Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 25855)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 25856)
@@ -165,311 +165,383 @@
 } #}}}
 
-# Windows compilers:
+# Windows compilers
 if [[ "$ISSM_ARCH" == "cygwin-intel" ]]; then
 	source $ISSM_DIR/externalpackages/windows/windows_environment.sh
 fi
 
-# Load ISSM scripts
+# ISSM scripts
 path_append "${ISSM_DIR}/scripts"
 
 ISSM_EXT_DIR="${ISSM_DIR}/externalpackages" # Redefine this constant if externalpackages are installed to a different directory
 
-SVN_DIR="${ISSM_EXT_DIR}/svn/install"
-if [ -d "${SVN_DIR}" ]; then
-	path_prepend   "${SVN_DIR}/bin"
-	ld_library_path_append "${SVN_DIR}/lib"
-fi
-
-GIT_DIR="${ISSM_EXT_DIR}/git/install"
-if [ -d "${GIT_DIR}" ]; then
-	path_prepend "${GIT_DIR}/bin"
-fi
-
-MPI_DIR="${ISSM_EXT_DIR}/mpich/install"
-if [ -d "${MPI_DIR}" ]; then
-	export MPI_DIR
-	export MPI_HOME=${MPI_DIR} # Needed by Dakota
-	export MPI_INC_DIR="$MPI_DIR/include"
-	path_prepend "${MPI_DIR}/bin"
-	cpath_prepend "${MPI_DIR}/include"
-	ld_library_path_append "${MPI_DIR}/lib"
-fi
-
-PETSC_DIR="${ISSM_EXT_DIR}/petsc/install"
-if [ -d "$PETSC_DIR" ]; then
-	export PETSC_DIR
-	ld_library_path_prepend "${PETSC_DIR}/lib"
-
-	# In case we have installed MPICH via PETSc
-	if [ -f "${PETSC_DIR}/bin/mpiexec" ]; then
-		MPI_DIR=${PETSC_DIR}
-		export MPI_DIR
-		export MPI_HOME=${MPI_DIR} # Needed by Dakota
-		export MPI_INC_DIR="${MPI_DIR}/include"
-		path_prepend "${MPI_DIR}/bin"
-		cpath_prepend "${MPI_DIR}/include"
-	fi
-fi
-
-LAPACK_DIR="${ISSM_EXT_DIR}/lapack/install"
-ld_library_path_append "${LAPACK_DIR}/lib"
-
-SCOTCH_DIR="${ISSM_EXT_DIR}/scotch/install"
-ld_library_path_append "$SCOTCH_DIR/lib"
-
-SLEPC_DIR="${ISSM_EXT_DIR}/slepc/install"
-ld_library_path_append "$SLEPC_DIR/lib"
-
-TAO_DIR="${ISSM_EXT_DIR}/tao/install"
-ld_library_path_append "$TAO_DIR/lib"
-
-DAKOTA_DIR="${ISSM_EXT_DIR}/dakota/install"
-if [ -d "${DAKOTA_DIR}" ]; then
-	path_append "${DAKOTA_DIR}/bin"
-	ld_library_path_append "${DAKOTA_DIR}/lib"
-	dyld_library_path_prepend "${DAKOTA_DIR}/lib"
-fi
-
-DOXYGEN_DIR="${ISSM_EXT_DIR}/doxygen/install"
-path_prepend "$DOXYGEN_DIR/bin"
-
-AUTOTOOLS_DIR="${ISSM_EXT_DIR}/autotools/install"
-path_prepend "$AUTOTOOLS_DIR/bin"
-
-SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
-path_append "$SDK_DIR"
-
-SSH_DIR="${ISSM_EXT_DIR}/ssh"
-path_append "$SSH_DIR"
-
-VALGRIND_DIR="${ISSM_EXT_DIR}/valgrind/install"
-path_prepend "$VALGRIND_DIR/bin"
-
-NCO_DIR="${ISSM_EXT_DIR}/nco/install/bin"
-path_prepend "$NCO_DIR/bin"
-
-CPPCHECK_DIR="${ISSM_EXT_DIR}/cppcheck/install"
-path_append "$CPPCHECK_DIR/bin"
-
-MERCURIAL_DIR="${ISSM_EXT_DIR}/mercurial/install"
-if [ -d "$MERCURIAL_DIR" ]; then
