Changeset 28161

Timestamp:

03/21/24 11:14:20 (12 months ago)

Author:

jdquinn

Message:

CHG: Support for macOS distributable configurations for both Intel and Silicon

Location:

issm/trunk-jpl

Files:

• etc/environment.sh (modified) (1 diff)
• externalpackages/boost/install-1.55-pleiades.sh (modified) (1 diff)
• externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.cmake (modified) (1 diff)
• externalpackages/dakota/configs/6.2/mac/cmake/BuildDakotaCustom.cmake (modified) (1 diff)
• externalpackages/dakota/configs/6.2/mac/static/BuildDakotaCustom.cmake (added)
• externalpackages/dakota/install-6.2-mac-static.sh (modified) (2 diffs)
• externalpackages/gmt/configs/6.0 (moved) (moved from issm/trunk-jpl/externalpackages/gmt/configs/6 )
• externalpackages/gmt/configs/6.0/static/mac/cmake/ConfigUser.static.cmake (modified) (14 diffs)
• externalpackages/gmt/configs/6.0/static/mac/patches (deleted)
• externalpackages/gmt/configs/6.5 (added)
• externalpackages/gmt/configs/6.5/static (added)
• externalpackages/gmt/configs/6.5/static/cmake (added)
• externalpackages/gmt/configs/6.5/static/cmake/modules (added)
• externalpackages/gmt/configs/6.5/static/cmake/modules/FindGDAL.cmake.patch (added)
• externalpackages/gmt/configs/6.5/static/cmake/modules/FindGSHHG.cmake.patch (added)
• externalpackages/gmt/configs/6.5/static/cmake/modules/FindNETCDF.cmake.patch (added)
• externalpackages/gmt/configs/6.5/static/mac (added)
• externalpackages/gmt/configs/6.5/static/mac/cmake (added)
• externalpackages/gmt/configs/6.5/static/mac/cmake/ConfigUserAdvancedTemplate.cmake.patch (added)
• externalpackages/gmt/install-6-mac-silicon-static.sh (deleted)
• externalpackages/gmt/install-6-mac-static.sh (moved) (moved from issm/trunk-jpl/externalpackages/gmt/install-6-mac-intel-static.sh ) (4 diffs)
• externalpackages/petsc/install-3.20-mac-static.sh (copied) (copied from issm/trunk-jpl/externalpackages/petsc/install-3.20-mac.sh ) (3 diffs)
• externalpackages/petsc/install-3.20-mac.sh (modified) (1 diff)
• jenkins/mac-intel-binaries-matlab (modified) (3 diffs)
• jenkins/mac-intel-binaries-python-3 (modified) (3 diffs)
• jenkins/mac-silicon-binaries-matlab (modified) (2 diffs)
• jenkins/mac-silicon-binaries-python-3 (modified) (2 diffs)
• m4/issm_options.m4 (modified) (2 diffs)
• packagers/linux/package-issm-linux-binaries-matlab.sh (modified) (3 diffs)
• packagers/linux/package-issm-linux-binaries-python-3.sh (modified) (3 diffs)
• packagers/mac/package-issm-mac-binaries-matlab.sh (modified) (2 diffs)
• packagers/mac/package-issm-mac-binaries-python-3.sh (modified) (2 diffs)

issm/trunk-jpl/etc/environment.sh ¶

@@ -203 +203 @@
 
         if [[ ${BUILD_TOOL_VER} -ge 15 ]]; then
-                export LDFLAGS="${LDFLAGS} -Wl,-ld_classic"
+                 # Add flag for classic linker only if it has not already been added
+                if [[ -z $(echo $LDFLAGS | /usr/bin/grep "\-Wl,\-ld_classic") ]]; then
+                        export LDFLAGS="${LDFLAGS} -Wl,-ld_classic"
+                fi
         else
                 export LDFLAGS="${LDFLAGS}" # At least set LDFLAGS to null string if it is not already set (used in installation of ISSM and some external packages). Can remove this when issues with new Xcode linker have settled.

