
+fi
+
+#GDAL
+GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
+if [ -d "$GDAL_DIR" ]; then
+	export PATH="$GDAL_DIR/bin:$PATH"
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GDAL_DIR/lib"
+fi
+
+#MERCURIAL
+MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
+if [ -d "$MERCURIAL_DIR" ]; then
+	export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
+	export PATH="$PATH:$MERCURIAL_DIR/"
+fi
+
+#BOOST
+BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
+BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
+if [ -d "$BOOST_DIR" ]; then
+	export BOOSTROOT
+	export BOOST_DIR
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$BOOST_DIR/lib"
+	export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$BOOST_DIR/lib"
+	export PATH="$PATH:$BOOST_DIR/bin"
+fi
+
+#XERCES
+XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
+XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
+if [ -d "$XERCESROOT" ]; then
+	export XERCESROOT 
+	export XERCESCROOT
+fi
+
+#xaifBooster
+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
+
+#angel
+ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
+if [ -d "$ANGELROOT" ]; then
+	export ANGELROOT
+fi
+
+#openanalysis
+OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
+if [ -d "$OPENANALYSISROOT" ]; then
+	export OPENANALYSISROOT
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OPENANALYSISROOT/lib"
+fi
+
+#JAVA
+JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
+if [ -d "$JVM_DIR" ]; then
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$JVM_DIR"
+fi
+
+#BBFTP
+BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
+if [ -d "$BBFTP_DIR" ]; then
+	export PATH="$PATH:$BBFTP_DIR/bin"
+fi
+
+#ADIC
+ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
+if [ -d "$ADIC_DIR" ]; then
+	export PATH="$PATH:$ADIC_DIR/bin"
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ADIC_DIR/lib"
+	export LD_RUN_PATH="$LD_RUN_PATH:$ADIC_DIR/lib"
+fi
+
+#COLPACK
+COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
+if [ -d "$COLPACK_DIR" ]; then
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$COLPACK_DIR/lib"
+	export LD_RUN_PATH="$LD_RUN_PATH:$COLPACK_DIR/lib"
+fi
+
+#ECLIPSE
+ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
+if [ -d "$ECLIPSE_DIR" ]; then
+	export PATH="$PATH:$ECLIPSE_DIR"
+fi
+
+#APPSCAN
+APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan"
+if [ -d "$APPSCAN_DIR" ]; then
+	export PATH="$PATH:$APPSCAN_DIR/install/bin"
+	export PATH="$PATH:$APPSCAN_DIR/bin"
+fi
+
+#RATS
+RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
+if [ -d "$RATS_DIR" ]; then
+	export PATH="$PATH:$RATS_DIR/bin"
+fi
+
+#DYSON
+DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
+if [ -d "$DYSON_DIR" ]; then
+	export PATH="$PATH:$DYSON_DIR"
+fi
+
+#CMAKE
+CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
+if [ -d "$CMAKE_DIR" ]; then
+	export PATH="$PATH:$CMAKE_DIR/bin"
+fi
+
+#SHAPELIB
+SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
+if [ -d "$SHAPELIB_DIR" ]; then
+	export PATH="$PATH:$SHAPELIB_DIR/exec"
+fi
+
+#CCCL
+CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
+if [ -d "$CCCL_DIR" ]; then
+	export PATH="$PATH:$CCCL_DIR/bin"
+fi
+
+#PACKAGEMAKER
+PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
+if [ -d "$PACKAGEMAKER_DIR" ]; then
+	export PATH="$PATH:$PACKAGEMAKER_DIR"
+fi
+
+#ANDROID_NDK:
+ANDROID_DIR="$ISSM_DIR/externalpackages/android"
+if [ -d "$ANDROID_DIR" ]; then
+	export ANDROID_NDK_DIR
+	export PATH="$PATH:$ANDROID_NDK_DIR/"
+fi
+
+#ANDROID_DIR
+ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
+if [ -d "$ANDROID_NDK_DIR" ]; then
+	export ANDROID_DIR
+fi
+
+#ANDROID_SDK
+ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk"
+if [ -d "$ANDROID_SDK_DIR" ]; then
+	export PATH="$PATH:$ANDROID_SDK_DIR/"
+fi
+
+#GSL
+GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
+if [ -d "$GSL_DIR" ]; then
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GSL_DIR/lib"
+	export LD_RUN_PATH="$LD_RUN_PATH:$GSL_DIR/lib"
+fi
+
+#GMAKE
+GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
+if [ -d "$GMAKE_DIR" ]; then
+	export PATH="$GMAKE_DIR/bin:$PATH"
+fi
+
+#PYTHON
+PYTHON_DIR="$ISSM_DIR/externalpackages/python/install"
+if [ -d "$PYTHON_DIR" ]; then
+	PYTHONSTARTUP="$ISSM_DIR/startup.py"
+	export PATH="$PYTHON_DIR/bin:$PATH"
+	export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python"
+	export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$ISSM_DIR/externalpackages/python/install/lib:$LD_LIBRARY_PATH
+	export PYTHONSTARTUP="$ISSM_DIR/startup.py"
+fi
+
+#MODELE
+MODELE_DIR="$ISSM_DIR/externalpackages/modelE"
+if [ -d "$MODELE_DIR" ]; then
+	export PATH="$MODELE_DIR/src/exec:$PATH"
+fi
+
+#GIT
+GIT_DIR="$ISSM_DIR/externalpackages/git"
+if [ -d "$GIT_DIR" ]; then
+	export PATH="$PATH:$GIT_DIR/install/bin"
+fi
+
+#NCVIEW
+NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview"
+if [ -d "$NCVIEW_DIR" ]; then
+	export PATH="$PATH:$NCVIEW_DIR/install"
+fi
+
+#TCLX
+TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4"
+if [ -d "$TCLX_DIR" ]; then
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$TCLX_DIR"
+	export LD_RUN_PATH="$LD_RUN_PATH:$TCLX_DIR"
+fi
+
 #ASPELL
-export PATH="$ASPELL_DIR/install/bin:$PATH"
-
+ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/"
+if [ -d "$ASPELL_DIR" ]; then
+	export PATH="$ASPELL_DIR/install/bin:$PATH"
+fi
 
 #ESMF
-export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf
-export ESMF_COMPILER=gfortran
-export ESMF_COMM=mpich2
+ESMF_DIR="$ISSM_DIR/externalpackages/esmf/esmf"
+if [ -d "$ESMF_DIR" ]; then
+	export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf
+	export ESMF_COMPILER=gfortran
+	export ESMF_COMM=mpich2
+fi
 
 #HDF5
-export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HDF5_DIR/lib"
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HDF5_DIR/lib"
-export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
-export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
-
+HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install
+if [ -d "$HDF5_DIR" ]; then
+	export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HDF5_DIR/lib"
+	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HDF5_DIR/lib"
+	export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
+	export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
+fi