Index: /issm/trunk-jpl/jenkins/pine_island-mac =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac (revision 25188) +++ /issm/trunk-jpl/jenkins/pine_island-mac (revision 25189) @@ -28,10 +28,4 @@ ' -# Test suites -MATLAB_TEST=1 -PYTHON_TEST=0 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - #-------------------# # External Packages # @@ -54,4 +48,10 @@ #---------# +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + # Number of CPUs used in ISSM compilation # @@ -71,4 +71,4 @@ # - test701 is skipped because it uses full Stokes equations # -MATLAB_NROPTIONS="'exclude',[435,701,702,703,IdFromString('Dakota')]" +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),435,701,702,703]" PYTHON_NROPTIONS="" Index: /issm/trunk-jpl/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 25188) +++ /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 25189) @@ -33,10 +33,4 @@ ' -# Test suites -MATLAB_TEST=1 -PYTHON_TEST=1 -JAVASCRIPT_TEST=0 -EXAMPLES_TEST=0 - #-------------------# # External Packages # @@ -61,4 +55,10 @@ # Testing # #---------# + +# Test suites +MATLAB_TEST=1 +PYTHON_TEST=1 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 # Number of CPUs used in ISSM compilation Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh =================================================================== --- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 25188) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 25189) @@ -9,5 +9,5 @@ MATLAB_PATH="/usr/local/MATLAB/R2019b" PACKAGE="ISSM-Solid_Earth" # Name of directory to copy distributable files to -PYTHON_NROPTIONS="--benchmark slr" +PYTHON_NROPTIONS="--benchmark 'slr'" TARBALL_NAME="issm-linux-solid_earth" TARBALL="${TARBALL_NAME}.tar.gz" Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh =================================================================== --- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh (revision 25188) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh (revision 25189) @@ -6,8 +6,8 @@ LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself LIBGFORTRAN_DIST="${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 any tests with transient solutions that require a restart +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" PACKAGE="ISSM" # Name of directory to copy distributable files to -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 418 420" # Exclude any tests with transient solutions that require a restart +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 418 420" TARBALL_NAME="issm-linux-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh =================================================================== --- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh (revision 25188) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh (revision 25189) @@ -6,5 +6,5 @@ LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself LIBGFORTRAN_DIST="${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="'exclude',[IdFromString('Dakota'),125,126]" # Exclude Dakota tests and any tests with transient solutions that require a restart +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" PACKAGE="ISSM" # Name of directory to copy distributable files to Index: /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh =================================================================== --- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh (revision 25188) +++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh (revision 25189) @@ -4,8 +4,8 @@ ## Constants # -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,235,418,420,444,445]" # Exclude any tests with transient solutions that require a restart, and any tests that are excluded in the standard build +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,235,418,420,444,445]" MATLAB_PATH="/Applications/MATLAB_R2018a.app" PACKAGE="ISSM" # Name of directory to copy distributable files to -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 417 418 420 444 445" # Exclude any tests with transient solutions that require a restart +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 417 418 420 444 445" TARBALL_NAME="issm-mac-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" Index: /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh =================================================================== --- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh (revision 25188) +++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh (revision 25189) @@ -4,5 +4,5 @@ ## Constants # -MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126,435,701,702,703]" # Exclude Dakota tests, any tests with transient solutions that require a restart, and any tests that are excluded in the standard build +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),435,701,702,703]" MATLAB_PATH="/Applications/MATLAB_R2018a.app" PACKAGE="ISSM" # Name of directory to copy distributable files to Index: /issm/trunk-jpl/scripts/test-issm-linux-binaries-solid_earth.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-linux-binaries-solid_earth.sh (revision 25189) +++ /issm/trunk-jpl/scripts/test-issm-linux-binaries-solid_earth.sh (revision 25189) @@ -0,0 +1,82 @@ +#!