Index: /issm/trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh (revision 24675) +++ /issm/trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh (revision 24676) @@ -40,2 +40,8 @@ mkdir ${BOOST_ROOT}/install/bin cp bjam ${BOOST_ROOT}/install/bin + +# Remove any dynamic libraries that may have been compiled +# +# TODO: Reconfigure so that dynamic libraries are not compiled at all +# +rm -f $(ls ${BOOST_ROOT}/install/lib/*.dylib) Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 24675) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 24676) @@ -10,10 +10,10 @@ ## Environment # -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/local/gfortran/lib -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install export DAK_BUILD=${DAK_ROOT}/build export DAK_INSTALL=${DAK_ROOT}/install export DAK_SRC=${DAK_ROOT}/src -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/local/gfortran/lib -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 24675) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 24676) @@ -10,10 +10,10 @@ ## Environment # -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/local/gfortran/lib -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install export DAK_BUILD=${DAK_ROOT}/build export DAK_INSTALL=${DAK_ROOT}/install export DAK_SRC=${DAK_ROOT}/src -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/local/gfortran/lib -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup Index: /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh (revision 24675) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh (revision 24676) @@ -36,5 +36,5 @@ --CFLAGS="-fPIC" \ --CXXFLAGS="-fPIC" \ - --FFLAGS="-fPIC" \ + --FFLAGS="-fPIC -static-libgfortran" \ --with-debugging=0 \ --with-valgrind=0 \ Index: /issm/trunk-jpl/jenkins/pine_island-mac =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac (revision 24675) +++ /issm/trunk-jpl/jenkins/pine_island-mac (revision 24676) @@ -14,5 +14,5 @@ --with-numthreads=4 \ --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -69,6 +69,6 @@ # # NOTE: -# - test701.m is skipped because it uses full Stokes equations +# - test701 is skipped because it uses full Stokes equations # -MATLAB_NROPTIONS="'exclude',[701,702,703,435,IdFromString('Dakota')]" -PYTHON_NROPTIONS="--exclude_name 'Dakota'" +MATLAB_NROPTIONS="'exclude',[435,701,702,703,IdFromString('Dakota')]" +PYTHON_NROPTIONS="" Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries (revision 24675) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries (revision 24676) @@ -9,10 +9,9 @@ # - We can disable dependency tracking in the Autotools because the binaries # should always be a one-time build. -# - libgfortran is copied to $ISSM_DIR/lib by packaging script. # + # ISSM CONFIGURATION ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ - --disable-static \ --enable-standalone-executables \ --enable-standalone-modules \ @@ -20,5 +19,5 @@ --disable-dependency-tracking \ --with-matlab-dir=${MATLAB_PATH} \ - --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \ + --with-fortran-lib="/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota (revision 24675) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota (revision 24676) @@ -9,10 +9,9 @@ # - We can disable dependency tracking in the Autotools because the binaries # should always be a one-time build. -# - libgfortran is copied to $ISSM_DIR/lib by packaging script. # + # ISSM CONFIGURATION ISSM_CONFIG='\ --prefix=${ISSM_DIR} \ - --disable-static \ --enable-standalone-executables \ --enable-standalone-modules \ @@ -22,5 +21,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \ + --with-fortran-lib="/usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libgfortran.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/libquadmath.a /usr/local/Cellar/gcc/9.3.0/lib/gcc/9/gcc/x86_64-apple-darwin15/9.3.0/libgcc.a" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ Index: /issm/trunk-jpl/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 24675) +++ /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 24676) @@ -16,5 +16,5 @@ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \ - --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \ + --with-fortran-lib="-L/usr/local/Cellar/gcc/9.3.0/lib/gcc/9 -lgfortran" \ --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ @@ -38,7 +38,7 @@ EXAMPLES_TEST=0 -#-----------------------------------# -# 3: External packages installation # -#-----------------------------------# +#-------------------# +# External Packages # +#-------------------# #List of external pakages to be installed and their installation scripts @@ -56,7 +56,7 @@ " -#-----------------# -# 4: test options # -#-----------------# +#---------# +# Testing # +#---------# # Number of CPUs used in ISSM compilation @@ -75,7 +75,7 @@ # # NOTE: -# - See test418.py for reason why it is excluded for now. -# - Error is large for test420. +# - See test418.py for reason why it is excluded for now +# - test701 is skipped because it uses full Stokes equations # -MATLAB_NROPTIONS="'exclude',[234,235,243,418,420,435,444,445,701,702],'id',[IdFromString('Dakota')]" -PYTHON_NROPTIONS="--exclude 234 235 243 418 420 435 444 445 701 702 --include_name 'Dakota'" +MATLAB_NROPTIONS="'exclude',[243 435 701 702 703,'id',[IdFromString('Dakota')]" +PYTHON_NROPTIONS="--exclude 243 418 435 701 702 703 --include_name 'Dakota'" 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 24675) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh (revision 24676) @@ -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="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,244,250,417,444,445]" # Exclude any tests with transient solutions that require a restart +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,243,244,250,417,444,445,701,702]" # Exclude any tests with transient solutions that require a restart MATLAB_PATH="/usr/local/MATLAB/R2019b" PACKAGE="ISSM" # Name of directory to copy distributable files to @@ -16,5 +16,5 @@ # - 418 fails with "malloc(): invalid next size (unsorted)"" # -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 244 250 417 418 444 445" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 243 244 250 417 418 435 444 445 701 702" TARBALL_NAME="issm-linux-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" 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 24675) +++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh (revision 24676) @@ -4,8 +4,6 @@ ## Constants # -LIBGFORTRAN="/usr/local/gfortran/lib/libgfortran.3.dylib" # Important that this is the library itself -LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.3.dylib" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it -MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,244,250,417,444,445]" # Exclude any tests with transient solutions that require a restart -MATLAB_PATH="/Applications/MATLAB_R2015b.app" +MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,244,250,417,435,444,445,701,702,703]" # Exclude any tests with transient solutions that require a restart, and any tests that are excluded in the standard build +MATLAB_PATH="/Applications/MATLAB_R2018a.app" PACKAGE="ISSM" # Name of directory to copy distributable files to @@ -13,8 +11,7 @@ # # NOTE: -# - All non-excluded tests were running until recent changes to QMU # - 418 fails with "malloc(): invalid next size (unsorted)"" # -PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 244 250 417 418 444 445" +PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 244 250 417 418 435 444 445 701 702 703" TARBALL_NAME="issm-mac-with_dakota" TARBALL="${TARBALL_NAME}.tar.gz" @@ -44,8 +41,4 @@ exit 1 fi - -# Add/modify required libraries -echo "Moving libgfortran to lib/" -cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null # Run tests Index: /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh =================================================================== --- /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh (revision 24675) +++ /issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh (revision 24676) @@ -4,8 +4,6 @@ ## Constants # -LIBGFORTRAN="/usr/local/gfortran/lib/libgfortran.3.dylib" # Important that this is the library itself -LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.3.dylib" # 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_PATH="/Applications/MATLAB_R2015b.app" +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_PATH="/Applications/MATLAB_R2018a.app" PACKAGE="ISSM" # Name of directory to copy distributable files to TARBALL_NAME="issm-mac" @@ -35,7 +33,4 @@ exit 1 fi - -echo "Moving libgfortran to lib/" -cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null # Run tests Index: /issm/trunk-jpl/src/c/Makefile.am =================================================================== --- /issm/trunk-jpl/src/c/Makefile.am (revision 24675) +++ /issm/trunk-jpl/src/c/Makefile.am (revision 24676) @@ -723,7 +723,7 @@ if STANDALONE_EXECUTABLES if MAC -AM_LDFLAGS += -Wl,-rpath,'$$ORIGIN' -else -AM_LDFLAGS += -static -Wl,--disable-new-dtags -Wl,-rpath,'$$ORIGIN' +AM_LDFLAGS += -Wl,-rpath,'@loader_path/../lib' +else +AM_LDFLAGS += -static -Wl,--disable-new-dtags -Wl,-rpath,'$$ORIGIN/../lib' endif endif Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am =================================================================== --- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am (revision 24675) +++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am (revision 24676) @@ -93,13 +93,13 @@ # will be linked to, whether we like it or not, if no static version is # available. -# - On macOC, static linking of binaries is not supported. +# - On macOS, static linking of binaries is not supported. # if STANDALONE_MODULES -#if MAC -#AM_LDFLAGS += -Wl,-rpath,'$$ORIGIN' -#else +if MAC +AM_LDFLAGS += -Wl,-rpath,'@rpath' +else AM_LDFLAGS += -Wl,-static -Wl,--disable-new-dtags -Wl,-rpath,'$$ORIGIN' endif -#endif +endif AM_CXXFLAGS += -D_HAVE_MATLAB_MODULES_ -fPIC Index: /issm/trunk-jpl/src/wrappers/python/Makefile.am =================================================================== --- /issm/trunk-jpl/src/wrappers/python/Makefile.am (revision 24675) +++ /issm/trunk-jpl/src/wrappers/python/Makefile.am (revision 24676) @@ -69,13 +69,13 @@ # will be linked to, whether we like it or not, if no static version is # available. -# - On macOC, static linking of binaries is not supported. +# - On macOS, static linking of binaries is not supported. # if STANDALONE_MODULES -#if MAC -#AM_LDFLAGS += -Wl,-rpath,'$$ORIGIN' -#else +if MAC +AM_LDFLAGS += -Wl,-rpath,'@rpath' +else AM_LDFLAGS += -Wl,-static -Wl,--disable-new-dtags -Wl,-rpath,'$$ORIGIN' endif -#endif +endif AM_LDFLAGS += --no-warnings