Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-solid_earth (revision 25195) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-solid_earth (revision 25196) @@ -40,20 +40,21 @@ EXTERNALPACKAGES=" - autotools install-debian-linux.sh - cmake install.sh - petsc install-3.12-linux-solid_earth-static.sh - boost install-1.7-linux-static.sh - triangle install-linux-static.sh - chaco install.sh - m1qn3 install.sh - semic install.sh - curl install-7.67-static.sh - netcdf install-4.7-parallel-static.sh - proj install-6.2-static.sh - gdal install-3.0-python-netcdf-static.sh - gshhg install.sh - gmt install-6.0-linux-static.sh - gmsh install-4-static.sh - shell2junit install.sh + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux-solid_earth-static.sh + boost install-1.7-linux-static.sh + triangle install-linux-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + curl install-7.67-static.sh + netcdf install-4.7-parallel-static.sh + netcdf-python install.sh + proj install-6.2-static.sh + gdal install-3.0-python-netcdf-static.sh + gshhg install.sh + gmt install-6.0-linux-static.sh + gmsh install-4-static.sh + shell2junit install.sh " 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 25195) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 25196) @@ -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" @@ -41,4 +41,22 @@ 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 @@ -141,4 +159,5 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -f ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} 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 25195) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh (revision 25196) @@ -133,4 +133,5 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -f ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh =================================================================== --- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh (revision 25195) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh (revision 25196) @@ -92,4 +92,5 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -f ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} 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 25195) +++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh (revision 25196) @@ -127,4 +127,5 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -f ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} Index: /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh =================================================================== --- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh (revision 25195) +++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh (revision 25196) @@ -87,4 +87,5 @@ rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package (we only need MEX-files) rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +rm -f ${PACKAGE}/test/SandBox # Remove testing sandbox from package echo "Creating tarball: ${TARBALL_NAME}" tar -czf ${TARBALL} ${PACKAGE} Index: /issm/trunk-jpl/scripts/devpath.py =================================================================== --- /issm/trunk-jpl/scripts/devpath.py (revision 25195) +++ /issm/trunk-jpl/scripts/devpath.py (revision 25196) @@ -7,5 +7,5 @@ # # export ISSM_DIR= -# export PATH="${PATH}:${ISSM_DIR}/bin" +# export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" # export PYTHONPATH="${ISSM_DIR}/scripts" # export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" Index: /issm/trunk-jpl/scripts/test-issm-linux-binaries-solid_earth.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-linux-binaries-solid_earth.sh (revision 25195) +++ /issm/trunk-jpl/scripts/test-issm-linux-binaries-solid_earth.sh (revision 25196) @@ -6,52 +6,51 @@ # -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'" +PYTHON_NROPTIONS="--benchmark slr" TARBALL_NAME="issm-linux-solid_earth" TARBALL="${TARBALL_NAME}.tar.gz" +export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" + cd ${INSTALL_DIR} -rm -rf ${PACKAGE_NAME} -tar -zxvf ${TARBALL} +# rm -rf ${PACKAGE_NAME} +# tar -zxvf ${TARBALL} cd ${PACKAGE_NAME}/test/NightlyRun -# Check that MATLAB tests run -echo "Running MATLAB tests" -rm matlab.log 2> /dev/null +# # Check that MATLAB tests run +# echo "Running MATLAB tests" +# rm matlab.log 2> /dev/null -# Run MATLAB tests redirecting output to logfile and suppressing output to console -${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 +# # 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` +# # 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 +# 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"` +# # 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 +# 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" Index: /issm/trunk-jpl/scripts/test-issm-linux-binaries-with_dakota.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-linux-binaries-with_dakota.sh (revision 25195) +++ /issm/trunk-jpl/scripts/test-issm-linux-binaries-with_dakota.sh (revision 25196) @@ -5,6 +5,4 @@ # 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="'id',[IdFromString('Dakota')]" @@ -15,4 +13,7 @@ TARBALL_NAME="issm-linux-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" + +export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" cd ${INSTALL_DIR} Index: /issm/trunk-jpl/scripts/test-issm-linux-binaries.