issm/trunk-jpl/externalpackages/boost/install-1.55-pleiades.sh ¶

@@ -2 +2 @@
 set -eu
 
-#Note of caution:  stop after boostrap phase, and run 
-#bjam --debug-configuration, to figure out which paths boost is using to include 
-#python. make sure everyone of these paths is covered by python. If not, just make 
-#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY 
-#to get the boost library to include python support without doing that. 
+# NOTE: Stop after bootstrap phase, and run,
+#
+#       bjam --debug-configuration
+#
+# to figure out which paths Boost is using to include Python. Make sure 
+# every one of these paths is covered by Python. If not, make symlinks in 
+# externalpackages/python to what Boost is expecting (assumes that you are 
+# using copy of Python installed as an external package of ISSM). There is 
+# NO WAY to get the Boost library to include Python support under this 
+# configuration without doing this
+#
 
 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"

issm/trunk-jpl/externalpackages/dakota/configs/6.2/linux/cmake/BuildDakotaCustom.cmake ¶

@@ -64 +64 @@
 set( DAKOTA_HAVE_MPI ON
      CACHE BOOL "Build with MPI enabled" FORCE)
-set( MPI_INCLUDE_PATH "$ENV{MPI_INSTALL}/include"
+set( MPI_INCLUDE_PATH "$ENV{MPI_HOME}/include"
      CACHE FILEPATH "Use MPI headers" FORCE)
-set( MPI_LIBRARY "-L$ENV{MPI_INSTALL}/lib -lmpich"
+set( MPI_LIBRARY "-L$ENV{MPI_HOME}/lib -lmpich"
      CACHE FILEPATH "Use MPI library" FORCE)
-set( MPI_EXTRA_LIBRARY "-L$ENV{MPI_INSTALL}/lib -lmpich"
+set( MPI_EXTRA_LIBRARY "-L$ENV{MPI_HOME}/lib -lmpich"
           CACHE FILEPATH "Use MPI extra libraries" FORCE)
 

issm/trunk-jpl/externalpackages/dakota/configs/6.2/mac/cmake/BuildDakotaCustom.cmake ¶

@@ -64 +64 @@
 set( DAKOTA_HAVE_MPI ON
      CACHE BOOL "Build with MPI enabled" FORCE)
-set( MPI_INCLUDE_PATH "$ENV{MPI_INSTALL}/include"
+set( MPI_INCLUDE_PATH "$ENV{MPI_HOME}/include"
      CACHE FILEPATH "Use MPI headers" FORCE)
-set( MPI_LIBRARY "-L$ENV{MPI_INSTALL}/lib -lmpich"
+set( MPI_LIBRARY "-L$ENV{MPI_HOME}/lib -lmpich"
      CACHE FILEPATH "Use MPI library" FORCE)
 

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

@@ -54 +54 @@
 
 # Copy customized source and configuration files specific to Mac to 'src' directory
-cp configs/${VER}/mac/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
+cp configs/${VER}/mac/static/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
 cp configs/${VER}/mac/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
 cp configs/${VER}/mac/cmake/InstallDarwinDylibs.cmake ${DAK_SRC}/cmake
@@ -85 +85 @@
         -DBUILD_STATIC_LIBS=ON \
         -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \
-        -DCMAKE_C_FLAGS="-fPIC -Wno-error=implicit-function-declaration -w" \
+        -DCMAKE_C_FLAGS="-fPIC -w -Wno-error=implicit-int -Wno-error=implicit-function-declaration" \
         -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
         -DCMAKE_CXX_FLAGS="-fPIC -fdelayed-template-parsing -w" \

issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/mac/cmake/ConfigUser.static.cmake ¶

@@ -1 +1 @@
 #
-#
-# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html)
+# Copyright (c) 1991-2022 by the GMT Team (https://www.generic-mapping-tools.org/team.html)
 # See LICENSE.TXT file for copying and redistribution conditions.
 #
@@ -16 +15 @@
 # ----------------------------------------------------------------------------
 