-	export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
-	path_append "$MERCURIAL_DIR"
-fi
-
-BOOST_DIR="${ISSM_EXT_DIR}/boost/install"
-BOOSTROOT="${ISSM_EXT_DIR}/boost/install"
-if [ -d "${BOOST_DIR}" ]; then
-	export BOOSTROOT
-	export BOOST_DIR
-	library_path_prepend "${BOOST_DIR}/lib"
-	ld_library_path_prepend "${BOOST_DIR}/lib"
-	dyld_library_path_prepend "${BOOST_DIR}/lib"
-	path_prepend "${BOOST_DIR}/bin"
+#########################
+# Command-line utilities
+#########################
+SSH_ROOT="${ISSM_EXT_DIR}/ssh"
+path_append "${SSH_ROOT}"
+
+SVN_ROOT="${ISSM_EXT_DIR}/svn/install"
+if [ -d "${SVN_ROOT}" ]; then
+	path_prepend "${SVN_ROOT}/bin"
+	ld_library_path_append "${SVN_ROOT}/lib"
+fi
+
+GIT_ROOT="${ISSM_EXT_DIR}/git/install"
+if [ -d "${GIT_ROOT}" ]; then
+	path_prepend "${GIT_ROOT}/bin"
+fi
+
+#############################
+# Compilers / runtime / SDKs
+#############################
+export ANDROID_DIR="${ISSM_EXT_DIR}/android"
+
+export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
+path_append "$ANDROID_NDK_DIR/arm-linux-android-install/bin"
+
+export ANDROID_SDK_ROOT="$ANDROID_DIR/android-sdk/install"
+path_append "$ANDROID_SDK_ROOT/"
+
+EMSCRIPTEN_ROOT="${ISSM_EXT_DIR}/emscripten/install"
+if [ -d ${EMSCRIPTEN_ROOT} ]; then
+	export EMSCRIPTEN_ROOT # Used in JavaScript build in installation of GSL, Triangle
+fi
+
+JVM_ROOT="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
+ld_library_path_append "${JVM_ROOT}"
+
+#############################
+# IDEs
+#############################
+ECLIPSE_ROOT="${ISSM_EXT_DIR}/eclipse/install"
+path_append "${ECLIPSE_ROOT}"
+
+#############################
+# Build systems
+#############################
+AUTOTOOLS_ROOT="${ISSM_EXT_DIR}/autotools/install"
+path_prepend "${AUTOTOOLS_ROOT}/bin"
+
+CMAKE_ROOT="${ISSM_EXT_DIR}/cmake/install"
+path_prepend "${CMAKE_ROOT}/bin"
+
+GMAKE_ROOT="${ISSM_EXT_DIR}/gmake/install"
+path_prepend "${GMAKE_ROOT}/bin"
+
+#############################
+# Packagers
+#############################
+PACKAGEMAKER_ROOT="${ISSM_EXT_DIR}/packagemaker/install"
+path_append "${PACKAGEMAKER_ROOT}"
+
+#############################
+# Libraries / binaries
+#############################
+MPI_ROOT="${ISSM_EXT_DIR}/mpich/install"
+if [ -d "${MPI_ROOT}" ]; then
+	export MPI_DIR=${MPI_ROOT}
+	export MPI_HOME=${MPI_ROOT} # Used in installation of Dakota
+	export MPI_INC_DIR="${MPI_ROOT}/include"
+	path_prepend "${MPI_ROOT}/bin"
+	cpath_prepend "${MPI_ROOT}/include"
+	ld_library_path_append "${MPI_ROOT}/lib"
+fi
+
+PETSC_ROOT="${ISSM_EXT_DIR}/petsc/install"
+if [ -d "$PETSC_ROOT" ]; then
+	export PETSC_ROOT # Used in installation of Gmsh