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-linux-binaries.sh (revision 25195) +++ /issm/trunk-jpl/scripts/test-issm-linux-binaries.sh (revision 25196) @@ -6,6 +6,4 @@ # -unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it - MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" MATLAB_PATH="/usr/local/MATLAB/R2019b" @@ -14,4 +12,7 @@ TARBALL_NAME="issm-linux" TARBALL="${TARBALL_NAME}.tar.gz" + +export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" cd ${INSTALL_DIR} Index: /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh (revision 25195) +++ /issm/trunk-jpl/scripts/test-issm-mac-binaries-with_dakota.sh (revision 25196) @@ -5,6 +5,4 @@ # NOTE: Tarball must already exist in INSTALL_DIR # - -unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,235,418,420,444,445]" @@ -15,4 +13,8 @@ TARBALL_NAME="issm-mac-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" + +export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" + cd ${INSTALL_DIR} @@ -53,5 +55,4 @@ export ISSM_DIR="${INSTALL_DIR}" -export PATH="${PATH}:${ISSM_DIR}/bin" export PYTHONPATH="${ISSM_DIR}/scripts" export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" Index: /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh =================================================================== --- /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh (revision 25195) +++ /issm/trunk-jpl/scripts/test-issm-mac-binaries.sh (revision 25196) @@ -6,5 +6,6 @@ # -unset ISSM_DIR # Ensure that ISSM_DIR is not set in case we are running on a machine and user profile that sets it +export ISSM_DIR="${INSTALL_DIR}/${PACKAGE_NAME}" +export PATH="${PATH}:${ISSM_DIR}/bin:${ISSM_DIR}/scripts" MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota'),435,701,702,703]" Index: /issm/trunk-jpl/src/m/Makefile.am =================================================================== --- /issm/trunk-jpl/src/m/Makefile.am (revision 25195) +++ /issm/trunk-jpl/src/m/Makefile.am (revision 25196) @@ -48,4 +48,5 @@ ${ISSM_DIR}/src/m/qmu/setupdesign/*.m \ ${ISSM_DIR}/src/m/regional/*.m \ + ${ISSM_DIR}/src/m/shp/*.m \ ${ISSM_DIR}/src/m/solve/*.m \ ${ISSM_DIR}/src/m/solvers/*.m \ Index: /issm/trunk-jpl/src/m/coordsystems/gmtmask.m =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gmtmask.m (revision 25195) +++ /issm/trunk-jpl/src/m/coordsystems/gmtmask.m (revision 25196) @@ -36,4 +36,6 @@ %Avoid bypassing of the ld library path by Matlab (:() + % + % TODO: Do we really need this (we can/already set it in etc/environment.sh)? if ismac, dyld_library_path_old=getenv('DYLD_LIBRARY_PATH'); @@ -42,7 +44,7 @@ %Find path to gmt, list all possible known paths to gmt (you may need to add yours to the list) - paths = {[issmdir() '/bin/gmt'],[issmdir() '/externalpackages/gmt/install/bin/gmt'],'/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt'}; + gmtpaths = {[issmdir '/bin/gmt'],[issmdir '/externalpackages/gmt/install/bin/gmt'],'/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt'}; gmtpath = ''; - for i=paths + for i=gmtpaths if exist(i{1},'file'), gmtpath = i{1}; @@ -51,5 +53,5 @@ end if isempty(gmtpath), - error('gmt not found, make sure it is properly installed, or add its path to this file (line 44)'); + error('gmt not found! Make sure it is properly installed, or add its path to this file.'); end Index: /issm/trunk-jpl/src/m/coordsystems/gmtmask.py =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gmtmask.py (revision 25195) +++ /issm/trunk-jpl/src/m/coordsystems/gmtmask.py (revision 25196) @@ -1,7 +1,8 @@ -from os import getenv, putenv +import os import subprocess import numpy as np +from issmdir import * from MatlabFuncs import * from model import * @@ -44,8 +45,6 @@ #Avoid bypassing of the ld library path by Matlab (:() - try: - issmdir - except NameError: - issmdir = getenv('ISSM_DIR') + issm_dir = issmdir() + try: ismac @@ -53,14 +52,33 @@ ismac = False + # TODO: Do we really need this (we can/already set it in etc/environment.sh)? if ismac: - dyld_library_path_old = getenv('DYLD_LIBRARY_PATH') - putenv('DYLD_LIBRARY_PATH', issmdir + '/externalpackages/curl/install/lib:' + issmdir + '/externalpackages/hdf5/install/lib:' + issmdir + '/externalpackages/netcdf/install/lib') + dyld_library_path_old = os.getenv('DYLD_LIBRARY_PATH') + os.putenv('DYLD_LIBRARY_PATH', issm_dir + '/externalpackages/curl/install/lib:' + issm_dir + '/externalpackages/hdf5/install/lib:' + issm_dir + '/externalpackages/netcdf/install/lib') + + #Find path to gmt (you may need to add yours to the list). + # + # NOTE: Assumes gmtselect is also in this directory. + # + gmtpaths = [ + issm_dir + '/bin/gmt', + issm_dir + '/externalpackages/gmt/install/bin/gmt', + '/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt' + ] + gmtpath = '' + for i in range(len(gmtpaths)): + if os.path.isfile(gmtpaths[i]): + gmtpath = gmtpaths[i] + break + + if gmtpath == '': + raise Exception('gmt not found! Make sure it is properly installed, or add its path to this file.') #figure out which vertices are on the ocean, which one on the continent: - subprocess.call(issmdir + '/externalpackages/gmt/install/bin/gmt gmtselect ./ all_vertices.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt', shell=True) + subprocess.call(gmtpath + ' gmtselect ./ all_vertices.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt', shell=True) #reset DYLD_LIBRARY_PATH to what it was: if ismac: - putenv('DYLD_LIBRARY_PATH', dyld_library_path_old) + os.putenv('DYLD_LIBRARY_PATH', dyld_library_path_old) #read the con_vertices.txt file and flag our mesh vertices on the continent