Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh (revision 25243) @@ -24,5 +24,5 @@ mkdir build install src -#Download from ISSM server +# Download source ${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz" Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 25243) @@ -11,13 +11,16 @@ # -# Find libgfortran and libgcc so we do not have to hardcode them +# Find libgfortran and libgcc so we do not have to hardcode them. # -# NOTE: Assumes user installed gfortran via Homebrew +# Should retrieve a copy of gfortran that is compiled from source before +# returning one that is installed via package manager. # -# TODO: Refactor this to work with other gfortran installations. +# TODO: +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. # -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) # Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager +LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) # Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager +LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 25243) @@ -10,13 +10,11 @@ ## Environment # -# Find libgfortran and so we do not have to hardcode it + +# Find libgfortran so that we do not have to hardcode it. # -# NOTE: -# - Assumes user installed gfortran via Homebrew. -# - Searches for libgfortran.a as it is easier to find it. +# Should retrieve a copy of gfortran that is compiled from source before +# returning one that is installed via package manager. # -# TODO: Refactor this to work with other gfortran installations. -# -LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) # Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager +LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/cmake/ConfigUser.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/cmake/ConfigUser.cmake (revision 25243) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/cmake/ConfigUser.cmake (revision 25243) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# 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 +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## 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 (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# 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 +# distribution type directory structure (doc and share separated) [on]: +#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) +#set (GMT_EXCLUDE_PCRE TRUE) +#set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# 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 "$ENV{ISSM_DIR}/externalpackages/netcdf/install") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install") + +# Set location of CURL (can be root directory or path to header file) [auto]: +#set (CURL_ROOT "curl_install_prefix") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack") +set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# 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) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +#set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +#set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#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) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# 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 +# message("Add Xcode definition for GMT") +#endif() +#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 +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +#set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/ConfigUser.static.cmake (revision 25243) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/ConfigUser.static.cmake (revision 25243) @@ -0,0 +1,308 @@ +# +# +# Copyright (c) 1991-2019 by the GMT Team (https://www.generic-mapping-tools.org/team.html) +# See LICENSE.TXT file for copying and redistribution conditions. +# +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation; version 3 or any later version. +# +# This program is distributed in the hope that it will be useful, but WITHOUT +# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License +# for more details. +# +# Contact info: www.generic-mapping-tools.org +# ---------------------------------------------------------------------------- + +# 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 +# (currently listed in .gitignore). +# +# Note: CMake considers an empty string, "FALSE", "OFF", "NO", or any