Index: /issm/trunk-jpl/externalpackages/curl/install-7.67-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7.67-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/curl/install-7.67-static.sh (revision 24919) @@ -0,0 +1,42 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="7.67.0" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz" + +# Unpack source +tar -zxvf curl-$VER.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv curl-$VER/* src +rm -rf curl-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-shared \ + --disable-dependency-tracking \ + --disable-manual \ + --disable-verbose + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Return to initial directory +cd ../.. Index: /issm/trunk-jpl/externalpackages/curl/install-7.67.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7.67.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/curl/install-7.67.sh (revision 24919) @@ -25,4 +25,6 @@ ./configure \ --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --disable-static \ + --disable-dependency-tracking \ --disable-manual \ --disable-verbose Index: sm/trunk-jpl/externalpackages/curl/install-macosx64.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-macosx64.sh (revision 24918) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf src install curl-7.39.0 -mkdir src install - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/curl-7.39.0.tar.gz' 'curl-7.39.0.tar.gz' - -#Untar -tar -zxvf curl-7.39.0.tar.gz - -#Move curl into src directory -mv curl-7.39.0/* src -rm -rf curl-7.39.0 - -#Configure curl -cd src - -export CFLAGS=" -arch x86_64" - -./configure \ - --prefix="$ISSM_DIR/externalpackages/curl/install" - -#Compile curl -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk-jpl/externalpackages/gdal/install-3.0-python-netcdf-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3.0-python-netcdf-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/gdal/install-3.0-python-netcdf-static.sh (revision 24919) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.0.2" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +NETCDF_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" + +## Environment +# +export CC=mpicc +export CXX=mpicxx + + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/gdal-${VER}.tar.gz" "gdal-${VER}.tar.gz" + +# Unpack source +tar -zxvf gdal-$VER.tar.gz + +# Move source into 'src' directory +mv gdal-$VER/* src +rm -rf gdal-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/gdal/install" \ + --disable-shared \ + --with-python \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk-jpl/externalpackages/gmsh/install-3.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-3.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/gmsh/install-3.sh (revision 24919) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.0.5" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_MPI=1 \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh (revision 24919) @@ -0,0 +1,37 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="4.5.6" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_MPI=1 \ + -DENABLE_BUILD_LIB=1 + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gmsh/install-4.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/gmsh/install-4.sh (revision 24919) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="4.5.6" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Untar source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Configure +cd install +cmake ../src \ + -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ + -DENABLE_MPI=1 \ + -DENABLE_BUILD_DYNAMIC=1 \ + -DENABLE_BUILD_SHARED=1 + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: sm/trunk-jpl/externalpackages/gmsh/install-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-static.sh (revision 24918) +++ (revision ) @@ -1,37 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install src -mkdir install - -#Download latest version -#svn co --username gmsh --password gmsh https://geuz.org/svn/gmsh/trunk src -#git clone http://gitlab.onelab.info/gmsh/gmsh.git src - -#Set gmsh version -GMSH_VER="3.0.5" - -#Remove tarball if it exists -rm -f gmsh-$GMSH_VER-source.tgz - -#Download last stable version that we know works -wget http://gmsh.info/src/gmsh-$GMSH_VER-source.tgz - -#Untar gmsh -tar -xvzf gmsh-$GMSH_VER-source.tgz - -#Rename gmsh source directory -mv gmsh-$GMSH_VER-source src - -#Configure -cd install -cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" -DENABLE_METIS=0 - -#Compile and install -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: sm/trunk-jpl/externalpackages/gmsh/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install.sh (revision 24918) +++ (revision ) @@ -1,36 +1,0 @@ -#!/bin/bash -set -eu - - -## Constants -# -VER="3.0.5" - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" - -# Untar source -tar -xvzf gmsh-${VER}-source.tgz - -# Move source to 'src' directory -mv gmsh-${VER}-source/* src -rm -rf gmsh-${VER}-source - -# Configure -cd install -cmake ../src \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ - -DENABLE_MPI=1 - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/cmake/ConfigUser.