-# Use this file to override variables in 'ConfigDefault.cmake' on a per-user
-# basis.  First copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake', then
-# edit 'ConfigUser.cmake'.  'ConfigUser.cmake' is not version controlled
+# INSTRUCTIONS TO USERS:
+#
+# 1. Copy 'ConfigUserTemplate.cmake' to 'ConfigUser.cmake' and make any edits
+#    related to install directory, the whereabouts of GSHHS, DCW.
+# 2. If you are an advanced user who wishes to tinker with the more advanced
+#    settings, then copy 'ConfigUserAdvancedTemplate.cmake' to 'ConfigUserAdvanced.cmake',
+#    explore and make changes to your ConfigUserAdvanced.cmake file
+#    to override variables in 'ConfigDefault.cmake' on a per-user basis.
+# 3. Follow the rest of the installation instructions in BUILDING.md.
+#
+# 'ConfigUser.cmake' and 'ConfigUserAdvanced.cmake' are not version controlled
 # (currently listed in .gitignore).
 #
@@ -27 +34 @@
 # OFF, or YES and NO for your booleans.
 
+# set (CMAKE_OSX_DEPLOYMENT_TARGET "12.3")
+
 ##
 ## Section 1: Installation paths
 ##
-
-# ============================================================================
-# Basic setup begins here.  All settings are optional.  In most cases, setting
-# CMAKE_INSTALL_PREFIX should be all you need to do in order to build GMT with
-# reasonable defaults enabled.  Note: If you need to specify directory names
-# with spaces (e.g., on Windows) then you must put them in quotes.
-# ============================================================================
-
-# Installation path (usually defaults to /usr/local) [auto]:
+# Set install name suffix used for directories and gmt executables [undefined]:
 set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}")
-
-# Set install name suffix used for directories and gmt executables
-# [undefined]:
-#set (GMT_INSTALL_NAME_SUFFIX "suffix")
 
 # Install into traditional directory structure. Disable to install a
@@ -49 +46 @@
 #set (GMT_INSTALL_TRADITIONAL_FOLDERNAMES OFF)
 
-# Install convenience links for GMT modules. Disable to install only the main
-# gmt program and access modules as "gmt modulename options" [TRUE]:
-#set (GMT_INSTALL_MODULE_LINKS FALSE)
-
 # Make executables relocatable on supported platforms (relative RPATH) [FALSE]:
 set (GMT_INSTALL_RELOCATABLE TRUE)
 
-# Exclude optional GDAL, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE]
-#set (GMT_EXCLUDE_GDAL TRUE)
+# Exclude optional GEOS, PCRE, PCRE2, FFTW3, LAPACK, BLAS, ZLIB dependencies even if you have them installed [FALSE]
+#set (GMT_EXCLUDE_GEOS TRUE)
 set (GMT_EXCLUDE_PCRE TRUE)
 set (GMT_EXCLUDE_PCRE2 TRUE)
@@ -84 +77 @@
 #set (GMT_DATADIR "share/gmt")
 
-# Set doc installation path [share/doc or
-# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]:
+# Set doc installation path [share/doc or share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]:
 #set (GMT_DOCDIR "share/doc/gmt")
 
-# Set manpage installation path [share/man or
-# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]:
+# Set manpage installation path [share/man or share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]:
 #set (GMT_MANDIR "share/doc/gmt/man")
 
@@ -108 +99 @@
 #set (GMT_DATA_SERVER "data_server_url")
 
-# Set path to GSHHG Shoreline Database [auto]:
-set (GSHHG_ROOT "$ENV{GSHHG_ROOT}")
-
-# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]:
-set (COPY_GSHHG TRUE)
-
-# Set path to DCW Digital Chart of the World for GMT [auto]:
-#set (DCW_ROOT "dcw-gmt_path")
-
-# Copy DCW files to ${GMT_DATADIR}/dcw [FALSE]:
-#set (COPY_DCW TRUE)
-
-# Copy GDAL's 'data' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]:
-#set (GDAL_DATA_PATH C:/programs/compa_libs/gdal_GIT/compileds/VC14_64/data)
-
-# Copy PROJ4's 'share' directory to ${GMT_DATADIR}/GDAL_DATA [FALSE]:
-#set (PROJ_DATA_PATH C:/programs/compa_libs/proj5_GIT/compileds/VC14_64/share/proj)
-
-# FOR WINDOWS ONLY
-# Set path to location of Ghostscript binaries (optional install)
-#set (GHOST_DATA_PATH C:/programs/compa_libs/ghostscript/bin)
-
-# FOR WINDOWS ONLY
-# Set path to location where the gmtmex is located.
-#set (GMTMEX_PATH "C:/progs_cygw/GMTdev/gmtmex/${GMTver}")
-
 # Set location of NetCDF (can be root directory, path to header file or path
 # to nc-config) [auto]:
-set (NETCDF_ROOT "$ENV{NETCDF_ROOT}")
+#set (NETCDF_ROOT "netcdf_install_prefix")
 