+	ld_library_path_prepend "${PETSC_ROOT}/lib"
+
+	# In case we have installed certain external packages via PETSc
+	#
+
+	# BLAS
+	NUM_BLAS_LIBS=$(find ${PETSC_ROOT}/lib -name libblas.* -o -name libfblas.* | wc -l)
+	if [ ${NUM_BLAS_LIBS} -gt 0 ]; then
+		export BLAS_ROOT="${PETSC_ROOT}" # Used in installation of Dakota, GMT
+	fi
+
+	# HDF5
+	NUM_HDF5_LIBS=$(find ${PETSC_ROOT}/lib -name libhdf5.* | wc -l)
+	if [ ${NUM_HDF5_LIBS} -gt 0 ]; then
+		export HDF5_ROOT="${PETSC_ROOT}" # Used in installation of NetCDF, GDAL
+		cpath_append "${PETSC_ROOT}/include"
+		library_path_append "${PETSC_ROOT}/lib"
+		dyld_library_path_append "${PETSC_ROOT}/lib"
+		ld_library_path_append "${PETSC_ROOT}/lib"
+	fi
+
+	# LAPACK
+	NUM_LAPACK_LIBS=$(find ${PETSC_ROOT}/lib -name liblapack.* -o -name libflapack.* | wc -l)
+	if [ ${NUM_LAPACK_LIBS} -gt 0 ]; then
+		export LAPACK_ROOT="${PETSC_ROOT}" # Used in installation of Dakota, GMT
+	fi
+
+	# METIS
+	NUM_METIS_LIBS=$(find ${PETSC_ROOT}/lib -name libmetis.* | wc -l)
+	if [ ${NUM_METIS_LIBS} -gt 0 ]; then
+		export METIS_ROOT="${PETSC_ROOT}" # Used in installation of Gmsh
+	fi
+
+	# MPICH
+	if [ -f "${PETSC_ROOT}/bin/mpiexec" ]; then
+		MPI_ROOT=${PETSC_ROOT}
+		export MPI_DIR=${MPI_ROOT}
+		export MPI_HOME=${MPI_ROOT} # Used in installation of Dakota
+		export MPI_INC_DIR="${MPI_ROOT}/include"
+		path_prepend "${MPI_ROOT}/bin"
+		cpath_prepend "${MPI_ROOT}/include"
+		ld_library_path_append "${MPI_ROOT}/lib"
+	fi
+
+	# ZLIB
+	NUM_ZLIB_LIBS=$(find ${PETSC_ROOT}/lib -name libz.* | wc -l)
+	if [ ${NUM_ZLIB_LIBS} -gt 0 ]; then
+		export ZLIB_ROOT="${PETSC_ROOT}" # Used in installation of NetCDF, GDAL
+	fi
+fi
+
+LAPACK_ROOT="${ISSM_EXT_DIR}/lapack/install"
+ld_library_path_append "${LAPACK_ROOT}/lib"
+
+SCOTCH_ROOT="${ISSM_EXT_DIR}/scotch/install"
+ld_library_path_append "${SCOTCH_ROOT}/lib"
+
+SLEPC_ROOT="${ISSM_EXT_DIR}/slepc/install"
+ld_library_path_append "${SLEPC_ROOT}/lib"
+
+TAO_ROOT="${ISSM_EXT_DIR}/tao/install"
+ld_library_path_append "${TAO_ROOT}/lib"
+
+DAKOTA_ROOT="${ISSM_EXT_DIR}/dakota/install"
+if [ -d "${DAKOTA_ROOT}" ]; then
+	path_append "${DAKOTA_ROOT}/bin"
+	ld_library_path_append "${DAKOTA_ROOT}/lib"
+	dyld_library_path_prepend "${DAKOTA_ROOT}/lib"
+fi
+
+NCO_ROOT="${ISSM_EXT_DIR}/nco/install/bin"
+path_prepend "${NCO_ROOT}/bin"
+
+CPPCHECK_ROOT="${ISSM_EXT_DIR}/cppcheck/install"
+path_append "${CPPCHECK_ROOT}/bin"
+
+MERCURIAL_ROOT="${ISSM_EXT_DIR}/mercurial/install"
+if [ -d "${MERCURIAL_ROOT}" ]; then
+	export PYTHONPATH="${PYTHONPATH}:${MERCURIAL_ROOT}/mercurial/pure/"
+	path_append "${MERCURIAL_ROOT}"
+fi
+
+BOOST_ROOT="${ISSM_EXT_DIR}/boost/install"
+if [ -d "${BOOST_ROOT}" ]; then
+	export BOOST_ROOT # Used in installation of Dakota