string +# ending in "-NOTFOUND" to be false (this happens to be case-insensitive, so +# "False", "off", "no", and "something-NotFound" are all false). Other values +# are true. Thus it does not matter whether you use TRUE and FALSE, ON and +# OFF, or YES and NO for your booleans. + +## +## 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 (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") + +# 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 +# distribution type directory structure (doc and share separated) [on]: +#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) +#set (GMT_EXCLUDE_PCRE TRUE) +#set (GMT_EXCLUDE_PCRE2 TRUE) +#set (GMT_EXCLUDE_FFTW3 TRUE) +#set (GMT_EXCLUDE_LAPACK TRUE) +#set (GMT_EXCLUDE_BLAS TRUE) +#set (GMT_EXCLUDE_ZLIB TRUE) + +# ============================================================================ +# Advanced configuration begins here. Usually it is not necessary to edit any +# settings below. You should know what you are doing if you do though. Note: +# installation paths are relative to ${CMAKE_INSTALL_PREFIX} unless absolute +# path is given. +# ============================================================================ + +# Set binary installation path [bin]: +#set (GMT_BINDIR "bin") + +# Set library installation path [lib or lib64]: +#set (GMT_LIBDIR "lib") + +# Set include installation path [include/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_INCLUDEDIR "include/gmt") + +# Set share installation path [share or share/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DATADIR "share/gmt") + +# Set doc installation path [share/doc or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}]: +#set (GMT_DOCDIR "share/doc/gmt") + +# Set manpage installation path [share/man or +# share/doc/gmt${GMT_INSTALL_NAME_SUFFIX}/man]: +#set (GMT_MANDIR "share/doc/gmt/man") + +# Install documentation files from this external location instead of creating +# new HTML documents from scratch [${GMT_SOURCE_DIR}/doc_release]: +#set (GMT_INSTALL_EXTERNAL_DOC OFF) + +# Install manual pages from this external location instead of creating the +# manpages from scratch [${GMT_SOURCE_DIR}/man_release]: +#set (GMT_INSTALL_EXTERNAL_MAN OFF) + +## +## Section 2: Build dependencies (should only be needed if CMake cannot +## automatically detect the rights version or path.) +## + +# Set URL to GMT Data server [auto]: +#set (GMT_DATA_SERVER "data_server_url") + +# Set path to GSHHG Shoreline Database [auto]: +set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") + +# 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 "$ENV{ISSM_DIR}/externalpackages/netcdf/install") + +# Set location of GDAL (can be root directory, path to header file or path to +# gdal-config) [auto]: +set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") + +# Set location of PCRE (can be root directory, path to header file or path to +# pcre-config) [auto]: +#set (PCRE_ROOT "pcre_install_prefix") +# Alternatively, set location of PCRE2 (can be root directory, path to header file or path to +# pcre2-config) [auto]: +#set (PCRE2_ROOT "pcre2_install_prefix") + +# Set location of single precision FFTW (can be root directory or path to +# header file) [auto]: +#set (FFTW3_ROOT "fftw_install_prefix") + +# Set location of ZLIB (can be root directory or path to header file) [auto]: +set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install") + +# Set location of CURL (can be root directory or path to header file) [auto]: +set (CURL_ROOT "$ENV{ISSM_DIR}/externalpackages/curl/install") + +# Set location of GLIB component gthread [auto]. This is an optional (and +# experimental) option which you need to enable: +#set (GMT_USE_THREADS TRUE) +# If pkg-config is not installed (e.g. on Windows) you need to specify these: +#set (GLIB_INCLUDE_DIR c:/path/to/glib-dev/include/glib-2.0) +#set (GLIB_LIBRARIES c:/path/to/glib-dev/lib/glib-2.0.lib) + +# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically +#set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack") +#set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas") + +## +## Section 3: GMT features +## + +# Enforce GPL or LGPL conformity. Use this to disable routines that cannot be +# redistributed under the terms of the GPL or LGPL such as Shewchuk's +# triangulation (valid values are GPL, LGPL and off) [off]: +#set (LICENSE_RESTRICTED GPL) + +# Allow building of OpenMP if compiler supports it +# set (GMT_ENABLE_OPENMP TRUE) + +# Configure default units (possible values are SI and US) [SI]: +#set (UNITS "US") + +# 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) + +# Create position independent code on all targets [auto] (needed for static +# build on non-x86): +set (CMAKE_POSITION_INDEPENDENT_CODE TRUE) + +# Build GMT shared lib with supplemental modules [TRUE]: +set (BUILD_SUPPLEMENTS FALSE) + +# Build/Install GMT Developer include files [TRUE]: +# This installs the extra include files and configured files needed by 3rd-party +# developers. Until we build a separate gmt-devel we include them in the main +# Distribution. +#set (BUILD_DEVELOPER FALSE) + +## +## Section 4: Advanced tweaking +## + +# +# Testing and development +# + +# Enable running examples/tests with "ctest" or "make check" (out-of-source). +# Need to set either DO_EXAMPLES, DO_TESTS or both and uncomment the following +# line. +#enable_testing() +#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) + +# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without +# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required +# for testing [OFF]: +#set (SUPPORT_EXEC_IN_BINARY_DIR ON) + +# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes +# that link against the full gmt libs (not just the API; for building codes +# that only need the GMT API, see the gmt-custom project). +#set (EXTRA_BUILD_DIRS apidemo) +# Uncomment the following line to enable running low-level C tests of the API +#set (DO_API_TESTS ON) + +# Directory in which to install the release sources per default +# [${GMT_BINARY_DIR}/gmt-${GMT_PACKAGE_VERSION}]: +#set (GMT_RELEASE_PREFIX "release-src-prefix") + +# If set to false, image conversion from PS images to PNG and PDF does +# not depend on the gmt binary target. Note: "make gmt" is then required +# before docs_depends [TRUE]. +#set (GMT_DOCS_DEPEND_ON_GMT FALSE) + +# +# Debugging +# + +# 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 +# message("Add Xcode definition for GMT") +#endif() +#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 +#set (CMAKE_C_FLAGS "-Wextra ${CMAKE_C_FLAGS}") # extra warnings +#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols +#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies +if (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized -flax-vector-conversions") # check uninitialized variables +else (HAVE_OPENMP) + set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables +endif (HAVE_OPENMP) + +# +# System specific tweaks +# + +# This is for GCC on Solaris to avoid "relocations remain against allocatable +# but non-writable sections" problems: +#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) + +# This may be needed to enable strdup and extended math functions with GCC and +# Suncc on Solaris: +#set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__EXTENSIONS__") + +# Do not warn when building with Windows SDK or Visual Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON) + +# Manually select runtime library when compiling with Windows SDK or Visual +# Studio Express: +#set (CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS c:/Windows/System32/msvcr100.dll) + +# If your NetCDF library is static (not recommended, applies to Windows only) +set (NETCDF_STATIC TRUE) + +# If want to rename the DLLs to something else than the default (e.g. to +# append the bitness - Windows only) +# WARNING: if using this option it is mandatory that the suffix starts with an underscore. +#if (WIN32) +# set (BITAGE 32) +# # Detect if we are building a 32 or 64 bits version +# if (CMAKE_SIZEOF_VOID_P EQUAL 8) +# set (BITAGE 64) +# endif () +# set (GMT_DLL_RENAME gmt_w${BITAGE}) +# set (PSL_DLL_RENAME psl_w${BITAGE}) +#endif(WIN32) + +# On Windows Visual C 2012 needs _ALLOW_KEYWORD_MACROS to build +#if(MSVC11) +# add_definitions(/D_ALLOW_KEYWORD_MACROS) +#endif(MSVC11) Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindGDAL.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindGDAL.cmake (revision 25243) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindGDAL.cmake (revision 25243) @@ -0,0 +1,187 @@ +# +# +# Locate gdal +# +# This module accepts the following environment variables: +# +# GDAL_DIR or GDAL_ROOT - Specify the location of GDAL +# +# This module defines the following CMake variables: +# +# GDAL_FOUND - True if libgdal is found +# GDAL_LIBRARY - A variable pointing to the GDAL library +# GDAL_INCLUDE_DIR - Where to find the headers + +#============================================================================= +# Copyright 2007-2009 Kitware, Inc. +# +# Distributed under the OSI-approved BSD License (the "License"); +# see accompanying file Copyright.txt for details. +# +# This software is distributed WITHOUT ANY WARRANTY; without even the +# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See COPYING-CMAKE-SCRIPTS for more information. +#============================================================================= +# Note: this file is not an exact copy of the original file from Kitware. +# It has been modified for the needs of GMT. + +# +# $GDAL_DIR is an environment variable that would +# correspond to the ./configure --prefix=$GDAL_DIR +# used in building gdal. +# +# Created by Eric Wing. I'm not a gdal user, but OpenSceneGraph uses it +# for osgTerrain so I whipped this module together for completeness. +# I actually don't know the conventions or where files are typically +# placed in distros. +# Any real gdal users are encouraged to correct this (but please don't +# break the OS X framework stuff when doing so which is what usually seems +# to happen). + +# This makes the presumption that you are include gdal.h like +# +#include "gdal.h" + +if (DEFINED GDAL_ROOT AND NOT GDAL_ROOT) + set (GDAL_LIBRARY "" CACHE INTERNAL "") + set (GDAL_INCLUDE_DIR "" CACHE INTERNAL "") + return() +endif (DEFINED GDAL_ROOT AND NOT GDAL_ROOT) + +if (UNIX AND NOT GDAL_FOUND) + # Use gdal-config to obtain the library version (this should hopefully + # allow us to -lgdal1.x.y where x.y are correct version) + # For some reason, libgdal development packages do not contain + # libgdal.so... + find_program (GDAL_CONFIG gdal-config + HINTS + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + PATH_SUFFIXES bin + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + ) + + if (GDAL_CONFIG) + execute_process (COMMAND ${GDAL_CONFIG} --cflags + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_CFLAGS) + if (GDAL_CONFIG_CFLAGS) + string (REGEX MATCHALL "-I[^ ]+" _gdal_dashI ${GDAL_CONFIG_CFLAGS}) + string (REGEX REPLACE "-I" "" _gdal_includepath "${_gdal_dashI}") + string (REGEX REPLACE "-I[^ ]+" "" _gdal_cflags_other ${GDAL_CONFIG_CFLAGS}) + endif (GDAL_CONFIG_CFLAGS) + execute_process (COMMAND ${GDAL_CONFIG} --libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_LIBS) + if (GDAL_CONFIG_LIBS) + string (REGEX MATCHALL "-l[^ ]+" _gdal_dashl ${GDAL_CONFIG_LIBS}) + string (REGEX REPLACE "-l" "" _gdal_lib "${_gdal_dashl}") + string (REGEX MATCHALL "-L[^ ]+" _gdal_dashL ${GDAL_CONFIG_LIBS}) + string (REGEX REPLACE "-L" "" _gdal_libpath "${_gdal_dashL}") + endif (GDAL_CONFIG_LIBS) + execute_process (COMMAND ${GDAL_CONFIG} --dep-libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE GDAL_CONFIG_DEP_LIBS) + if (GDAL_CONFIG_DEP_LIBS) + string (REGEX MATCHALL "-l[^ ]+" _gdal_dashl ${GDAL_CONFIG_DEP_LIBS}) + string (REGEX REPLACE "-l" "" _gdal_dep_lib "${_gdal_dashl}") + string (REGEX MATCHALL "-L[^ ]+" _gdal_dashL ${GDAL_CONFIG_DEP_LIBS}) + string (REGEX REPLACE "-L" "" _gdal_dep_libpath "${_gdal_dashL}") + endif (GDAL_CONFIG_DEP_LIBS) + endif (GDAL_CONFIG) + if (_gdal_dep_lib) + list (REMOVE_DUPLICATES _gdal_dep_lib) + list (REMOVE_ITEM _gdal_dep_lib gdal) + endif (_gdal_dep_lib) +endif (UNIX AND NOT GDAL_FOUND) + +find_path (GDAL_INCLUDE_DIR gdal.h + HINTS + ${_gdal_includepath} + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + PATH_SUFFIXES + include/gdal + include/GDAL + include + PATHS + ~/Library/Frameworks/gdal.framework/Headers + /Library/Frameworks/gdal.framework/Headers + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +find_library (GDAL_LIBRARY + NAMES ${_gdal_lib} gdal gdal_i gdal1.5.0 gdal1.4.0 gdal1.3.2 GDAL + HINTS + ${GDAL_DIR} + ${GDAL_ROOT} + $ENV{GDAL_DIR} + $ENV{GDAL_ROOT} + ${_gdal_libpath} + PATH_SUFFIXES lib + PATHS + ~/Library/Frameworks/gdal.framework + /Library/Frameworks/gdal.framework + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +# find all libs that gdal-config --dep-libs reports +foreach (_extralib ${_gdal_dep_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} + ${ZLIB_ROOT} + $ENV{ZLIB_ROOT} + ${CURL_ROOT} + $ENV{CURL_ROOT} + PATH_SUFFIXES lib + PATHS + ${_gdal_dep_libpath} + ) + list (APPEND GDAL_LIBRARY ${_found_lib_${_extralib}}) +endforeach (_extralib) + +# append manually-supplied libs +# find all manually-supplied libs +if (GDAL_EXTRA_LIBS) + # Ensure -l is precedeced by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _gdal_extra_lib_dashl ${GDAL_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _gdal_extra_lib "${_gdal_extra_lib_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _gdal_extra_lib_dashL ${GDAL_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _gdal_extra_libpath "${_gdal_extra_lib_dashL}") + foreach (_extralib ${_gdal_extra_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_gdal_extra_libpath} + ) + list (APPEND GDAL_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) +endif (GDAL_EXTRA_LIBS) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (GDAL DEFAULT_MSG GDAL_LIBRARY GDAL_INCLUDE_DIR) + +set (GDAL_LIBRARIES ${GDAL_LIBRARY}) +set (GDAL_INCLUDE_DIRS ${GDAL_INCLUDE_DIR}) Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindGSHHG.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindGSHHG.cmake (revision 25243) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindGSHHG.cmake (revision 25243) @@ -0,0 +1,95 @@ +# +# +# Locate GSHHG shorelines +# +# This module accepts the following environment variables: +# +# GSHHG_ROOT, GSHHGDIR - Specify the location of GSHHG +# +# This module defines the following CMake variables: +# +# GSHHG_FOUND - True if GSHHG is found +# GSHHG_PATH - A variable pointing to the GSHHG path +# GSHHG_VERSION - String of the GSHHG version found +# GSHHG_MIN_REQUIRED_VERSION_{MAJOR, MINOR, PATCH} +# - Major, minor, and patch version required + +# get GSHHG path +find_path (GSHHG_PATH + NAMES binned_GSHHS_c.nc + HINTS ${GSHHG_ROOT} $ENV{GSHHG_ROOT} $ENV{GSHHGDIR} + PATH_SUFFIXES + gmt-gshhg + gshhg + gshhg-gmt + gshhg-gmt-nc4 + share/gmt/gshhg + share/gmt-gshhg + share/gshhg + share/gshhg-gmt + share/gshhg-gmt-nc4 + PATHS + ${CMAKE_SOURCE_DIR} + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + DOC "Global Self-consistent Hierarchical High-resolution Geography" +) + +# get GSHHG file +if (GSHHG_PATH) + find_file (_GSHHG_FILE + NAMES binned_GSHHS_c.nc + HINTS ${GSHHG_PATH}) +endif (GSHHG_PATH) + +# The minimum required GSHHG version +set (GSHHG_MIN_REQUIRED_VERSION_MAJOR 2 CACHE INTERNAL "GSHHG required version major") +set (GSHHG_MIN_REQUIRED_VERSION_MINOR 2 CACHE INTERNAL "GSHHG required version minor") +set (GSHHG_MIN_REQUIRED_VERSION_PATCH 0 CACHE INTERNAL "GSHHG required version patch") +set (GSHHG_MIN_REQUIRED_VERSION + "${GSHHG_MIN_REQUIRED_VERSION_MAJOR}.${GSHHG_MIN_REQUIRED_VERSION_MINOR}.${GSHHG_MIN_REQUIRED_VERSION_PATCH}") + +# Temporary hack to bypass failure of compilation of code to find GSHHG +set (GSHHG_FOUND TRUE) +set (GSHHG_VERSION "2.3.4" CACHE INTERNAL "GSHHG version") + +# check GSHHG version +if (_GSHHG_FILE AND NOT GSHHG_FOUND) + try_run (_EXIT_GSHHG_VERSION _COMPILED_GSHHG_VERSION + ${CMAKE_BINARY_DIR}/CMakeTmp + ${CMAKE_CURRENT_SOURCE_DIR}/gshhg_version.c + CMAKE_FLAGS + -DINCLUDE_DIRECTORIES=${NETCDF_INCLUDE_DIR} + -DLINK_LIBRARIES=${NETCDF_LIBRARIES} + COMPILE_DEFINITIONS -DSTANDALONE + COMPILE_OUTPUT_VARIABLE _GSHHG_VERSION_COMPILE_OUT + RUN_OUTPUT_VARIABLE _GSHHG_VERSION_STRING + ARGS \"${_GSHHG_FILE}\" ${GSHHG_MIN_REQUIRED_VERSION}) + + if (NOT _COMPILED_GSHHG_VERSION OR _EXIT_GSHHG_VERSION STREQUAL FAILED_TO_RUN) + message(FATAL_ERROR "Cannot determine GSHHG version:\n + ${_GSHHG_VERSION_COMPILE_OUT}\n + ${_GSHHG_VERSION_STRING}") + endif () + + # check version string + if (_COMPILED_GSHHG_VERSION) + # strip whitespace + string (STRIP ${_GSHHG_VERSION_STRING} GSHHG_VERSION) + if (_EXIT_GSHHG_VERSION EQUAL 0) + # found GSHHG of required version or higher + set (GSHHG_VERSION ${GSHHG_VERSION} CACHE INTERNAL "GSHHG version") + elseif (_EXIT_GSHHG_VERSION EQUAL -1) + # found GSHHG but version is too old + message (WARNING "GSHHG found but it is too old (${GSHHG_VERSION}). " + "Need at least ${GSHHG_MIN_REQUIRED_VERSION}.") + endif (_EXIT_GSHHG_VERSION EQUAL 0) + endif (_COMPILED_GSHHG_VERSION) +endif (_GSHHG_FILE AND NOT GSHHG_FOUND) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (GSHHG DEFAULT_MSG + GSHHG_PATH GSHHG_VERSION) Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindNETCDF.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindNETCDF.cmake (revision 25243) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/static/cmake/modules/FindNETCDF.cmake (revision 25243) @@ -0,0 +1,170 @@ +# +# +# Locate netcdf +# +# This module accepts the following environment variables: +# +# NETCDF_DIR or NETCDF_ROOT - Specify the location of NetCDF +# +# This module defines the following CMake variables: +# +# NETCDF_FOUND - True if libnetcdf is found +# NETCDF_LIBRARY - A variable pointing to the NetCDF library +# NETCDF_INCLUDE_DIR - Where to find the headers +# NETCDF_INCLUDE_DIRS - Where to find the headers +# NETCDF_DEFINITIONS - Extra compiler flags + +#============================================================================= +# Inspired by FindGDAL +# +# Distributed under the OSI-approved bsd license (the "License") +# +# This software is distributed WITHOUT ANY WARRANTY; without even the +# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See COPYING-CMAKE-SCRIPTS for more information. +#============================================================================= + +# This makes the presumption that you are include netcdf.h like +# +#include "netcdf.h" + +if (UNIX AND NOT NETCDF_FOUND) + # Use nc-config to obtain the libraries + find_program (NETCDF_CONFIG nc-config + HINTS + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES bin + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local + ) + + if (NETCDF_CONFIG) + execute_process (COMMAND ${NETCDF_CONFIG} --cflags + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE NETCDF_CONFIG_CFLAGS) + if (NETCDF_CONFIG_CFLAGS) + string (REGEX MATCHALL "(^| )-I[^ ]+" _netcdf_dashI ${NETCDF_CONFIG_CFLAGS}) + string (REGEX REPLACE "(^| )-I" "" _netcdf_includepath "${_netcdf_dashI}") + string (REGEX REPLACE "(^| )-I[^ ]+" "" _netcdf_cflags_other ${NETCDF_CONFIG_CFLAGS}) + endif (NETCDF_CONFIG_CFLAGS) + execute_process (COMMAND ${NETCDF_CONFIG} --libs + ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE + OUTPUT_VARIABLE NETCDF_CONFIG_LIBS) + if (NETCDF_CONFIG_LIBS) + # Ensure -l is precedeced by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_dashl ${NETCDF_CONFIG_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _netcdf_lib "${_netcdf_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _netcdf_dashL ${NETCDF_CONFIG_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _netcdf_libpath "${_netcdf_dashL}") + endif (NETCDF_CONFIG_LIBS) + endif (NETCDF_CONFIG) + if (_netcdf_lib) + list (REMOVE_DUPLICATES _netcdf_lib) + list (REMOVE_ITEM _netcdf_lib netcdf) + endif (_netcdf_lib) +endif (UNIX AND NOT NETCDF_FOUND) + +find_path (NETCDF_INCLUDE_DIR netcdf.h + HINTS + ${_netcdf_includepath} + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES + include/netcdf + include/netcdf-4 + include/netcdf-3 + include + PATHS + /sw # Fink + /opt/local # DarwinPorts + /opt/csw # Blastwave + /opt + /usr/local +) + +find_library (NETCDF_LIBRARY + NAMES netcdf + HINTS + ${_netcdf_libpath} + ${NETCDF_DIR} + ${NETCDF_ROOT} + $ENV{NETCDF_DIR} + $ENV{NETCDF_ROOT} + PATH_SUFFIXES lib + PATHS + /sw + /opt/local + /opt/csw + /opt + /usr/local +) + +# find all libs that nc-config reports +foreach (_extralib ${_netcdf_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + HINTS + ${HDF5_ROOT} + $ENV{HDF5_ROOT} + ${ZLIB_ROOT} + $ENV{ZLIB_ROOT} + ${CURL_ROOT} + $ENV{CURL_ROOT} + PATH_SUFFIXES lib + PATHS + ${_netcdf_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) +endforeach (_extralib) + +# find all manually-supplied libs +if (NETCDF_EXTRA_LIBS) + # Ensure -l is precedeced by whitespace to not match + # '-l' in '-L/usr/lib/x86_64-linux-gnu/hdf5/serial' + string (REGEX MATCHALL "(^| )-l[^ ]+" _netcdf_extra_lib_dashl ${NETCDF_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-l" "" _netcdf_extra_lib "${_netcdf_extra_lib_dashl}") + string (REGEX MATCHALL "(^| )-L[^ ]+" _netcdf_extra_lib_dashL ${NETCDF_EXTRA_LIBS}) + string (REGEX REPLACE "(^| )-L" "" _netcdf_extra_libpath "${_netcdf_extra_lib_dashL}") + foreach (_extralib ${_netcdf_extra_lib}) + find_library (_found_lib_${_extralib} + NAMES ${_extralib} + PATH_SUFFIXES lib + PATHS + ${_netcdf_extra_libpath} + ) + list (APPEND NETCDF_LIBRARY ${_found_lib_${_extralib}}) + endforeach (_extralib) +endif (NETCDF_EXTRA_LIBS) + +if (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + # Ensure that NetCDF with version 4 extensions is installed + include (CMakePushCheckState) + include (CheckSymbolExists) + cmake_push_check_state() # save state of CMAKE_REQUIRED_* + set (CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${NETCDF_INCLUDE_DIR}) + set (CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${NETCDF_LIBRARY}) + set (HAVE_NETCDF4 HAVE_NETCDF4) # to force check_symbol_exists again + check_symbol_exists (nc_def_var_deflate netcdf.h HAVE_NETCDF4) + cmake_pop_check_state() # restore state of CMAKE_REQUIRED_* + if (NOT HAVE_NETCDF4) + message (SEND_ERROR "Library found but netCDF-4/HDF5 format unsupported. Do not configure netCDF-4 with --disable-netcdf-4.") + endif (NOT HAVE_NETCDF4) +endif (NETCDF_LIBRARY AND NETCDF_INCLUDE_DIR AND NOT HAVE_NETCDF4) + +include (FindPackageHandleStandardArgs) +find_package_handle_standard_args (NETCDF + DEFAULT_MSG NETCDF_LIBRARY NETCDF_INCLUDE_DIR HAVE_NETCDF4) + +set (NETCDF_LIBRARIES ${NETCDF_LIBRARY}) +set (NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR}) +string (REPLACE "-DNDEBUG" "" NETCDF_DEFINITIONS "${_netcdf_cflags_other}") Index: /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux-static.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux-static.sh (revision 25243) @@ -2,4 +2,9 @@ set -eu + +# TODO: +# - Apply changes made to ./install-6.0-mac-static.sh and customized +# configuration files to this file. +# ## Constants @@ -17,5 +22,5 @@ ZLIB_ROOT="${PETSC_ROOT}" -GDAL_LIBRARY="${GDAL_ROOT}/lib/libgdal.a;${NETCDF_ROOT}/lib/libnetcdf.a;${HDF5_ROOT}/lib/libhdf5_hl.a;${HDF5_ROOT}/lib/libhdf5.a;${PROJ_ROOT}/lib/libproj.a;${ZLIB_ROOT}/lib/libz.a;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libdl.so;${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a;/usr/lib/x86_64-linux-gnu/libsqlite3.a;/usr/lib/x86_64-linux-gnu/libexpat.a;/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25;" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs`, removing duplicate libs, then adding libmpicxx as, otherwise, various symbols in libgdal are undefined (compiled with mpicxx) +GDAL_LIBRARY="${GDAL_ROOT}/lib/libgdal.a;${NETCDF_ROOT}/lib/libnetcdf.a;${HDF5_ROOT}/lib/libhdf5_hl.a;${HDF5_ROOT}/lib/libhdf5.a;${PROJ_ROOT}/lib/libproj.a;${ZLIB_ROOT}/lib/libz.a;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libdl.so;${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a;/usr/lib/x86_64-linux-gnu/libsqlite3.a;/usr/lib/x86_64-linux-gnu/libexpat.a;/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25;" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs NETCDF_LIBRARY="${NETCDF_ROOT}/lib/libnetcdf.a;/usr/lib/x86_64-linux-gnu/libm.so;${CURL_ROOT}/lib/libcurl.a;${HDF5_ROOT}/lib/libhdf5_hl.a;${HDF5_ROOT}/lib/libhdf5.a;${ZLIB_ROOT}/lib/libz.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a;/usr/lib/x86_64-linux-gnu/libdl.so" # Determined by running `$NETCDF_ROOT/bin/nc-config --libs` @@ -39,6 +44,6 @@ # Copy custom configuration files -cp ./configs/6.0/linux/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake -cp ./configs/6.0/linux/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules +cp ./configs/6.0/static/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6.0/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules # Configure Index: /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux.sh (revision 25243) @@ -28,5 +28,5 @@ # Copy custom configuration files -cp ./configs/6.0/linux/cmake/ConfigUser.cmake ./src/cmake +cp ./configs/6.0/cmake/ConfigUser.cmake ./src/cmake # Configure Index: /issm/trunk-jpl/externalpackages/gmt/install-6.0-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6.0-mac-static.sh (revision 25243) +++ /issm/trunk-jpl/externalpackages/gmt/install-6.0-mac-static.sh (revision 25243) @@ -0,0 +1,78 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Apply changes to this file and customized configuration files to +# ./install-6.0-linux-static.sh +# + +## Constants +# +VER="6.0.0" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +BLASLAPACK_ROOT="${PETSC_ROOT}" +HDF5_ROOT="${PETSC_ROOT}" + +# Find libgfortran and libgcc so we do not have to hardcode them +# +# Should retrieve a copy of gfortran that is compiled from