 # Set location of GDAL (can be root directory, path to header file or path to
 # gdal-config) [auto]:
-set (GDAL_ROOT "$ENV{GDAL_ROOT}")
+#set (GDAL_ROOT "gdal_install_prefix")
+
+# Set location of GEOS (can be root directory, path to header file or path to
+# geos-config) [auto]:
+#set (GEOS_ROOT "geos_install_prefix")
 
 # Set location of PCRE (can be root directory, path to header file or path to
@@ -167 +136 @@
 
 # Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically
-#set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack")
-#set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas")
+#set (LAPACK_LIBRARY "V:/lapack-3.5.0/build/lib/liblapack.lib")
+#set (BLAS_LIBRARY "V:/lapack-3.5.0/build/lib/libblas.lib")
 
 ##
@@ -180 +149 @@
 
 # Allow building of OpenMP if compiler supports it
-# set (GMT_ENABLE_OPENMP TRUE)
+#set (GMT_ENABLE_OPENMP TRUE)
 
 # Configure default units (possible values are SI and US) [SI]:
@@ -187 +156 @@
 # Enable building of shared libraries [TRUE] (disable to use static libraries;
 # not recommended; on non-x86 architectures uncomment the next option as well):
-set (BUILD_SHARED_LIBS FALSE)
+# NOTE: currently only support shared libraries
+#set (BUILD_SHARED_LIBS FALSE)
 
 # Create position independent code on all targets [auto] (needed for static
@@ -194 +164 @@
 
 # Build GMT shared lib with supplemental modules [TRUE]:
-set (BUILD_SUPPLEMENTS FALSE)
+#set (BUILD_SUPPLEMENTS FALSE)
 
 # Build/Install GMT Developer include files [TRUE]:
@@ -216 +186 @@
 #set (DO_EXAMPLES TRUE)
 #set (DO_TESTS TRUE)
-#set (DO_ANIMATIONS TRUE)
 # Number of parallel test jobs with "make check":
 #set (N_TEST_JOBS 4)
+
+# Ignore the "GMT_KNOWN_FAILURE" comment in tests to let tests fail normally
+# Can only be "ON" or "OFF" in uppercase!
+#set (GMT_ENABLE_KNOWN2FAIL OFF)
 
 # Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without
@@ -225 +198 @@
 #set (SUPPORT_EXEC_IN_BINARY_DIR ON)
 
-# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes
-# that link against the full gmt libs (not just the API; for building codes
-# that only need the GMT API, see the gmt-custom project).
-#set (EXTRA_BUILD_DIRS apidemo)
 # Uncomment the following line to enable running low-level C tests of the API
 #set (DO_API_TESTS ON)
+
+# Uncomment the following line to enable running tests of the GMT supplements
+#set (DO_SUPPLEMENT_TESTS ON)
+
+# Uncomment the following line if you need to run the full tests suite using
+# the gmtserver "test" distribution instead of the default server.
+# You may wish to rename existing cache and server dirs so you can restore afterwards
+# set (GMT_DATA_SERVER "test")
+
+# List extra sub-dirs of 'src' with a CMakeLists.txt to build custom modules
+# that link against the full gmt libs. (For building codes that only need the GMT API,
+# see the https://github.com/GenericMappingTools/custom-supplements project).
+# These supplemental modules can be built into separate libraries.
+#set (SUPPL_EXTRA_DIRS newsuppl1 newsuppl2 ...)
 