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/cmake/ConfigUser.cmake (revision 24918) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/cmake/ConfigUser.cmake (revision 24919) @@ -136,5 +136,5 @@ # Set location of NetCDF (can be root directory, path to header file or path # to nc-config) [auto]: -set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install") +set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") # Set location of GDAL (can be root directory, path to header file or path to Index: /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/cmake/ConfigUser.static.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/cmake/ConfigUser.static.cmake (revision 24919) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/cmake/ConfigUser.static.cmake (revision 24919) @@ -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/linux/static/cmake/modules/FindGSHHG.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/static/cmake/modules/FindGSHHG.cmake (revision 24919) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6.0/linux/static/cmake/modules/FindGSHHG.cmake (revision 24919) @@ -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: sm/trunk-jpl/externalpackages/gmt/configs/ConfigUser.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/ConfigUser.cmake (revision 24918) +++ (revision ) @@ -1,240 +1,0 @@ -# -# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ -# -# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe -# 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: gmt.soest.hawaii.edu -# ---------------------------------------------------------------------------- - -# 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 svn:ignore property) -# -# 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. -# ============================================================================ - -# 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) [TRUE]: -#set (GMT_INSTALL_RELOCATABLE FALSE) - -# ============================================================================ -# 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${GMT_INSTALL_NAME_SUFFIX}/man]: -#set (GMT_MANDIR "share/doc/gmt/man") - -# Install documentation files from this external location instead of creating -# new PDF and HTML documents from scratch [${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 [${GMT_SOURCE_DIR}/man_release]: -#set (GMT_INSTALL_EXTERNAL_MAN OFF) - -## -## Section 2: Build dependencies (should only be needed if CMake cannot -## automatically detect the rights version or path.) -## - -# Set path to GSHHG Shoreline Database [auto]: -set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") - -# Copy GSHHG files to $/coast [FALSE]: -#set (COPY_GSHHG TRUE) - -# Set path to DCW Digital Chart of the World for GMT [auto]: -#set (DCW_ROOT "$ENV{ISSM_DIR}/externalpackages/dcw/install") - -# Copy DCW files to $/dcw [FALSE]: -#set (COPY_DCW TRUE) - -# Set location of NetCDF (can be root directory, path to header file or path -# to nc-config) [auto]: -set (NETCDF_ROOT "$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") - -# 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 "zlib_install_prefix") - -## -## 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) - -# 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): -#set (BUILD_SHARED_LIBS TRUE) - -# Build GMT shared lib with supplemental modules [TRUE]: -#set (BUILD_SUPPLEMENTS TRUE) - -## -## 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) -# Number of parallel test jobs with "make check": -#set (N_TEST_JOBS 4) - -# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without -# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required -# for testing [OFF]: -#set (SUPPORT_EXEC_IN_BINARY_DIR ON) - -# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes -# that link against the full gmt libs (not just the API; for building codes -# that only need the GMT API, see the gmtextension project). -#set (EXTRA_BUILD_DIRS apidemo) - -# Directory in which to install the release sources per default -# [${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: -#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 ${CMAKE_C_FLAGS}") # extra warnings -#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols -#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables -#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies - -# -# System specific tweaks -# - -# This is for GCC on Solaris to avoid "relocations remain against allocatable -# but non-writable sections" problems: -#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) - -# This may be needed to enable strdup and extended math functions with GCC and -# Suncc on Solaris: -#set (CMAKE_C_FLAGS "${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) -#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) - -# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: sm/trunk-jpl/externalpackages/gmt/configs/ConfigUser.cmake-static =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/ConfigUser.cmake-static (revision 24918) +++ (revision ) @@ -1,240 +1,0 @@ -# -# $Id: ConfigUserTemplate.cmake 12904 2014-02-17 20:52:35Z fwobbe $ -# -# Copyright (c) 1991-2014 by