Changeset 24676

Timestamp:

03/31/20 12:42:27 (5 years ago)

Author:

jdquinn

Message:

CHG: Support for Mac binaries

Location:

issm/trunk-jpl

Files:

• externalpackages/boost/install-1.72-mac-static.sh (modified) (1 diff)
• externalpackages/dakota/install-6.2-mac-static.sh (modified) (1 diff)
• externalpackages/dakota/install-6.2-mac.sh (modified) (1 diff)
• externalpackages/petsc/install-3.12-mac-static.sh (modified) (1 diff)
• jenkins/pine_island-mac (modified) (2 diffs)
• jenkins/pine_island-mac-binaries (modified) (2 diffs)
• jenkins/pine_island-mac-binaries-with_dakota (modified) (2 diffs)
• jenkins/pine_island-mac-dakota (modified) (4 diffs)
• packagers/linux/package-issm-linux-binaries-with_dakota.sh (modified) (2 diffs)
• packagers/mac/package-issm-mac-binaries-with_dakota.sh (modified) (3 diffs)
• packagers/mac/package-issm-mac-binaries.sh (modified) (2 diffs)
• src/c/Makefile.am (modified) (1 diff)
• src/wrappers/matlab/Makefile.am (modified) (1 diff)
• src/wrappers/python/Makefile.am (modified) (1 diff)

issm/trunk-jpl/externalpackages/boost/install-1.72-mac-static.sh

@@ -40 +40 @@
 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)

issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh

@@ -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

issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh

@@ -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

issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh

@@ -36 +36 @@
         --CFLAGS="-fPIC" \
         --CXXFLAGS="-fPIC" \
-        --FFLAGS="-fPIC" \
+        --FFLAGS="-fPIC -static-libgfortran" \
         --with-debugging=0 \
         --with-valgrind=0 \

issm/trunk-jpl/jenkins/pine_island-mac

@@ -14 +14 @@
         --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 +69 @@
 #
 # 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=""

issm/trunk-jpl/jenkins/pine_island-mac-binaries

@@ -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 +19 @@
         --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" \

issm/trunk-jpl/jenkins/pine_island-mac-binaries-with_dakota

@@ -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 +21 @@
         --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" \

issm/trunk-jpl/jenkins/pine_island-mac-dakota

@@ -16 +16 @@
         --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 +38 @@
 EXAMPLES_TEST=0
 
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
+#-------------------#
+# External Packages #
+#-------------------#
 
 #List of external pakages to be installed and their installation scripts
@@ -56 +56 @@
 "
 
-#-----------------#
-# 4: test options #
-#-----------------#
+#---------#
+# Testing #
+#---------#
 
 # Number of CPUs used in ISSM compilation
@@ -75 +75 @@
 #
 # 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'"

issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh

@@ -6 +6 @@
 LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself
 LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it
-MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,244,250,417,444,445]" # Exclude any tests with transient solutions that require a restart
+MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,243,244,250,417,444,445,701,702]" # Exclude any tests with transient solutions that require a restart
 MATLAB_PATH="/usr/local/MATLAB/R2019b"
 PACKAGE="ISSM" # Name of directory to copy distributable files to
@@ -16 +16 @@
 # - 418 fails with "malloc(): invalid next size (unsorted)""
 #
-PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 244 250 417 418 444 445"
+PYTHON_NROPTIONS="--include_name 'Dakota' --exclude 234 243 244 250 417 418 435 444 445 701 702"
 TARBALL_NAME="issm-linux-with_dakota"
 TARBALL="${TARBALL_NAME}.tar.gz"

issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-with_dakota.sh

@@ -4 +4 @@
 ## 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 +11 @@
 #
 # 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 +41 @@
         exit 1
 fi
-
-# Add/modify required libraries
-echo "Moving libgfortran to lib/"
-cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
 
 # Run tests

issm/trunk-jpl/packagers/mac/package-issm-mac-binaries.sh

@@ -4 +4 @@
 ## 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 +33 @@
         exit 1
 fi
-
-echo "Moving libgfortran to lib/"
-cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
 
 # Run tests

issm/trunk-jpl/src/c/Makefile.am

@@ -723 +723 @@
 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

issm/trunk-jpl/src/wrappers/matlab/Makefile.am

@@ -93 +93 @@
 #       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

issm/trunk-jpl/src/wrappers/python/Makefile.am

@@ -69 +69 @@
 #       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