 # Directory in which to install the release sources per default
@@ -245 +228 @@
 #
 
-# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel
-# [Release]:
+# Set build type can be: empty, Debug, Release, RelWithDebInfo or MinSizeRel [Release]:
 #set (CMAKE_BUILD_TYPE Debug)
 
 # Extra debugging for developers:
 #if ( CMAKE_GENERATOR STREQUAL "Xcode" )
-##      So Xcode can find the supplemental plug-ins during debug sessions
-#       add_definitions(-DXCODER)
-#   add_definitions(-DDEBUG_MODERN)                     # To set PPID == 0 during Xcode test
+#   #   So Xcode can find the supplemental plug-ins during debug sessions
+#       add_definitions(-DXCODER)                       # Handle a debug plugin directory
+#       add_definitions(-DDEBUG_MODERN)                 # To set PPID == 0 during Xcode test
 #       message("Add Xcode definition for GMT")
 #endif()
+# Uncomment these two statements if you are a developer debugging GMT:
 #add_definitions(-DDEBUG)
 #add_definitions(-DMEMDEBUG) # Turn on memory tracking see gmt_support.c for extra info
-#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement") # recommended even for release build
+#add_definitions(-DUSE_COMMON_LONG_OPTIONS)     # Turn on testing of upcoming long-option syntax for common GMT options
+#add_definitions(-DUSE_MODULE_LONG_OPTIONS)     # Turn on testing of upcoming long-option syntax for module options
+#add_definitions(-DEXPORT_GMTLIB)                               # Turn on to access normally un-exported or static gmtlib functions from external tools
+#add_definitions(-DNO_THEMES)                   # Turn off implementation of GMT_THEME for debugging
+# Uncomment this statement if you are a developer debugging PSL and want exact line coordinates:
+#add_definitions(-DPSL_EXACT_LINE)
+
+#set (CMAKE_C_FLAGS "-Wall -Wdeclaration-after-statement ${CMAKE_C_FLAGS}") # recommended even for release build
 #set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}")            # extra warnings
 #set (CMAKE_C_FLAGS_DEBUG -ggdb3)                          # gdb debugging symbols
 #set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE)                  # debug link dependencies
-if (HAVE_OPENMP)
-        set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions")  # check uninitialized variables
-else (HAVE_OPENMP)
-        set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized")  # check uninitialized variables
-endif (HAVE_OPENMP)
+#if (HAVE_OPENMP)
+#       set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions")  # check uninitialized variables
+#else (HAVE_OPENMP)
+#       set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized")  # check uninitialized variables
+#endif (HAVE_OPENMP)
 
 #
@@ -301 +291 @@
 # set (GMT_DLL_RENAME gmt_w${BITAGE})
 # set (PSL_DLL_RENAME psl_w${BITAGE})
+# set (SUPP_DLL_RENAME supplements_w${BITAGE})
 #endif(WIN32)
 

issm/trunk-jpl/externalpackages/gmt/install-6-mac-static.sh ¶

@@ -5 +5 @@
 ## Constants
 #
-VER="6.0.0"
+VER="6.5.0"
 
-# Find libgfortran and libgcc so we do not have to hardcode them
+# Find certain libraries so we do not have to hardcode them
 #
 # TODO:
@@ -18 +18 @@
 LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
 LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* 2>/dev/null | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
+echo "Finding libssl..."
+LIBSSL=$(find /usr /opt -name libssl* 2>/dev/null | egrep -n libssl.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
 
 GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6/static/cmake/modules/FindGDAL.cmake)
@@ -44 +46 @@
 rm -rf gmt-${VER}
 
-# Copy custom configuration files
-cp ./configs/6/static/mac/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake
-cp ./configs/6/static/cmake/modules/FindGDAL.cmake ./src/cmake/modules
-cp ./configs/6/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules
-cp ./configs/6/static/cmake/modules/FindNETCDF.cmake ./src/cmake/modules
+# Copy custom configuration files to source
+cp ./src/cmake/ConfigUserAdvancedTemplate.cmake ./src/cmake/ConfigUser.cmake
+
+# Patch source
+patch ./src/cmake/ConfigUser.cmake < ./configs/${VER%.*}/static/mac/cmake/ConfigUserAdvancedTemplate.cmake.patch
+patch ./src/cmake/modules/FindGDAL.cmake < ./configs/${VER%.*}/static/cmake/modules/FindGDAL.cmake.patch
+patch ./src/cmake/modules/FindGSHHG.cmake < ./configs/${VER%.*}/static/cmake/modules/FindGSHHG.cmake.patch
+patch ./src/cmake/modules/FindNETCDF.cmake < ./configs/${VER%.*}/cmake/modules/FindNETCDF.cmake.patch
 