+	export BOOST_DIR=${BOOST_ROOT}
+	export BOOSTROOT=${BOOST_ROOT}
+	library_path_prepend "${BOOST_ROOT}/lib"
+	ld_library_path_prepend "${BOOST_ROOT}/lib"
+	dyld_library_path_prepend "${BOOST_ROOT}/lib"
+	path_prepend "${BOOST_ROOT}/bin"
+fi
+
+GSL_ROOT="${ISSM_EXT_DIR}/gsl/install"
+if [ -d "${GSL_ROOT}" ]; then
+	export GSL_HOME="${GSL_ROOT}" # Used in installation of Dakota
+	ld_library_path_append "${GSL_ROOT}/lib"
+fi
+
+NETCDF_ROOT="${ISSM_EXT_DIR}/netcdf/install"
+if [ -d "${NETCDF_ROOT}" ]; then
+	export NETCDF_ROOT # Used in installation of GDAL, GMT
+	path_append "${NETCDF_ROOT}/bin"
+	cpath_append "${NETCDF_ROOT}/include"
+	library_path_append "${NETCDF_ROOT}/lib"
+	dyld_library_path_append "${NETCDF_ROOT}/lib"
+	ld_library_path_append "${NETCDF_ROOT}/lib"
+fi
+
+NETCDF_CXX_ROOT="${ISSM_EXT_DIR}/netcdf-cxx/install"
+if [ -d "${NETCDF_CXX_ROOT}" ]; then
+	ld_library_path_append "${NETCDF_CXX_ROOT}/lib"
+fi
+
+NETCDF_PYTHON_ROOT="${ISSM_EXT_DIR}/netcdf-python/install"
+if [ -d "${NETCDF_PYTHON_ROOT}" ]; then
+	if [ -d "${NETCDF_PYTHON_ROOT}/lib/python2.7/site-packages" ]; then
+		ld_library_path_append "${NETCDF_PYTHON_ROOT}/lib/python2.7/site-packages"
+	fi
+fi
+
+CURL_ROOT="${ISSM_EXT_DIR}/curl/install"
+if [ -d "${CURL_ROOT}" ]; then
+	export CURL_ROOT # Used in installation of NetCDF, GDAL, GMT
+	ld_library_path_append "${CURL_ROOT}/lib"
+	dyld_library_path_append "${CURL_ROOT}/lib"
+	path_append "${CURL_ROOT}/bin"
+fi
+
+HDF5_ROOT="${ISSM_EXT_DIR}/hdf5/install"
+if [ -d "${HDF5_ROOT}" ]; then
+	export HDF5_ROOT # Used in installation of NetCDF, GDAL
+	cpath_append "${HDF5_ROOT}/include"
+	library_path_append "${HDF5_ROOT}/lib"
+	dyld_library_path_append "${HDF5_ROOT}/lib"
+	ld_library_path_append "${HDF5_ROOT}/lib"
+fi
+
+ZLIB_ROOT="${ISSM_EXT_DIR}/zlib/install"
+if [ -d "${ZLIB_ROOT}" ]; then
+	export ZLIB_ROOT # Used in installation of NetCDF, GDAL, GMT
+fi
+
+SQLITE_ROOT="${ISSM_EXT_DIR}/sqlite/install"
+if [ -d "${SQLITE_ROOT}" ]; then
+	path_append "${SQLITE_ROOT}/bin"
+	library_path_append "${SQLITE_ROOT}/lib"
+	ld_library_path_append "${SQLITE_ROOT}/lib"
+fi
+
+PROJ_ROOT="${ISSM_EXT_DIR}/proj/install"
+if [ -d "${PROJ_ROOT}" ]; then
+	export PROJ_ROOT # Used in installation of GDAL
+	dyld_library_path_append "${PROJ_ROOT}/lib"
+	ld_library_path_append "${PROJ_ROOT}/lib"
+fi
+
+GDAL_ROOT="${ISSM_EXT_DIR}/gdal/install"
+if [ -d "${GDAL_ROOT}" ]; then
+	export GDAL_ROOT # Used in installation of GMT
+	path_prepend "${GDAL_ROOT}/bin"
+	ld_library_path_append "${GDAL_ROOT}/lib"
+fi
+
+GSHHG_ROOT="${ISSM_EXT_DIR}/gshhg/install"
+if [ -d "${GSHHG_ROOT}" ]; then
+	export GSHHG_ROOT # Used in installation of GMT
+fi
+
