Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python
===================================================================
--- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python	(revision 25809)
+++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python	(revision 25809)
@@ -0,0 +1,87 @@
+#--------------------#
+# ISSM Configuration #
+#--------------------#
+
+# NOTE:
+# - We can disable dependency tracking in the Autotools because the binaries
+#	should always be a one-time build.
+# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is
+#	copied by packaging script.
+#
+ISSM_CONFIG='\
+	--prefix=${ISSM_DIR} \
+	--enable-standalone-executables \
+	--enable-standalone-modules \
+	--enable-standalone-libraries \
+	--disable-dependency-tracking \
+	--with-pic \
+	--with-python-dir=/usr \
+	--with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \
+	--with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \
+	--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
+	--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
+	--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
+	--with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
+	--with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
+	--with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
+	--with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
+	--with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
+	--with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
+	--with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
+'
+#-------------------#
+# External Packages #
+#-------------------#
+
+EXTERNALPACKAGES="
+	autotools	install-debian-linux.sh
+	cmake		install.sh
+	petsc		install-3.12-linux-static.sh
+	gsl			install-static.sh
+	boost		install-1.7-linux-static.sh
+	dakota		install-6.2-linux-static.sh
+	curl		install-7-static.sh
+	netcdf		install-4.7-parallel-static.sh
+	proj		install-6.2-static.sh
+	gdal		install-3-python-netcdf-static.sh
+	gshhg		install.sh
+	gmt			install-6-linux-static.sh
+	gmsh		install-4-linux-static.sh
+	triangle	install-linux-static.sh
+	chaco		install.sh
+	m1qn3		install.sh
+	semic		install.sh
+	shell2junit	install.sh
+"
+
+#---------#
+# Testing #
+#---------#
+
+# Test suites
+MATLAB_TEST=0
+PYTHON_TEST=0
+JAVASCRIPT_TEST=0
+EXAMPLES_TEST=0
+
+# Number of CPUs used in ISSM compilation
+#
+# NOTE: One is usually safer as some packages are very sensitive to parallel
+# 		compilation.
+#
+NUMCPUS_INSTALL=8
+
+# Number of CPUs used in the nightly runs
+NUMCPUS_RUN=1
+
+# Nightly run options
+#
+# See documentation in test/NightlyRun/runme.* for more information.
+#
+MATLAB_NROPTIONS=""
+PYTHON_NROPTIONS=""
Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-matlab.sh
===================================================================
--- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-matlab.sh	(revision 25808)
+++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-matlab.sh	(revision 25809)
@@ -12,4 +12,11 @@
 # - Packages and compresses executables and libraries.
 # - Transmits it to ISSM Web site for distribution.
+#
+# Options:
+# -s/--skiptests		Skip tests (use if this script fails for some reason 
+#						after tests have successfully passed to save time)
+# -t/--transferonly		Transfer package to ISSM Web site only (use if 
+#						transfer fails for some reason to skip testing and
+#						signing)
 ################################################################################
 
Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python.sh
===================================================================
--- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python.sh	(revision 25809)
+++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python.sh	(revision 25809)
@@ -0,0 +1,191 @@
+#!/bin/bash
+
+################################################################################
+# To be used after running,
+#
+#	${ISSM_DIR}/jenkins/jenkins.sh ${ISSM_DIR}/jenkins/ross-debian_linux-binaries-matlab
+#
+# in the context of a Jenkins project.
+#
+# When no runtime errors occur, performs the following:
+# - Checks resulting executables and libraries against test suite.
+# - Packages and compresses executables and libraries.
+# - Transmits it to ISSM Web site for distribution.
+#
+# Options:
+# -s/--skiptests		Skip tests (use if this script fails for some reason 
+#						after tests have successfully passed to save time)
+# -t/--transferonly		Transfer package to ISSM Web site only (use if 
+#						transfer fails for some reason to skip testing and
+#						signing)
+################################################################################
+
+# Expand aliases within the context of this script
+shopt -s expand_aliases
+
+## Override certain aliases
+#
+alias grep=$(which grep)
+
+## Constants
+#
+LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself
+LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it
+PYTHON_NROPTIONS="--benchmark all --exclude 125 126 234 235 418 420 435 444 445 701 702 703 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1201 1202 1203 1204 1205 1206 1207 1208 1301 1302 1303 1304 1401 1402 1601 1602 2002 2003 2005 2006 2010 2020 2021 2051 2052 2053 2101 2102 3001:3200 3201 3202 3300 3480 3481 4001 4002 4003" # NOTE: Combination of test suites from basic, Dakota, and Solid Earth builds, with tests that require a restart and those that require the JVM excluded
+PKG="ISSM-Linux-Python" # Name of directory to copy distributable files to
+
+COMPRESSED_PKG="${PKG}.tar.gz"
+
+## Environment
+#
+export PATH="${ISSM_DIR}/bin:$(getconf PATH)" # Ensure that we pick up binaries from 'bin' directory rather than 'externalpackages'
+
+## Parse options
+#
+if [ $# -gt 1 ]; then
+	echo "Can use only one option at a time"
+	exit 1
+fi
+
+skip_tests=0
+transfer_only=0
+while [ $# -gt 0 ]; do
+    case $1 in
+        -s|--skiptests) skip_tests=1; shift ;;
+        -t|--transferonly) transfer_only=1; shift ;;
+        *) echo "Unknown parameter passed: $1"; exit 1 ;;
+    esac
+    shift
+done
+
+if [ ${transfer_only} -eq 0 ]; then
+	# Check if MATLAB exists
+	if ! [ -d ${MATLAB_PATH} ]; then
+		echo "${MATLAB_PATH} does not point to a MATLAB installation! Please modify MATLAB_PATH variable in $(basename $0) and try again."