 # Configure
@@ -65 +70 @@
         -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
         -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
-        -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \
+        -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a;${LIBSSL}" \
         -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
         -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \

issm/trunk-jpl/externalpackages/petsc/install-3.20-mac-static.sh ¶

@@ -24 +24 @@
 rm -rf petsc-${VER}
 
-# Apply patches
-patch src/config/BuildSystem/config/setCompilers.py < configs/3.20/mac/intel/src/config/BuildSystem/config/setCompilers.py.patch
-
 # Configure
 #
 # NOTE:
-# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. 
-#       (may need to remove it for earlier versions not using the C99 standard).
+# - Cannot use --with-fpic option when compiling static libs,
+#
+#               Cannot determine compiler PIC flags if shared libraries is turned off
+#               Either run using --with-shared-libraries or --with-pic=0 and supply the
+#               compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS
 #
 cd ${PETSC_DIR}
@@ -38 +38 @@
         --PETSC_DIR="${PETSC_DIR}" \
         --LDFLAGS="${LDFLAGS}" \
+        --with-shared-libraries=0 \
+        --CFLAGS="-fPIC" \
+        --CXXFLAGS="-fPIC" \
+        --FFLAGS="-fPIC" \
         --with-debugging=0 \
         --with-valgrind=0 \
         --with-x=0 \
         --with-ssl=0 \
-        --with-pic=1 \
         --download-fblaslapack=1 \
         --download-mpich="https://www.mpich.org/static/downloads/4.2.0/mpich-4.2.0.tar.gz" \
@@ -55 +58 @@
 make install
 
+# Need to make symlinks from libmpich* to libmpi*
+ln -s ${PREFIX}/lib/libmpi.a ${PREFIX}/lib/libmpich.a
+ln -s ${PREFIX}/lib/libmpicxx.a ${PREFIX}/lib/libmpichcxx.a
+ln -s ${PREFIX}/lib/libmpifort.a ${PREFIX}/lib/libmpichf90.a
+
 # Need to make sure classic linker is used (should be able to remove this once MPICH fixes it)
 if [[ ${LDFLAGS} =~ "-Wl,-ld_classic" ]]; then

issm/trunk-jpl/externalpackages/petsc/install-3.20-mac.sh ¶

@@ -23 +23 @@
 mv petsc-${VER}/* ${PETSC_DIR}
 rm -rf petsc-${VER}
-
-# Apply patches
-patch src/config/BuildSystem/config/setCompilers.py < configs/3.20/mac/intel/src/config/BuildSystem/config/setCompilers.py.patch
 
 # Configure

issm/trunk-jpl/jenkins/mac-intel-binaries-matlab ¶

@@ -1 +1 @@
 MATLAB_PATH="/Applications/MATLAB_R2023b.app"
+LIBGFORTRAN_PATH="/usr/local/Cellar/gcc/13.2.0/lib/gcc/current"
+LIBGCC_PATH="${LIBGFORTRAN_PATH}/gcc/x86_64-apple-darwin21/13"
 
 #--------------------#
@@ -20 +22 @@
         --disable-dependency-tracking \
         --with-matlab-dir=${MATLAB_PATH} \
-        --with-fortran-lib="/usr/local/Cellar/gcc/13.2.0/lib/gcc/current/libgfortran.a /usr/local/Cellar/gcc/13.2.0/lib/gcc/current/libquadmath.a /usr/local/Cellar/gcc/13.2.0/lib/gcc/current/gcc/x86_64-apple-darwin21/13/libgcc.a" \
+        --with-fortran-lib="${LIBGFORTRAN_PATH}/libgfortran.a ${LIBGFORTRAN_PATH}/libquadmath.a ${LIBGCC_PATH}/libgcc.a" \
         --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
         --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
@@ -58 +60 @@
         gdal            install-3-static.sh
         gshhg           install.sh
-        gmt                     install-6-mac-intel-static.sh
+        gmt                     install-6-mac-static.sh
         gmsh            install-4-mac-static.sh
         triangle        install-mac-static.sh