+GMT_ROOT="${ISSM_EXT_DIR}/gmt/install"
+if [ -d "${GMT_ROOT}" ]; then
+	path_prepend "${GMT_ROOT}/bin"
+	ld_library_path_append "${GMT_ROOT}/lib"
+	dyld_library_path_append "${GMT_ROOT}/lib"
+fi
+
+GMSH_ROOT="${ISSM_EXT_DIR}/gmt/install"
+if [ -d "${GMSH_ROOT}" ]; then
+	path_append "${GMSH_ROOT}/bin"
+	ld_library_path_append "${GMSH_ROOT}/lib"
+	dyld_library_path_append "${GMSH_ROOT}/lib"
+fi
+
+TRIANGLE_ROOT="${ISSM_EXT_DIR}/triangle/install"
+if [ -d "${TRIANGLE_ROOT}" ]; then
+	ld_library_path_append "${TRIANGLE_ROOT}/lib"
+	dyld_library_path_append "${TRIANGLE_ROOT}/lib"
+fi
+
+ANGELROOT="${ISSM_EXT_DIR}/angel/angel"
+if [ -d "${ANGELROOT}" ]; then
+	export ANGELROOT
+fi
+
+OPENANALYSISROOT="${ISSM_EXT_DIR}/openanalysis/install"
+if [ -d "${OPENANALYSISROOT}" ]; then
+	export OPENANALYSISROOT
+	ld_library_path_append "${OPENANALYSISROOT}/lib"
+fi
+
+BBFTP_ROOT="${ISSM_EXT_DIR}/bbftp/install"
+path_append "${BBFTP_ROOT}/bin"
+
+ADIC_ROOT="${ISSM_EXT_DIR}/adic/install"
+path_append "${ADIC_ROOT}/bin"
+ld_library_path_append "${ADIC_ROOT}/lib"
+
+COLPACK_ROOT="${ISSM_EXT_DIR}/colpack/install"
+ld_library_path_append "${COLPACK_ROOT}/lib"
+
+APPSCAN_ROOT="${ISSM_EXT_DIR}/appscan/install"
+path_append "${APPSCAN_ROOT}/bin"
+
+RATS_ROOT="${ISSM_EXT_DIR}/rats/install"
+path_append "${RATS_ROOT}/bin"
+
+DYSON_ROOT="${ISSM_EXT_DIR}/dyson/"
+path_append "${DYSON_ROOT}"
+
+SHAPELIB_ROOT="${ISSM_EXT_DIR}/shapelib/install"
+path_append "${SHAPELIB_ROOT}/exec"
+
+CCCL_ROOT="${ISSM_EXT_DIR}/cccl/install"
+path_append "${CCCL_ROOT}/bin"
+
+MODELE_ROOT="${ISSM_EXT_DIR}/modelE/install"
+path_append "${MODELE_ROOT}/src/exec"
+
+NCVIEW_ROOT="${ISSM_EXT_DIR}/ncview/install"
+path_append "${NCVIEW_ROOT}"
+
+TCLX_ROOT="${ISSM_EXT_DIR}/tclx/install/lib/tclx8.4"
+ld_library_path_append "${TCLX_ROOT}"
+
+ASPELL_ROOT="${ISSM_EXT_DIR}/aspell/install"
+path_append "${ASPELL_ROOT}/bin"
+
+ESMF_ROOT="${ISSM_EXT_DIR}/esmf/install"
+if [ -d "${ESMF_ROOT}" ]; then
+	path_prepend "${ESMF_ROOT}/bin"
+	ld_library_path_append "${ESMF_ROOT}/lib/libO/Linux.gfortran.64.mpich.default/"
+fi
+
+CVS_ROOT="${ISSM_EXT_DIR}/cvs/install"
+path_prepend "${CVS_ROOT}/bin"
+
+APR_ROOT="${ISSM_EXT_DIR}/apr/install"
+path_append "${APR_ROOT}/bin"
+ld_library_path_append "${APR_ROOT}/lib"
+
+APR_UTIL_ROOT="${ISSM_EXT_DIR}/apr-util/install"
+path_prepend "${APR_UTIL_ROOT}/bin"
+ld_library_path_append "${APR_UTIL_ROOT}/lib"
+
+YAMS_ROOT="${ISSM_EXT_DIR}/yams/install"
+path_append "${YAMS_ROOT}"
+
+SWIG_ROOT="${ISSM_EXT_DIR}/swig/install"
+path_append "${SWIG_ROOT}"
+
+INISHELL_ROOT="${ISSM_EXT_DIR}/inishell/install"
+path_append "${INISHELL_ROOT}"
+
+EXPAT_ROOT="${ISSM_EXT_DIR}/expat/install"