P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis and F. Wobbe -# 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: gmt.soest.hawaii.edu -# ---------------------------------------------------------------------------- - -# 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 svn:ignore property) -# -# 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. -# ============================================================================ - -# 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) [TRUE]: -#set (GMT_INSTALL_RELOCATABLE FALSE) - -# ============================================================================ -# 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${GMT_INSTALL_NAME_SUFFIX}/man]: -#set (GMT_MANDIR "share/doc/gmt/man") - -# Install documentation files from this external location instead of creating -# new PDF and HTML documents from scratch [${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 [${GMT_SOURCE_DIR}/man_release]: -#set (GMT_INSTALL_EXTERNAL_MAN OFF) - -## -## Section 2: Build dependencies (should only be needed if CMake cannot -## automatically detect the rights version or path.) -## - -# Set path to GSHHG Shoreline Database [auto]: -set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") - -# Copy GSHHG files to $/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 $/dcw [FALSE]: -#set (COPY_DCW TRUE) - -# Set location of NetCDF (can be root directory, path to header file or path -# to nc-config) [auto]: -set (NETCDF_ROOT "$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") - -# 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 "zlib_install_prefix") - -## -## 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) - -# 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): -set (BUILD_SHARED_LIBS FALSE) - -# Build GMT shared lib with supplemental modules [TRUE]: -#set (BUILD_SUPPLEMENTS 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) -# Number of parallel test jobs with "make check": -#set (N_TEST_JOBS 4) - -# Enable this option to run GMT programs from within ${GMT_BINARY_DIR} without -# installing or setting GMT_SHAREDIR and GMT_USERDIR first. This is required -# for testing [OFF]: -#set (SUPPORT_EXEC_IN_BINARY_DIR ON) - -# List extra sub-dirs of 'src' with a CMakeList.txt to build non-module codes -# that link against the full gmt libs (not just the API; for building codes -# that only need the GMT API, see the gmtextension project). -#set (EXTRA_BUILD_DIRS apidemo) - -# Directory in which to install the release sources per default -# [${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: -#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 ${CMAKE_C_FLAGS}") # extra warnings -#set (CMAKE_C_FLAGS_DEBUG -ggdb3) # gdb debugging symbols -#set (CMAKE_C_FLAGS_RELEASE "-ggdb3 -O2 -Wuninitialized") # check uninitialized variables -#set (CMAKE_LINK_DEPENDS_DEBUG_MODE TRUE) # debug link dependencies - -# -# System specific tweaks -# - -# This is for GCC on Solaris to avoid "relocations remain against allocatable -# but non-writable sections" problems: -#set (USER_GMTLIB_LINK_FLAGS -mimpure-text) - -# This may be needed to enable strdup and extended math functions with GCC and -# Suncc on Solaris: -#set (CMAKE_C_FLAGS "${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) -#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) - -# vim: textwidth=78 noexpandtab tabstop=2 softtabstop=2 shiftwidth=2 Index: sm/trunk-jpl/externalpackages/gmt/install-5.1-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-5.1-linux.sh (revision 24918) +++ (revision ) @@ -1,40 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="5.1.1" - -# 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 source customizations -cp configs/5.1/linux/cmake/ConfigUser.cmake src/cmake - -# Configure -cd src -mkdir build -cd build -cmake .. - -# Install -if [ $# -eq 0 ]; then - make install -else - make -j $1 install -fi - -# Return to initial directory -cd ../.. Index: /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux-static.sh (revision 24919) @@ -0,0 +1,77 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="6.0.0" + +PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +BLASLAPACK_ROOT="${PETSC_ROOT}" +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" +GDAL_ROOT="${ISSM_DIR}/externalpackages/gdal/install" +HDF5_ROOT="${PETSC_ROOT}" +NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" +PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" +ZLIB_ROOT="${PETSC_ROOT}" + +GDAL_LIBRARY="${GDAL_ROOT}/lib/libgdal.a;/usr/lib/x86_64-linux-gnu/libcrypto.