source before returning one that is installed via package manager +# +# TODO: +# - Test if -static-libgfortran flag will avoid all of this. +# - Otherwise, refactor this to work with other gfortran installations. +# +LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) +LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} +LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) + +GDAL_EXTRA_LIBS="-lc++" # `$GDAL_ROOT/bin/gdal-config --dep-libs` does not report need to link to libc++ (see also customized configuration file ./configs/6.0/static/cmake/modules/FindGDAL.cmake) +NETCDF_EXTRA_LIBS="-lsqlite3 -lpthread -ldl -lidn2 -lldap -liconv" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6.0/static/cmake/modules/FindNETCDF.cmake) + +# Environment +# +export CC=mpicc + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmt-${VER}.tar.gz" "gmt-${VER}.tar.gz" + +# Unpack source +tar -zxvf gmt-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv gmt-${VER}/* src +rm -rf gmt-${VER} + +# Copy custom configuration files +cp ./configs/6.0/static/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6.0/static/cmake/modules/FindGDAL.cmake ./src/cmake/modules +cp ./configs/6.0/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules +cp ./configs/6.0/static/cmake/modules/FindNETCDF.cmake ./src/cmake/modules + +# Configure +cd src +mkdir build +cd build + +cmake \ + -DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ + -DHDF5_ROOT="${HDF5_ROOT}" \ + -DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gmt/install-6.0-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6.0-mac.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/gmt/install-6.0-mac.sh (revision 25243) @@ -28,5 +28,5 @@ # Copy custom configuration files -cp ./configs/6.0/linux/cmake/ConfigUser.cmake ./src/cmake +cp ./configs/6.0/cmake/ConfigUser.cmake ./src/cmake # Configure Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-mac-parallel-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-mac-parallel-static.sh (revision 25243) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-mac-parallel-static.sh (revision 25243) @@ -0,0 +1,74 @@ +#!/bin/bash +set -eu + + +# Dependencies +# - MPI implementation (for parallel I/O support) +# - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) +# - zlib (1.2.5 or later, for netCDF-4 compression) +# - curl (7.18.0 or later, for DAP remote access client support) +# +# For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# + +# NOTE: +# - Certain configuration tests fail if libraries are not supplied explicitly + +# Constants +# +VER="4.7.2" + +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +# Environment +# +export CC=mpicc +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" + +export CURLLIB="${CURL_ROOT}/lib/libcurl.a" +export HDF5LIB="${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a" +export ZLIB="${ZLIB_ROOT}/lib/libz.a" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf-c-${VER}.tar.gz" "netcdf-c-${VER}.tar.gz" + +# Unpack source +tar -zxvf netcdf-c-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv netcdf-c-$VER/* src/ +rm -rf netcdf-c-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-shared \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-doxygen \ + --enable-netcdf4 \ + --disable-testsets \ + --disable-examples \ + --disable-filter-testing + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 25242) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 25243) @@ -21,4 +21,5 @@ # VER="4.7.2" + CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" @@ -29,5 +30,9 @@ export CC=mpicc export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" -export LIBS="${CURL_ROOT}/lib/libcurl.a ${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a ${ZLIB_ROOT}/lib/libz.a /usr/lib/x86_64-linux-gnu/libssl.a /usr/lib/x86_64-linux-gnu/libcrypto.a -L/usr/lib/x86_64-linux-gnu -ldl" +export LIBS="/usr/lib/x86_64-linux-gnu/libssl.a /usr/lib/x86_64-linux-gnu/libcrypto.a -L/usr/lib/x86_64-linux-gnu -ldl" + +export CURLLIB="${CURL_ROOT}/lib/libcurl.a" +export HDF5LIB="${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a" +export ZLIB="${ZLIB_ROOT}/lib/libz.a" # Download source @@ -55,5 +60,6 @@ --enable-netcdf4 \ --disable-testsets \ - --disable-examples + --disable-examples \ + --disable-filter-testing # Compile and install