Index: /issm/trunk-jpl/etc/environment.csh
===================================================================
--- /issm/trunk-jpl/etc/environment.csh	(revision 12973)
+++ /issm/trunk-jpl/etc/environment.csh	(revision 12974)
@@ -1,140 +1,91 @@
 #ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
-source $ISSM_DIR/etc/environment_variables.csh
 
-#Do we have any command line arguments? (such as MATLAB_DIR=otherdirthandefault), source them before exporting the variables 
-#to environment.
-
-#foreach i ($@)
-#eval $i
-#end
-
-#CRON utilities
-setenv PATH {$PATH}:{$ISSM_DIR}/cron
-
-#SCRIPTS utilities
+#Load ISSM scripts
 setenv PATH {$PATH}:{$ISSM_DIR}/scripts
 
 #MATLAB
-setenv MATLAB_DIR {$MATLAB_DIR}
-setenv PATH {$MATLAB_DIR}/bin:{$PATH}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MATLAB_DIR/lib
+set MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
+if (-d MATLAB_DIR) then
+	setenv MATLAB_DIR {$MATLAB_DIR}
+	setenv PATH {$MATLAB_DIR}/bin:{$PATH}
+	setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64
+endif
 
 #MPI
-setenv MPI_DIR {$MPI_DIR}
-setenv PATH {$MPI_DIR}/bin:{$PATH}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MPI_DIR/lib
-setenv MANPATH {$MANPATH}:$MPI_DIR/man
-setenv MPIRUN_NPROCS 8
+set MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
+if (-d $MPI_DIR) then
+	setenv MPI_DIR {$MPI_DIR}
+	setenv PATH {$MPI_DIR}/bin:{$PATH}
+	setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$MPI_DIR/lib
+	setenv MANPATH {$MANPATH}:$MPI_DIR/man
+endif
 
 #PETSC
-setenv PETSC_DIR {$PETSC_DIR}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib/{$ISSM_ARCH}
+set PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
+if (-d $PETSC_DIR) then
+	setenv PETSC_DIR {$PETSC_DIR}
+	setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$PETSC_DIR/lib/{$ISSM_ARCH}
+endif
 
 #SLEPC
-setenv SLEPC_DIR {$SLEPC_DIR}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib/{$ISSM_ARCH}
-
+set SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
+if (-d $SLEPC_DIR) then
+	setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:$SLEPC_DIR/lib/{$ISSM_ARCH}
+endif
 
 #Dakota
-setenv DAKOTA_DIR {$DAKOTA_DIR}
-setenv PATH {$PATH}:{$DAKOTA_DIR}/bin
-setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref
-
-#Qhull
-setenv QHULL_DIR {$QHULL_DIR}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$QHULL_DIR}/lib
-
+set DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
+if (-d $DAKOTA_DIR) then
+	setenv PATH {$PATH}:{$DAKOTA_DIR}/bin
+	setenv MANPATH {$MANPATH}:{$MPI_DIR}/man:{$DAKOTA_DIR}/docs/man:{$DAKOTA_DIR}/docs/man-ref
+endif
 