+ld_library_path_prepend "${EXPAT_ROOT}"
+dyld_library_path_prepend "${EXPAT_ROOT}"
+
+NEOPZ_ROOT="${ISSM_EXT_DIR}/neopz/install"
+if [ -d "${NEOPZ_ROOT}" ]; then
+	export REFPATTERNDIR="${NEOPZ_ROOT}/include/refpatterns"
 fi
 
 XERCESROOT="${ISSM_EXT_DIR}/xerces/install"
-if [ -d "$XERCESROOT" ]; then
+if [ -d "${XERCESROOT}" ]; then
 	export XERCESROOT
 	export XERCESCROOT="${ISSM_EXT_DIR}/xerces/src"
 fi
 
-
 XAIFBOOSTERROOT="${ISSM_EXT_DIR}/xaifbooster"
-XAIF_DIR="${XAIFBOOSTERROOT}/xaifBooster"
-if [ -d "$XAIF_DIR" ]; then
+XAIF_ROOT="${XAIFBOOSTERROOT}/xaifBooster"
+if [ -d "${XAIF_ROOT}" ]; then
 	export XAIFBOOSTERROOT
-	export XAIF_DIR
-	export XAIFBOOSTER_HOME=$XAIF_DIR
+	export XAIF_DIR="${XAIF_ROOT}"
+	export XAIFBOOSTER_HOME="${XAIF_ROOT}"
 	export PLATFORM="x86-Linux"
 fi
 
-ANGELROOT="${ISSM_EXT_DIR}/angel/angel"
-if [ -d "$ANGELROOT" ]; then
-	export ANGELROOT
-fi
-
-OPENANALYSISROOT="${ISSM_EXT_DIR}/openanalysis/install"
-if [ -d "$OPENANALYSISROOT" ]; then
-	export OPENANALYSISROOT
-	ld_library_path_append "$OPENANALYSISROOT/lib"
-fi
-
-JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
-ld_library_path_append "$JVM_DIR"
-
-BBFTP_DIR="${ISSM_EXT_DIR}/bbftp/install"
-path_append "$BBFTP_DIR/bin"
-
-ADIC_DIR="${ISSM_EXT_DIR}/adic/install"
-path_append "$ADIC_DIR/bin"
-ld_library_path_append "$ADIC_DIR/lib"
-
-COLPACK_DIR="${ISSM_EXT_DIR}/colpack/install"
-ld_library_path_append "$COLPACK_DIR/lib"
-
-ECLIPSE_DIR="${ISSM_EXT_DIR}/eclipse/install"
-path_append "$ECLIPSE_DIR"
-
-APPSCAN_DIR="${ISSM_EXT_DIR}/appscan/install"
-path_append "$APPSCAN_DIR/bin"
-
-RATS_DIR="${ISSM_EXT_DIR}/rats/install"
-path_append "$RATS_DIR/bin"
-
-DYSON_DIR="${ISSM_EXT_DIR}/dyson/"
-path_append "$DYSON_DIR"
-
-CMAKE_DIR="${ISSM_EXT_DIR}/cmake/install"
-path_prepend "$CMAKE_DIR/bin"
-
-SHAPELIB_DIR="${ISSM_EXT_DIR}/shapelib/install"
-path_append "$SHAPELIB_DIR/exec"
-
-CCCL_DIR="${ISSM_EXT_DIR}/cccl/install"
-path_append "$CCCL_DIR/bin"
-
-PACKAGEMAKER_DIR="${ISSM_EXT_DIR}/packagemaker/install"
-path_append "$PACKAGEMAKER_DIR"
-
-#android-dev-dir
-export ANDROID_DIR="${ISSM_EXT_DIR}/android"
-
-export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install"
-path_append "$ANDROID_NDK_DIR/arm-linux-android-install/bin"
-
-export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install"
-path_append "$ANDROID_SDK_DIR/"
-
-GSL_DIR="${ISSM_EXT_DIR}/gsl/install"
-ld_library_path_append "$GSL_DIR/lib"
-
-GMAKE_DIR="${ISSM_EXT_DIR}/gmake/install"
-path_prepend "$GMAKE_DIR/bin"
-
-MODELE_DIR="${ISSM_EXT_DIR}/modelE/install"
-path_append "$MODELE_DIR/src/exec"
-
-NCVIEW_DIR="${ISSM_EXT_DIR}/ncview/install"
-path_append "$NCVIEW_DIR"
-
-TCLX_DIR="${ISSM_EXT_DIR}/tclx/install/lib/tclx8.4"