+		exit 1
+	fi
+
+	# Clean up from previous packaging
+	echo "Cleaning up existing assets"
+	cd ${ISSM_DIR}
+	rm -rf ${PKG} ${COMPRESSED_PKG}
+	mkdir ${PKG}
+
+	# Add/modify required binaries and libraries
+	cd ${ISSM_DIR}/bin
+
+	echo "Modify generic"
+	cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py
+
+	echo "Moving MPICH binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
+		cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec .
+		cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy .
+	elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then
+		cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec .
+		cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy .
+	else
+		echo "MPICH not found"
+		exit 1
+	fi
+
+	echo "Moving GDAL binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/gdal/install/bin/gdal-config ]; then
+		cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdalsrsinfo .
+		cp ${ISSM_DIR}/externalpackages/gdal/install/bin/gdaltransform .
+	else
+		echo "GDAL not found"
+		exit 1
+	fi
+
+	echo "Moving GMT binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt-config ]; then
+		cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmt .
+		cp ${ISSM_DIR}/externalpackages/gmt/install/bin/gmtselect .
+	else
+		echo "GMT not found"
+		exit 1
+	fi
+
+	echo "Moving Gmsh binaries to bin/"
+	if [ -f ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh ]; then
+		cp ${ISSM_DIR}/externalpackages/gmsh/install/bin/gmsh .
+	else
+		echo "Gmsh not found"
+		exit 1
+	fi
+
+	echo "Moving libgfortran to lib/"
+	cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+
+
+	# Run tests
+	if [ ${skip_tests} -eq 0 ]; then
+		echo "Running tests"
+		cd ${ISSM_DIR}/test/NightlyRun
+		rm python.log 2> /dev/null
+
+		# Set Python environment
+		export PYTHONPATH="${ISSM_DIR}/src/m/dev"
+		export PYTHONSTARTUP="${PYTHONPATH}/devpath.py"
+		export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured
+
+		# Run tests, redirecting output to logfile and suppressing output to console
+		./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1
+
+		# Check that Python did not exit in error
+		pythonExitCode=`echo $?`
+		pythonExitedInError=`grep -E "Error|Standard exception|Traceback|bad interpreter" python.log | wc -l`
+
+		if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then
+			echo "----------Python exited in error!----------"
+			cat python.log
+			echo "-----------End of python.log-----------"
+
+			# Clean up execution directory
+			rm -rf ${ISSM_DIR}/execution/*
+
+			exit 1
+		fi
+
+		# Check that all tests passed
+		numTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+
+		if [[ ${numTestsFailed} -ne 0 ]]; then
+			echo "One or more tests FAILED"
+			exit 1
+		else
+			echo "All tests PASSED"
+		fi
+	else
+		echo "Skipping tests"
+	fi
+
+	# Create package
+	cd ${ISSM_DIR}
+	svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
+	echo "Copying assets to package: ${PKG}"
+	cp -rf bin examples lib scripts test ${PKG}/
+	mkdir ${PKG}/execution
+	${ISSM_DIR}/scripts/py_to_pyc.sh ${PKG}/bin # Compile Python source files
+	echo "Cleaning up unneeded/unwanted files"
+	rm -f ${PKG}/bin/*.py # Remove all Python scripts
+	rm -f ${PKG}/bin/generic_static.* # Remove static versions of generic cluster classes
+	rm -f ${PKG}/lib/*.a # Remove static libraries from package
+	rm -f ${PKG}/lib/*.la # Remove libtool libraries from package
+	rm -rf ${PKG}/test/SandBox # Remove testing sandbox from package
+
+	# Compress package
+	echo "Compressing package"
+	tar -czf ${COMPRESSED_PKG} ${PKG}
+	ls -lah ${ISSM_DIR}/${COMPRESSED_PKG}
+fi
+
+# Transfer package to ISSM Web site
+echo "Transferring package to ISSM Web site"
+scp -i ~/.ssh/debian_linux-vm_to_ross ${COMPRESSED_PKG} jenkins@ross.ics.uci.edu:/var/www/html/${COMPRESSED_PKG}
+
+if [ $? -ne 0 ]; then
+	echo "Transfer failed! Verify connection then build this project again."
+	exit 1
+fi