 #Doxygen
-setenv DOXYGEN_DIR {$DOXYGEN_DIR}
-setenv MANPATH {$MANPATH}:{$DOXYGEN_DIR}/man
-setenv PATH {$PATH}:{$DOXYGEN_DIR}/bin
-
-#MTOC
-setenv MTOC_DIR {$MTOC_DIR}
-setenv PATH {$PATH}:{$MTOC_DIR}
-
-#MATLAB
-setenv MATLAB_DIR {$MATLAB_DIR}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$MATLAB_DIR}/bin/glnxa64
-setenv PATH {$PATH}:{$MATLAB_DIR}/bin
-
-#TRIANGLE
-setenv TRIANGLE_DIR {$TRIANGLE_DIR}
-
-#METIS
-setenv METIS_DIR {$METIS_DIR}
-	
-#BLAS
-setenv BLAS_DIR {$BLAS_DIR}
-
-#LAPACK
-setenv LAPACK_DIR {$LAPACK_DIR}
-
-#SCALAPACK
-setenv SCALAPACK_DIR {$SCALAPACK_DIR}
-
-#PLAPACK
-setenv PLAPACK_DIR {$PLAPACK_DIR}
-
-#BLACS
-setenv BLACS_DIR {$BLACS_DIR}
-
-#YAMS
-setenv YAMS_DIR {$YAMS_DIR}
-setenv PATH {$PATH}:{$YAMS_DIR}
-
-#TEX2IM
-setenv TEX2IM_DIR {$TEX2IM_DIR}
-setenv PATH {$PATH}:{$TEX2IM_DIR}
-
-#SOWING
-setenv SOWING_DIR {$SOWING_DIR}
-setenv PATH {$PATH}:{$SOWING_DIR}/bin
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$SOWING_DIR}/lib
-setenv MANPATH {$MANPATH}:{$SOWING_DIR}/man
-
-#Chaco
-setenv CHACO_DIR {$CHACO_DIR}
-setenv PATH {$PATH}:{$CHACO_DIR}
-
-#MeshPart
-setenv MESHPART_DIR {$MESHPART_DIR}
-setenv PATH {$PATH}:{$MESHPART_DIR}
-
-#SCOTCH
-setenv SCOTCH_DIR {$SCOTCH_DIR}
-setenv PATH {$PATH}:{$SCOTCH_DIR}
-setenv MANPATH {$MANPATH}:{$SCOTCH_DIR}/man
+set DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
+if (-d $DOXYGEN_DIR) then
+	setenv MANPATH {$MANPATH}:{$DOXYGEN_DIR}/man
+	setenv PATH {$PATH}:{$DOXYGEN_DIR}/bin
+endif
 
 #AUTOCONF
-setenv AUTOCONF_DIR {$AUTOCONF_DIR}
-setenv PATH {$AUTOCONF_DIR}/bin:{$PATH}
+set AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install"
+if (-d $AUTOCONF_DIR) then
+	setenv PATH {$AUTOCONF_DIR}/bin:{$PATH}
+endif
 
 #AUTOMAKE
-setenv AUTOMAKE_DIR {$AUTOMAKE_DIR}
-setenv PATH {$AUTOMAKE_DIR}/bin:{$PATH}
-
-#BORLAND
-setenv BORLAND_DIR {$BORLAND_DIR}
-setenv PATH {$PATH}:{$BORLAND_DIR}/Bin
+set AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install"
+if (-d $AUTOMAKE_DIR) then
+	setenv PATH {$AUTOMAKE_DIR}/bin:{$PATH}
+endif
 
 #SSH
-setenv SSH_DIR {$SSH_DIR}
-setenv PATH {$PATH}:{$SSH_DIR}
+set SSH_DIR="$ISSM_DIR/externalpackages/ssh"
+if (-d $SSH_DIR) then
+	setenv PATH {$PATH}:{$SSH_DIR}
+endif
 
 #VALGRIND
-setenv VALGRIND_DIR {$VALGRIND_DIR}
-setenv PATH {$PATH}:{$VALGRIND_DIR}
+set VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin"
+if (-d $VALGRIND_DIR) then
+	setenv PATH {$PATH}:{$VALGRIND_DIR}
+endif
 
 #MERCURIAL
-#setenv PYTHONPATH {$PYTHONPATH}:{$MERCURIAL_DIR}/mercurial/pure/
-setenv PYTHONPATH {$MERCURIAL_DIR}/mercurial/pure/
-setenv PATH {$PATH}:{$MERCURIAL_DIR}
+set MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
+if (-d $MERCURIAL_DIR) then
+	setenv PYTHONPATH {$MERCURIAL_DIR}/mercurial/pure/
+	setenv PATH {$PATH}:{$MERCURIAL_DIR}
+endif
 
 #GSL
-setenv GSL_DIR {$GSL_DIR}
-setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_DIR}/lib
+set GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
+if (-d $GSL_DIR) then
+	setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:{$GSL_DIR}/lib
+endif
 
 #CMAKE
-setenv PATH {$PATH}:{$CMAKE_DIR}/bin
+set CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
+if (-d $CMAKE_DIR) then
+	setenv PATH {$PATH}:{$CMAKE_DIR}/bin
+endif
Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 12973)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 12974)
@@ -5,6 +5,4 @@
 	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
 fi
-
-#source $ISSM_DIR/etc/environment_variables.sh
 