-ld_library_path_append "$TCLX_DIR"
-
-ASPELL_DIR="${ISSM_EXT_DIR}/aspell/install"
-path_append "$ASPELL_DIR/bin"
-
-NETCDF_DIR="${ISSM_EXT_DIR}/netcdf/install"
-if [ -d "${NETCDF_DIR}" ]; then
-	path_append "${NETCDF_DIR}/bin"
-	cpath_append "${NETCDF_DIR}/include"
-	library_path_append "${NETCDF_DIR}/lib"
-	dyld_library_path_append "${NETCDF_DIR}/lib"
-	ld_library_path_append "${NETCDF_DIR}/lib"
-fi
-
-NETCDF_CXX_DIR="${ISSM_EXT_DIR}/netcdf-cxx/install"
-if [ -d "${NETCDF_CXX_DIR}" ]; then
-	ld_library_path_append "${NETCDF_CXX_DIR}/lib"
-fi
-
-NETCDF_PYTHON_DIR="${ISSM_EXT_DIR}/netcdf-python/install"
-if [ -d "${NETCDF_PYTHON_DIR}" ]; then
-	if [ -d "${NETCDF_PYTHON_DIR}/lib/python2.7/site-packages" ]; then
-		ld_library_path_append "${NETCDF_PYTHON_DIR}/lib/python2.7/site-packages"
-	fi
-fi
-
-HDF5_DIR="${ISSM_EXT_DIR}/hdf5/install"
-if [ -d "${HDF5_DIR}" ]; then
-	cpath_append "${HDF5_DIR}/include"
-	library_path_append "${HDF5_DIR}/lib"
-	dyld_library_path_append "${HDF5_DIR}/lib"
-	ld_library_path_append "${HDF5_DIR}/lib"
-fi
-
-SQLITE_DIR="${ISSM_EXT_DIR}/sqlite/install"
-if [ -d "${SQLITE_DIR}" ]; then
-	path_append "${SQLITE_DIR}/bin"
-	library_path_append "${SQLITE_DIR}/lib"
-	ld_library_path_append "${SQLITE_DIR}/lib"
-fi
-
-PROJ_DIR="${ISSM_EXT_DIR}/proj/install"
-if [ -d "${PROJ_DIR}" ]; then
-	dyld_library_path_prepend "${PROJ_DIR}/lib"
-	ld_library_path_prepend "${PROJ_DIR}/lib"
-fi
-
-GDAL_DIR="${ISSM_EXT_DIR}/gdal/install"
-if [ -d "${GDAL_DIR}" ]; then
-	path_prepend "${GDAL_DIR}/bin"
-	ld_library_path_append "${GDAL_DIR}/lib"
-fi
-
-ESMF_DIR="${ISSM_EXT_DIR}/esmf/install"
-if [ -d "${ESMF_DIR}" ]; then
-	path_prepend "${ESMF_DIR}/bin"
-	ld_library_path_append "${ESMF_DIR}/lib/libO/Linux.gfortran.64.mpich.default/"
-fi
-
-GMT_DIR="${ISSM_EXT_DIR}/gmt/install"
-if [ -d "${GMT_DIR}" ]; then
-	export GMT_DIR
-	path_prepend "${GMT_DIR}/bin"
-fi
-
-GMSH_DIR="${ISSM_EXT_DIR}/gmsh/install"
-if [ -d "${GMSH_DIR}" ]; then
-	path_append "${ISSM_EXT_DIR}/gmsh/install"
-fi
-
-CVS_DIR="${ISSM_EXT_DIR}/cvs/install"
-path_prepend "$CVS_DIR/bin"
-
-APR_DIR="${ISSM_EXT_DIR}/apr/install"
-path_append "$APR_DIR/bin"
-ld_library_path_append "$APR_DIR/lib"
-
-APR_UTIL_DIR="${ISSM_EXT_DIR}/apr-util/install"
-path_prepend "$APR_UTIL_DIR/bin"
-ld_library_path_append "$APR_UTIL_DIR/lib"
-
-YAMS_DIR="${ISSM_EXT_DIR}/yams/install"
-path_append "$YAMS_DIR"
-
-SWIG_DIR="${ISSM_EXT_DIR}/swig/install"
-path_append "$SWIG_DIR"
-
-#AUX-CONFIG
+VALGRIND_ROOT="${ISSM_EXT_DIR}/valgrind/install"
+path_prepend "${VALGRIND_ROOT}/bin"
+
+DOXYGEN_ROOT="${ISSM_EXT_DIR}/doxygen/install"
+path_prepend "${DOXYGEN_ROOT}/bin"
+
 path_append "${ISSM_DIR}/aux-config"
-
