Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh
===================================================================
--- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh	(revision 24698)
+++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh	(revision 24698)
@@ -0,0 +1,162 @@
+#!/bin/bash
+
+
+## Constants
+#
+LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself
+LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it
+MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,243,420,435,444,445,701,702,703]" # Exclude any tests with transient solutions that require a restart
+MATLAB_PATH="/usr/local/MATLAB/R2019b"
+PACKAGE="ISSM" # Name of directory to copy distributable files to
+
+# Exclude any tests with transient solutions that require a restart
+#
+# NOTE:
+# - All non-excluded tests were running until recent changes to QMU
+# - 418 fails with "malloc(): invalid next size (unsorted)""
+#
+PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 243 418 420 435 444 445 701 702 703"
+TARBALL_NAME="issm-linux-with_dakota"
+TARBALL="${TARBALL_NAME}.tar.gz"
+
+# Clean up from previous packaging
+echo "Cleaning up existing assets"
+cd ${ISSM_DIR}
+rm -rf ${PACKAGE}
+mkdir ${PACKAGE}
+
+# Add/modify required binaries
+cd ${ISSM_DIR}/bin
+
+echo "Modifying generic"
+cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
+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
+
+# Add/modify required libraries
+echo "Moving libgfortran to lib/"
+cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+
+# Run tests
+echo "Running tests"
+cd ${ISSM_DIR}/test/NightlyRun
+
+# Check that MATLAB tests run
+echo "Running MATLAB tests"
+
+rm matlab.log 2> /dev/null
+
+# Run MATLAB tests redirecting output to logfile and suppressing output to console
+${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null
+
+# Check that MATLAB did not exit in error
+matlabExitCode=`echo $?`
+matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab.log | wc -l`
+
+if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
+	echo "----------MATLAB exited in error!----------"
+	cat matlab.log
+	echo "-----------End of matlab.log-----------"
+
+	# Clean up execution directory
+	rm -rf ${ISSM_DIR}/execution/*
+
+	exit 1
+fi
+
+# Check that all MATLAB tests passed
+numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"`
+
+if [[ ${numMatlabTestsFailed} -ne 0 ]]; then
+	echo "One or more MATLAB tests FAILED"
+	exit 1;
+else
+	echo "All MATLAB tests PASSED"
+fi
+
+# Check that Python tests run
+echo "Running Python tests"
+
+export PATH="${PATH}:${ISSM_DIR}/bin"
+export PYTHONPATH="${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
+
+rm python.log 2> /dev/null
+./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1
+
+# Check that Python did not exit in error
+pythonExitCode=`echo $?`
+pythonExitedInError=`grep -E "Error|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 Python tests passed
+numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"`
+
+if [[ ${numPythonTestsFailed} -ne 0 ]]; then
+	echo "One or more Python tests FAILED"
+	exit 1;
+else
+	echo "All Python tests PASSED"
+fi
+
+# Create tarball
+cd ${ISSM_DIR}
+rm -f ${TARBALL}
+svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package)
+echo "Copying assets to package: ${PACKAGE}"
+cp -rf bin examples lib scripts test ${PACKAGE}/
+echo "Cleaning up unneeded/unwanted files"
+python -m compileall ${PACKAGE}/bin # Precompile all Python scripts to bytecode
+rm -f ${PACKAGE}/bin/*.py # Remove all Python scripts
+rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes
+rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package
+rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package
+echo "Creating tarball: ${TARBALL_NAME}"
+tar -czf ${TARBALL} ${PACKAGE}
+ls -lah ${ISSM_DIR}/${TARBALL}
+
+echo "Shipping binaries to website"
+
+# We're using public key authentication method to upload the tarball The
+# following lines check to see if the SSH Agent is running. If not, then it is
+# started and relevant information is forwarded to a script.
+pgrep "ssh-agent" > /dev/null
+if [ $? -ne 0 ]; then
+	echo "SSH Agent is not running. Starting it..."
+	ssh-agent > ~/.ssh/agent.sh
+else
+	echo "SSH Agent is running..."
+fi
+
+source ~/.ssh/agent.sh
+ssh-add ~/.ssh/debian_linux-vm_to_ross
+
+scp ${TARBALL} ross.ics.uci.edu:/var/www/html/${TARBALL}
+
+if [ $? -ne 0 ]; then
+	echo "The upload failed."
+	echo "Perhaps the SSH Agent was started by some other means."
+	echo "Try killing the agent and running again."
+fi