/bin/bash + +# This script is intended to test binaries downloaded to a user-end machine. +# +# NOTE: Tarball must already exist in INSTALL_DIR +# + +unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it + +MATLAB_NROPTIONS="'benchmark','slr'" +MATLAB_PATH="/usr/local/MATLAB/R2019b" +INSTALL_DIR=~/Downloads +PACKAGE_NAME="ISSM-Solid_Earth" +PYTHON_NROPTIONS="--benchmark 'slr'" +TARBALL_NAME="issm-linux-solid_earth" +TARBALL="${TARBALL_NAME}.tar.gz" + +cd ${INSTALL_DIR} +rm -rf ${PACKAGE_NAME} +tar -zxvf ${TARBALL} +cd ${PACKAGE_NAME}/test/NightlyRun + +# Check that MATLAB tests run +echo "Running MATLAB tests" +rm matlab.log 2> /dev/null + +# Run MATLAB tests redirecting output to logfile and suppressing output to console +${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ../../bin; addpath ../../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|Error" 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-----------" + exit 1 +fi + +# Check that all MATLAB tests passed +numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numMatlabTestsFailed} -ne 0 ]]; then + echo "One or more MATLAB tests FAILED" + exit 1 +else + echo "All MATLAB tests PASSED" +fi + +# Check that Python tests run +echo "Running Python tests" + +export ISSM_DIR="${INSTALL_DIR}" +export PATH="${PATH}:${ISSM_DIR}/bin" +export PYTHONPATH="${ISSM_DIR}/scripts" +export PYTHONSTARTUP="${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 "runme.py: error" 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-----------" + exit 1 +fi + +# Check that all Python tests passed +numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numPythonTestsFailed} -ne 0 ]]; then + echo "One or more Python tests FAILED" + exit 1 +else + echo "All Python tests PASSED" +fi Index: /issm/trunk-jpl/scripts/test-issm-linux-binaries-with_dakota.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-linux-binaries-with_dakota.sh (revision 25188) +++ /issm/trunk-jpl/scripts/test-issm-linux-binaries-with_dakota.sh (revision 25189) @@ -6,15 +6,11 @@ # -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,235,243,244,250,417,420,444,445,701,702,703]" # Exclude any tests with transient solutions that require a restart +unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it + +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" INSTALL_DIR=~/Downloads PACKAGE_NAME="ISSM" - -# Exclude any tests with transient solutions that require a restart -# -# NOTE: -# - 418 fails with "malloc(): invalid next size (unsorted)"" -# -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 235 243 244 250 417 418 420 444 445 701 702 703" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 418 420" TARBALL_NAME="issm-linux-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" Index: /issm/trunk-jpl/scripts/test-issm-linux-binaries.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-linux-binaries.sh (revision 25188) +++ /issm/trunk-jpl/scripts/test-issm-linux-binaries.sh (revision 25189) @@ -6,5 +6,7 @@ # -MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126]" # Exclude Dakota tests and any tests with transient solutions that require a restart +unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it + +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" INSTALL_DIR=~/Downloads Index: /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh (revision 25188) +++ /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh (revision 25189) @@ -6,15 +6,11 @@ # -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,235,243,244,250,417,418,420,435,444,445,701,702,703]" # Regular test suite, plus any tests with transient solutions that require a restart +unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it + +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,235,418,420,444,445]" MATLAB_PATH="/Applications/MATLAB_R2019b.app" INSTALL_DIR=~/Downloads PACKAGE_NAME="ISSM" - -# Exclude any tests with transient solutions that require a restart -# -# NOTE: -# - 418 fails with "malloc(): invalid next size (unsorted)"" -# -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 235 243 244 250 417 418 420 435 444 445 701 702 703" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 417 418 420 444 445" TARBALL_NAME="issm-mac-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" Index: /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh (revision 25188) +++ /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh (revision 25189) @@ -6,5 +6,7 @@ # -MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),125,126]" # Exclude Dakota tests and any tests with transient solutions that require a restart +unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it + +MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),435,701,702,703]" MATLAB_PATH="/Applications/MATLAB_R2019b.app" INSTALL_DIR=~/Downloads Index: /issm/trunk-jpl/src/m/coordsystems/epsg2proj.m =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/epsg2proj.m (revision 25188) +++ /issm/trunk-jpl/src/m/coordsystems/epsg2proj.m (revision 25189) @@ -19,5 +19,5 @@ version_major=str2num(r); - [s,r]=system(['gdalsrsinfo epsg:' num2str(epsg) ' | grep PROJ.4 | tr -d ''\n'' | sed ''s/PROJ.4 : //''']); + [s,r]=system(['gdalsrsinfo epsg:' num2str(epsg) ' | command grep PROJ.4 | tr -d ''\n'' | sed ''s/PROJ.4 : //''']); if s~=0, Index: /issm/trunk-jpl/src/m/coordsystems/epsg2proj.py =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/epsg2proj.py (revision 25188) +++ /issm/trunk-jpl/src/m/coordsystems/epsg2proj.py (revision 25189) @@ -29,5 +29,5 @@ version_major=int(outs) - subproc_args = shlex.split("gdalsrsinfo epsg:{} | grep PROJ.4 | tr -d '\n' | sed 's/PROJ.4 : //'".format(epsg)) + subproc_args = shlex.split("gdalsrsinfo epsg:{} | command grep PROJ.4 | tr -d '\n' | sed 's/PROJ.4 : //'".format(epsg)) subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) outs, errs = subproc.communicate() Index: /issm/trunk-jpl/src/m/coordsystems/gdalinfo.m =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gdalinfo.m (revision 25188) +++ /issm/trunk-jpl/src/m/coordsystems/gdalinfo.m (revision 25189) @@ -8,5 +8,5 @@ %first, get pixel size: - [s,r]=system(sprintf('gdalinfo %s | grep "Pixel Size"',imagename)); + [s,r]=system(sprintf('gdalinfo %s | command grep "Pixel Size"',imagename)); if s, error('gdalinfo error message: could not run system command gdalinfo to find pixel size'); end d=sscanf(r,'Pixel Size = (%g,%g)'); @@ -14,5 +14,5 @@ %get upper left: - [s,r]=system(sprintf('gdalinfo %s | grep "Upper Left"',imagename)); + [s,r]=system(sprintf('gdalinfo %s | command grep "Upper Left"',imagename)); if s, error('gdalinfo error message: could not run system command gdalinfo to find upper left'); end d=sscanf(r,'Upper Left ( %g,%g) %s'); @@ -21,5 +21,5 @@ %get lower right: - [s,r]=system(sprintf('gdalinfo %s | grep "Lower Right"',imagename)); + [s,r]=system(sprintf('gdalinfo %s | command grep "Lower Right"',imagename)); if s, error('gdalinfo error message: could not run system command gdalinfo to find lower right'); end d=sscanf(r,'Lower Right ( %g,%g) %s'); @@ -28,5 +28,5 @@ %Size: - [s,r]=system(sprintf('gdalinfo %s | grep "Size is"',imagename)); + [s,r]=system(sprintf('gdalinfo %s | command grep "Size is"',imagename)); if s, error('gdalinfo error message: could not run system command gdalinfo to find size'); end d=sscanf(r,'Size is %g, %g'); Index: /issm/trunk-jpl/src/m/coordsystems/gmtmaskparallel.m =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gmtmaskparallel.m (revision 25188) +++ /issm/trunk-jpl/src/m/coordsystems/gmtmaskparallel.m (revision 25189) @@ -52,5 +52,5 @@ %concatenate: - system('cat oce_vertices*.txt | grep -v Command | awk ''{printf("%s\n",$3);}''> vertices.txt'); + system('cat oce_vertices*.txt | command grep -v Command | awk ''{printf("%s\n",$3);}''> vertices.txt'); %read the vertices.txt file and flag our mesh vertices on the continent Index: /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m =================================================================== --- /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m (revision 25188) +++ /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m (revision 25189) @@ -16,5 +16,5 @@ % Get Gmsh version - [s,r]=system(['gmsh -info | grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']); + [s,r]=system(['gmsh -info | command grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']); if s~=0, error(r); Index: /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py (revision 25188) +++ /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py (revision 25189) @@ -26,5 +26,5 @@ # Get Gmsh version - subproc_args = "gmsh -info | grep 'Version' | sed -e 's/Version[[:blank:]]*:[[:blank:]]//' | cut -d '.' -f1" + subproc_args = "gmsh -info | command grep 'Version' | sed -e 's/Version[[:blank:]]*:[[:blank:]]//' | cut -d '.' -f1" subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) outs, errs = subproc.communicate() Index: /issm/trunk-jpl/src/m/miscellaneous/converttopowerof2.m =================================================================== --- /issm/trunk-jpl/src/m/miscellaneous/converttopowerof2.m (revision 25188) +++ /issm/trunk-jpl/src/m/miscellaneous/converttopowerof2.m (revision 25189) @@ -11,6 +11,6 @@ %figure out the size of the tiff - [status,width]=system(['tiffinfo ' tiffname ' 2>/dev/null | grep "Image Width" | awk ''{printf("%s\n",$3);}''']); - [status,length]=system(['tiffinfo ' tiffname ' 2>/dev/null | grep "Image Width" | awk ''{printf("%s\n",$6);}''']); + [status,width]=system(['tiffinfo ' tiffname ' 2>/dev/null | command grep "Image Width" | awk ''{printf("%s\n",$3);}''']); + [status,length]=system(['tiffinfo ' tiffname ' 2>/dev/null | command grep "Image Width" | awk ''{printf("%s\n",$6);}''']); width=str2num(width); length=str2num(length); Index: /issm/trunk-jpl/src/m/plot/googlemaps.m =================================================================== --- /issm/trunk-jpl/src/m/plot/googlemaps.m (revision 25188) +++ /issm/trunk-jpl/src/m/plot/googlemaps.m (revision 25189) @@ -225,9 +225,9 @@ %Put everything in model -[status output]=system('gdalinfo temp2.tiff | grep "Upper Left"'); +[status output]=system('gdalinfo temp2.tiff | command grep "Upper Left"'); ul = sscanf(output,'Upper Left (%f, %f)'); -[status output]=system('gdalinfo temp2.tiff | grep "Lower Right"'); +[status output]=system('gdalinfo temp2.tiff | command grep "Lower Right"'); lr = sscanf(output,'Lower Right (%f, %f)'); -[status output]=system('gdalinfo temp2.tiff | grep "Size is"'); +[status output]=system('gdalinfo temp2.tiff | command grep "Size is"'); si = sscanf(output,'Size is %i, %i'); x_m=linspace(ul(1),lr(1),si(1));