-#INISHELL
-path_append "${ISSM_EXT_DIR}/inishell/install"
-
-#SHELL2JUNIT
 path_append "${ISSM_EXT_DIR}/shell2junit/install"
-
-#EXPAT
-ld_library_path_prepend "${ISSM_EXT_DIR}/expat/install"
-dyld_library_path_prepend "${ISSM_EXT_DIR}/expat/install"
-
-#CURL
-CURL_DIR="${ISSM_EXT_DIR}/curl/install"
-if [ -d "${CURL_DIR}" ]; then
-	ld_library_path_prepend "${CURL_DIR}/lib"
-	dyld_library_path_prepend "${CURL_DIR}/lib"
-	path_prepend "${CURL_DIR}/bin"
-fi
-
-#NEOPZ
-NEOPZ_DIR="${ISSM_EXT_DIR}/neopz/install"
-if [ -d "$NEOPZ_DIR" ]; then
-	export REFPATTERNDIR="$NEOPZ_DIR/include/refpatterns"
-fi
-
-TRIANGLE_DIR="${ISSM_EXT_DIR}/triangle/install"
-if [ -d "${TRIANGLE_DIR}" ]; then
-	ld_library_path_append "${TRIANGLE_DIR}/lib"
-	dyld_library_path_append "${TRIANGLE_DIR}/lib"
-fi
Index: /issm/trunk-jpl/externalpackages/gmt/install-6-mac-static.sh
===================================================================
--- /issm/trunk-jpl/externalpackages/gmt/install-6-mac-static.sh	(revision 25855)
+++ /issm/trunk-jpl/externalpackages/gmt/install-6-mac-static.sh	(revision 25856)
@@ -7,9 +7,4 @@
 VER="6.0.0"
 
-PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
-
-BLASLAPACK_ROOT="${PETSC_ROOT}"
-HDF5_ROOT="${PETSC_ROOT}"
-
 # Find libgfortran and libgcc so we do not have to hardcode them
 #
@@ -17,4 +12,5 @@
 #
 # TODO:
+# - Move this to etc/environment.sh
 # - Test if -static-libgfortran flag will avoid all of this.
 # - Otherwise, refactor this to work with other gfortran installations.
@@ -30,4 +26,7 @@
 #
 export CC=mpicc
+export CURL_INCLUDE_DIRS="${CURL_ROOT}/include"
+export CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;-framework CoreFoundation;-framework Security;-lldap;-lz"
+export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed.
 
 # Download source
@@ -38,6 +37,6 @@
 
 # Cleanup
-rm -rf install src
-mkdir install src
+rm -rf ${PREFIX} src
+mkdir -p ${PREFIX} src
 
 # Move source to 'src' directory
@@ -56,9 +55,16 @@
 cd build
 
+# NOTE:
+# - The CMake modules used to find and probe the BLAS and LAPACK libraries do
+#	not seem to handle the situation where BLAS_LIBRARY and LAPACK_LIBRARY are
+#	set but we are working with static libraries
+#	(see customized ConfigUser.static.cmake). Using BLAS_LIBRARIES and
+#	LAPACK_LIBRARIES is a workaround.
+#
 cmake \
-	-DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
+	-DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
 	-DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
 	-DHDF5_ROOT="${HDF5_ROOT}" \
-	-DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
+	-DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
 	-DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \
 	..