issm/trunk-jpl/jenkins/mac-intel-binaries-python-3 ¶

@@ +1 @@
+MATLAB_PATH="/Applications/MATLAB_R2023b.app"
+LIBGFORTRAN_PATH="/usr/local/Cellar/gcc/13.2.0/lib/gcc/current"
+LIBGCC_PATH="${LIBGFORTRAN_PATH}/gcc/x86_64-apple-darwin21/13"
+
 #--------------------#
 # ISSM Configuration #
@@ -20 +24 @@
         --with-python-dir=/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9 \
         --with-python-numpy-dir=/Library/Python/3.9/site-packages/numpy/core/include/numpy \
-        --with-fortran-lib="/usr/local/Cellar/gcc/13.2.0/lib/gcc/current/libgfortran.a /usr/local/Cellar/gcc/13.2.0/lib/gcc/current/libquadmath.a /usr/local/Cellar/gcc/13.2.0/lib/gcc/current/gcc/x86_64-apple-darwin21/13/libgcc.a" \
+        --with-fortran-lib="${LIBGFORTRAN_PATH}/libgfortran.a ${LIBGFORTRAN_PATH}/libquadmath.a ${LIBGCC_PATH}/libgcc.a" \
         --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
         --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
@@ -58 +62 @@
         gdal            install-3-python-static.sh
         gshhg           install.sh
-        gmt                     install-6-mac-intel-static.sh
+        gmt                     install-6-mac-static.sh
         gmsh            install-4-mac-static.sh
         triangle        install-mac-static.sh

issm/trunk-jpl/jenkins/mac-silicon-binaries-matlab ¶

@@ -1 +1 @@
 MATLAB_PATH="/Applications/MATLAB_R2023b.app"
-LIBGFORTRAN_PATH="/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13"
-LIBGCC_PATH="${LIBGFORTRAN_PATH}/aarch64-apple-darwin22/13"
+LIBGFORTRAN_PATH="/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current"
+LIBGCC_PATH="${LIBGFORTRAN_PATH}/gcc/aarch64-apple-darwin23/13"
 
 #--------------------#
@@ -63 +63 @@
         gdal            install-3-static.sh
         gshhg           install.sh
-        gmt                     install-6-mac-silicon-static.sh
+        gmt                     install-6-mac-static.sh
         gmsh            install-4-mac-static.sh
         triangle        install-mac-static.sh

issm/trunk-jpl/jenkins/mac-silicon-binaries-python-3 ¶

@@ -1 @@
-LIBGFORTRAN_PATH="/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/13"
-LIBGCC_PATH="${LIBGFORTRAN_PATH}/aarch64-apple-darwin22/13"
+MATLAB_PATH="/Applications/MATLAB_R2023b.app"
+LIBGFORTRAN_PATH="/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current"
+LIBGCC_PATH="${LIBGFORTRAN_PATH}/gcc/aarch64-apple-darwin23/13"
 
 #--------------------#
@@ -62 +63 @@
         gdal            install-3-python-static.sh
         gshhg           install.sh
-        gmt                     install-6-mac-silicon-static.sh
+        gmt                     install-6-mac-static.sh
         gmsh            install-4-mac-static.sh
         triangle        install-mac-static.sh

issm/trunk-jpl/m4/issm_options.m4 ¶

@@ -198 +198 @@
                         dnl When standard Dakota installation has been updated to new 
                         dnl version, remove the following
-                        export CFLAGS="-Wno-deprecated-register -Wno-return-type"
-                        export CXXFLAGS="-Wno-deprecated-register -Wno-return-type"
+                        if test -z "${CFLAGS}"; then
+                                export CFLAGS="-Wno-deprecated-register -Wno-return-type"
+                        else
+                                export CFLAGS="${CFLAGS} -Wno-deprecated-register -Wno-return-type"
+                        fi
+                        if test -z "${CXXFLAGS+x}"; then
+                                export CXXFLAGS="-Wno-deprecated-register -Wno-return-type"
+                        else
+                                export CXXFLAGS="${CXXFLAGS} -Wno-deprecated-register -Wno-return-type"
+                        fi
                         dnl NOTE: Commenting out the following, for now, as ISSM seems to 
                         dnl       compile and run fine, but certain errors (e.g. file not 
@@ -541 +549 @@
         dnl Boost libraries and header files
         if test "x${HAVE_BOOST}" == "xyes"; then
+                if test -z "${CXXFLAGS+x}"; then
+                        export CXXFLAGS="-Wno-deprecated"
+                else
+                        export CXXFLAGS="${CXXFLAGS} -Wno-deprecated"
+                fi
                 BOOSTINCL="-I${BOOST_ROOT}/include"
                 #BOOSTLIB="-L$BOOST_ROOT/lib -lboost_python"

issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-matlab.sh ¶

@@ -17 +17 @@
 # See also:
 # - packagers/linux/complete-issm-linux-binaries-matlab.sh
+#
+# TODO:
+# - Make sure that all TPL licenses are copied to package
 ################################################################################
 
@@ -71 +74 @@
 cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
 
+echo "Moving libgfortran to lib/"
+cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+
 echo "Moving MPICH binaries to bin/"
 if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
@@ -109 +115 @@
 fi
 
-echo "Moving libgfortran to lib/"
-cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
-
 echo "Moving GSHHG assets to share/"
-if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+if [ -d ${ISSM_DIR}/externalpackages/gshhg/install ]; then
         mkdir ${ISSM_DIR}/share 2> /dev/null
-        cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+        cp -R ${ISSM_DIR}/externalpackages/gshhg/install/*.nc ${ISSM_DIR}/share
 else
         echo "GSHHG not found"

issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-python-3.sh ¶

@@ -17 +17 @@
 # See also:
 # - packagers/linux/complete-issm-linux-binaries-python-3.sh
+#
+# TODO:
+# - Make sure that all TPL licenses are copied to package
 ################################################################################
 
@@ -64 +67 @@
 cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py
 
+echo "Moving libgfortran to lib/"
+cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
+
 echo "Moving MPICH binaries to bin/"
 if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then
@@ -102 +108 @@
 fi
 
-echo "Moving libgfortran to lib/"
-cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
-
 echo "Moving GSHHG assets to share/"
-if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+if [ -d ${ISSM_DIR}/externalpackages/gshhg/install ]; then
         mkdir ${ISSM_DIR}/share 2> /dev/null
-        cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+        cp -R ${ISSM_DIR}/externalpackages/gshhg/install/*.nc ${ISSM_DIR}/share
 else
         echo "GSHHG not found"

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

@@ -19 +19 @@
 # See also:
 # - packagers/mac/<ARCH>/complete-issm-mac-<ARCH>-binaries-matlab.sh
+#
+# TODO:
+# - Make sure that all TPL licenses are copied to package
 ################################################################################
 
@@ -116 +119 @@
 
 echo "Moving GSHHG assets to share/"
-if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+if [ -d ${ISSM_DIR}/externalpackages/gshhg/install ]; then
         mkdir ${ISSM_DIR}/share 2> /dev/null
-        cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+        cp -R ${ISSM_DIR}/externalpackages/gshhg/install/*.nc ${ISSM_DIR}/share
 else
         echo "GSHHG not found"

issm/trunk-jpl/packagers/mac/package-issm-mac-binaries-python-3.sh ¶

@@ -18 +18 @@
 # See also:
 # - packagers/mac/<ARCH>/complete-issm-mac-<ARCH>-binaries-python-3.sh
+#
+# TODO:
+# - Make sure that all TPL licenses are copied to package
 ################################################################################
 
@@ -108 +111 @@
 
 echo "Moving GSHHG assets to share/"
-if [ -d ${ISSM_DIR}/externalpackages/gmt/install/share/coast ]; then
+if [ -d ${ISSM_DIR}/externalpackages/gshhg/install ]; then
         mkdir ${ISSM_DIR}/share 2> /dev/null
-        cp -R ${ISSM_DIR}/externalpackages/gmt/install/share/coast ${ISSM_DIR}/share
+        cp -R ${ISSM_DIR}/externalpackages/gshhg/install/*.nc ${ISSM_DIR}/share
 else
         echo "GSHHG not found"