Index: sm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh
===================================================================
--- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh	(revision 24696)
+++ 	(revision )
@@ -1,162 +1,0 @@
-#!/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