 #Some basic path, in case it is not included by default
Index: sm/trunk-jpl/etc/environment_variables.csh
===================================================================
--- /issm/trunk-jpl/etc/environment_variables.csh	(revision 12973)
+++ 	(revision )
@@ -1,93 +1,0 @@
-#
-#
-#This routine can only be run if the ISSM_DIR variable has been correctly set!
-#
-#
-
-#MATLAB
-set MATLAB_DIR={$ISSM_DIR}/externalpackages/matlab/install
-
-#MPI
-set MPI_DIR={$ISSM_DIR}/externalpackages/mpich2/install
-
-#PETSC
-set PETSC_DIR={$ISSM_DIR}/externalpackages/petsc/install
-
-#SLEPC
-set SLEPC_DIR={$ISSM_DIR}/externalpackages/slepc/install
-
-#Dakota
-set DAKOTA_DIR={$ISSM_DIR}/externalpackages/dakota/install
-
-#Qhull
-set QHULL_DIR={$ISSM_DIR}/externalpackages/qhull/install
-
-#Doxygen
-set DOXYGEN_DIR={$ISSM_DIR}/externalpackages/doxygen/install
-
-#MTOC
-set MTOC_DIR={$ISSM_DIR}/externalpackages/mtoc/install
-
-#Triangle
-set TRIANGLE_DIR={$ISSM_DIR}/externalpackages/triangle/install
-
-#METIS
-set METIS_DIR={$ISSM_DIR}/externalpackages/metis/install
-
-#BLAS
-set BLAS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack
-
-#LAPACK
-set LAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/fblaslapack/$ISSM_ARCH
-
-#SCALAPACK
-set SCALAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/SCALAPACK/$ISSM_ARCH
-
-#PLAPACK
-set PLAPACK_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/PLAPACKR32
-
-#BLACS
-set BLACS_DIR={$ISSM_DIR}/externalpackages/petsc/install/externalexternalpackages/blacs-dev/$ISSM_ARCH
-
-#sowing
-set SOWING_DIR={$ISSM_DIR}/externalpackages/sowing/install
-
-#YAMS
-set YAMS_DIR={$ISSM_DIR}/externalpackages/yams/install
-
-#TEX2IM
-set TEX2IM_DIR={$ISSM_DIR}/externalpackages/tex2im/install
-
-#Chaco
-set CHACO_DIR={$ISSM_DIR}/externalpackages/chaco/install
-
-#MeshPart
-set MESHPART_DIR={$ISSM_DIR}/externalpackages/meshpart/install
-
-#SCOTCH
-set SCOTCH_DIR={$ISSM_DIR}/externalpackages/scotch/install
-
-#Development packages
-#automake
-set AUTOMAKE_DIR={$ISSM_DIR}/externalpackages/automake/install
-
-#autoconf
-set AUTOCONF_DIR={$ISSM_DIR}/externalpackages/autoconf/install
-
-#borland
-set BORLAND_DIR=/cygdrive/c/Borland
-
-#ssh
-set SSH_DIR={$ISSM_DIR}/externalpackages/ssh
-
-#mercurial
-set MERCURIAL_DIR={$ISSM_DIR}/externalpackages/mercurial/install
-
-#valgrind
-set VALGRIND_DIR={$ISSM_DIR}/externalpackages/valgrind/install/bin
-
-#gsl
-set GSL_DIR={$ISSM_DIR}/externalpackages/gsl/install
-
-#cmake
-set CMAKE_DIR={$ISSM_DIR}/externalpackages/cmake/install
Index: sm/trunk-jpl/etc/environment_variables.sh
===================================================================
--- /issm/trunk-jpl/etc/environment_variables.sh	(revision 12973)
+++ 	(revision )
@@ -1,212 +1,0 @@
-#
-#
-#This routine can only be run if the ISSM_DIR variable has been correctly set!
-#
-#
-
-#MATLAB
-MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
-
-#MPI
-MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
-
-#PETSC
-PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
-
-#SLEPC
-SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
-
-#Dakota
-DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
-
-#Qhull
-QHULL_DIR="$ISSM_DIR/externalpackages/qhull/install"
-
-#Doxygen
-DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
-
-#MTOC
-MTOC_DIR="$ISSM_DIR/externalpackages/mtoc/install"
-
-#Triangle
-TRIANGLE_DIR="$ISSM_DIR/externalpackages/triangle/install"
-
-#METIS
-METIS_DIR="$ISSM_DIR/externalpackages/metis/install"
-
-#BLAS
-BLAS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack"
-
-#LAPACK
-LAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH"
-
-#SCALAPACK
-SCALAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/SCALAPACK/$ISSM_ARCH"
-
-#PLAPACK
-PLAPACK_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32"
-
-#BLACS
-BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH"
-
-#sowing
-SOWING_DIR="$ISSM_DIR/externalpackages/sowing/install"
-
-#BLACS
-BLACS_DIR="$ISSM_DIR/externalpackages/petsc/install/externalpackages/blacs-dev/$ISSM_ARCH"
-
-#YAMS
-YAMS_DIR="$ISSM_DIR/externalpackages/yams/install"
-
-#BAMG
-BAMG_DIR="$ISSM_DIR/externalpackages/bamg/install"
-
-#Chaco
-CHACO_DIR="$ISSM_DIR/externalpackages/chaco/install"
-
-#MeshPart
-MESHPART_DIR="$ISSM_DIR/externalpackages/meshpart/install"
-
-#SCOTCH
-SCOTCH_DIR="$ISSM_DIR/externalpackages/scotch/install"
-
-#Development packages
-#automake
-AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install"
-
-#libtool
-LIBTOOL_DIR="$ISSM_DIR/externalpackages/libtool/install"
-
-#autoconf
-AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install"
-
-#borland
-#BORLAND_DIR="/cygdrive/c/Borland/"
-
-#intel
-#INTEL_DIR="C:/IntelInstall/Compiler/11.1/038/bin/ia32/"
-
-#TEX2IM			 
-TEX2IM_DIR="$ISSM_DIR/externalpackages/tex2im/install" 
-
-#sdk
-#SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
-
-#ssh 
-SSH_DIR="$ISSM_DIR/externalpackages/ssh"
-
-#valgrind
-VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install/bin"
-
-#graphviz
-GRAPHVIZ_DIR="$ISSM_DIR/externalpackages/graphviz/install/bin"
-
-#cppcheck
-CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
-
-#gdal
-GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
-
-#mercurial
-MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
-
-#boost
-BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
-BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
-
-#OpenAnalysis
-OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
-
-#xerces
-XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
-XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
-
-#xaifBooster
-XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/"
-XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
-XAIFBOOSTER_HOME="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
-PLATFORM=x86-Linux
-
-#angel
-ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
-
-#java
-JVM_DIR=/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/
-
-#bbftp
-BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
-
-#adic2
-ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
-
-#colpack
-COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
-
-#eclipse
-ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
-
-#flaim
-FLAIM_DIR="$ISSM_DIR/externalpackages/flaim/install"
-
-#appscan
-APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan"
-
-#cppcheck
-CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
-
-#rats
-RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
-
-#dyson
-DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
-
-#cmake
-CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
-
-#shapelib
-SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
-
-#cccl
-CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
-
-#packagemaker
-PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
-
-#android-dev-dir
-ANDROID_DIR="$ISSM_DIR/externalpackages/android"
-
-#android-ndk
-ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
-
-#android-sdk
-ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk"
-
-#gsl
-GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
-
-#gnu make
-GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
-
-#PYTHON
-PYTHON_VER=2.7
-PYTHON_DIR="$ISSM_DIR/externalpackages/python/install"
-PYTHONSTARTUP="$ISSM_DIR/startup.py"
-
-#MODELE
-MODELE_DIR="$ISSM_DIR/externalpackages/modelE"
-
-
-#GIT
-GIT_DIR="$ISSM_DIR/externalpackages/git"
-
-#NCVIEW
-NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview"
-
-#TCLX
-TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4"
-
-#ASPELL
-ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/"
-
-#HDF5
-export HDF5_DIR=$ISSM_DIR/externalpackages/hdf5/install