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 adding libmpicxx as, otherwise, various symbols in libgdal are undefined (compiled with mpicxx) +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` + +# 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/linux/cmake/ConfigUser.static.cmake ./src/cmake/ConfigUser.cmake +cp ./configs/6.0/linux/static/cmake/modules/FindGSHHG.cmake ./src/cmake/modules + +# Configure +cd src +mkdir build +cd build + +# NOTE: +# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake +# that, ostensibly, allows for supplying the path to curl when it is in a +# non-standard location. That said, newer versions of CMake will ignore said +# variable and instead try to find curl itself. Passing in the two options +# below overrides this behavior. +# - The CMake modules used to find and probe the BLAS and LAPACK libraries do +# not seem to handle the situation where BLAS_LIBRARY and LAPACK_LIBRARY are +# set but we are working with static libraries +# (see customized ConfigUser.static.cmake). Using BLAS_LIBRARIES and +# LAPACK_LIBRARIES is a workaround. +# +cmake \ + -DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;/usr/lib/x86_64-linux-gnu/libgfortran.so" \ + -DCURL_LIBRARY="${CURL_ROOT}/lib" \ + -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \ + -DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;/usr/lib/x86_64-linux-gnu/libgfortran.so" \ + -DGDAL_LIBRARY="${GDAL_LIBRARY}" \ + -DNETCDF_LIBRARY="${NETCDF_LIBRARY}" \ + .. + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/gmt/install-6.0-linux.sh (revision 24919) @@ -3,11 +3,13 @@ -## Environment -# -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" - ## Constants # VER="6.0.0" + +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" + +# Environment +# +export CC=mpicc # Download source @@ -33,9 +35,11 @@ cd build -# NOTE: There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake -# that, ostensibly, allows for supplying the path to curl when it is in a -# a non-standard location. That said, newer versions of CMake will -# ignore said variable and instead try to find curl itself. Passing in -# the two options below overrides this behavior. +# NOTE: +# - There is a CMake variable named CURL_ROOT in src/cmake/ConfigUser.cmake +# that, ostensibly, allows for supplying the path to curl when it is in a +# non-standard location. That said, newer versions of CMake will ignore said +# variable and instead try to find curl itself. Passing in the two options +# below overrides this behavior. +# cmake \ -DCURL_LIBRARY="${CURL_ROOT}/lib" \ Index: sm/trunk-jpl/externalpackages/gmt/install-jenkins.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-jenkins.sh (revision 24918) +++ (revision ) @@ -1,32 +1,0 @@ -#!/bin/bash -set -eu - -#Erase install -rm -rf install src gmt - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gmt-5.1.1.tar.gz' 'gmt-5.1.1.tar.gz' - -#install directory -mkdir src -tar -zxvf gmt-5.1.1.tar.gz -mv gmt-5.1.1/* src -rm -rf gmt-5.1.1 - -#configure: -cp configs/ConfigUser.cmake-jenkins ./src/cmake/ConfigUser.cmake - -cd src -mkdir build -cd build -cmake ../ - -#compile -if [ $# -eq 0 ]; then - make install -else - make -j $1 install -fi - -#come back: -cd ../../ Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 24919) @@ -0,0 +1,70 @@ +#!/bin/bash +set -eu + + +# Dependencies +# - MPI implementation (for parallel I/O support) +# - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) +# - zlib (1.2.5 or later, for netCDF-4 compression) +# - curl (7.18.0 or later, for DAP remote access client support) +# +# For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# + +# NOTE: +# - Certain configuration tests fail if libraries are not supplied explicitly + +# Constants +# +VER="4.7.2" +CURL_ROOT="${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${ZLIB_ROOT}/include" +export LIBS="${CURL_ROOT}/lib/libcurl.a ${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a ${ZLIB_ROOT}/lib/libz.a /usr/lib/x86_64-linux-gnu/libssl.a /usr/lib/x86_64-linux-gnu/libcrypto.a -L/usr/lib/x86_64-linux-gnu -ldl" + +# Download source +$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-dependency-tracking \ + --disable-shared \ + --enable-parallel-tests \ + --disable-filter-testing \ + --disable-dap-remote-tests \ + --disable-doxygen + +# Compile and install +if [ $# -eq 0 ]; then + make + make check + make install +else + make -j $1 + make -j $1 check + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 24919) @@ -0,0 +1,68 @@ +#!/bin/bash +set -eu + + +# Dependencies +# - MPI implementation (for parallel I/O support) +# - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) +# - zlib (1.2.5 or later, for netCDF-4 compression) +# - curl (7.18.0 or later, for DAP remote access client support) +# +# For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# + +# NOTE: +# - Certain configuration tests fail if libraries are not supplied explicitly + +# Constants +# +VER="4.7.2" +CURL_ROOT="${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${ZLIB_ROOT}/include" +export LIBS="${CURL_ROOT}/lib/libcurl.a ${HDF5_ROOT}/lib/libhdf5_hl.a ${HDF5_ROOT}/lib/libhdf5.a ${ZLIB_ROOT}/lib/libz.a /usr/lib/x86_64-linux-gnu/libssl.a /usr/lib/x86_64-linux-gnu/libcrypto.a -L/usr/lib/x86_64-linux-gnu -ldl" + +# Download source +$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-dependency-tracking \ + --enable-fast-install \ + --disable-testsets \ + --disable-examples \ + --disable-shared \ + --disable-doxygen + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi + +# Return to initial directory +cd .. Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 24919) @@ -11,17 +11,20 @@ # For most ISSM installations, only hdf5 will be necessary # +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# # Constants # VER="4.7.2" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" # Environment # export CC=mpicc -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh (revision 24919) @@ -11,4 +11,7 @@ # For most ISSM installations, only hdf5 will be necessary # +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# # Constants @@ -16,12 +19,12 @@ VER="4.7.2" CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" # Environment # export CC=mpicc -export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include" -export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -43,4 +46,6 @@ ./configure \ --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ --disable-doxygen Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh (revision 24919) @@ -4,4 +4,5 @@ # Dependencies +# - MPI implementation (for parallel I/O support) # - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) # - zlib (1.2.5 or later, for netCDF-4 compression) @@ -10,4 +11,7 @@ # For most ISSM installations, only hdf5 will be necessary # +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building +# # Constants @@ -15,11 +19,11 @@ VER="4.7.2" CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/hdf5/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install" +HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" # Environment # -export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include" -export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -41,4 +45,6 @@ ./configure \ --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ --disable-doxygen Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh (revision 24919) @@ -4,4 +4,5 @@ # Dependencies +# - MPI implementation (for parallel I/O support) # - hdf5 (1.8.9 / 1.10.1 or later, for netCDF-4 support) # - zlib (1.2.5 or later, for netCDF-4 compression) @@ -9,4 +10,7 @@ # # For most ISSM installations, only hdf5 will be necessary +# +# Sources: +# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building # @@ -20,6 +24,6 @@ # Environment # -export CPPFLAGS="-I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include -I${CURL_ROOT}/include" -export LDFLAGS="-L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib -L${CURL_ROOT}/lib" +export CPPFLAGS="-I${CURL_ROOT}/include -I${HDF5_ROOT}/include -I${ZLIB_ROOT}/include" +export LDFLAGS="-L${CURL_ROOT}/lib -L${HDF5_ROOT}/lib -L${ZLIB_ROOT}/lib" # Download source @@ -41,4 +45,6 @@ ./configure \ --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ --disable-doxygen Index: sm/trunk-jpl/externalpackages/netcdf/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install.sh (revision 24918) +++ (revision ) @@ -1,30 +1,0 @@ -#!/bin/bash -set -eu -#you need hdf5 compiled - -#Some cleanup -rm -rf src install netcdf-4.3.2 -mkdir install src - -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/netcdf-4.3.2.tar.gz" "netcdf-4.3.2.tar.gz" - -#Untar -tar -zxvf netcdf-4.3.2.tar.gz - -#Move netcdf to install directory -rm -rf src/* -mv netcdf-4.3.2/* src/ -rm -rf netcdf-4.3.2 - -#Configure and compile -cd src -./configure \ - --prefix="$ISSM_DIR/externalpackages/netcdf/install" \ - --disable-doxygen -if [ $# -eq 0 ]; then - make -else - make -j $1 -fi -make install Index: /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-solid_earth-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-solid_earth-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-solid_earth-static.sh (revision 24919) @@ -0,0 +1,54 @@ +#!/bin/bash +set -eu + + +## Constants +# +VER="3.12.3" + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" + +# Unpack source +tar -zxvf petsc-${VER}.tar.gz + +# Cleanup +rm -rf install src +mkdir install src + +# Move source to 'src' directory +mv petsc-${VER}/* src/ +rm -rf petsc-${VER} + +# Configure +# +# NOTE: Cannot use --with-fpic option when compiling static libs, +# +# Cannot determine compiler PIC flags if shared libraries is turned off +# Either run using --with-shared-libraries or --with-pic=0 and supply the +# compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS +# +cd src +./config/configure.py \ + --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ + --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --with-shared-libraries=0 \ + --CFLAGS="-fPIC" \ + --CXXFLAGS="-fPIC" \ + --FFLAGS="-fPIC" \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --download-fblaslapack=1 \ + --download-mpich=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-scalapack=1 \ + --download-mumps=1 \ + --download-zlib=1 \ + --download-hdf5=1 + +# Compile and install +make +make install Index: /issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh (revision 24919) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="6.2.1" + +## Environnment +# +export CC=mpicc +export CXX=mpicxx +# NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently +# requires, +# +# SQLITE3_LIBS="-lsqlite3". +# +# On Ubuntu Linux, install the SQLite3 binary, libraries and headers +# with, +# +# `apt-get install sqlite3 libsqlite3-dev` +# +export SQLITE3_LIBS="-lsqlite3" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/proj-${VER}.tar.gz" "proj-${VER}.tar.gz" + +# Unpack source +tar -zxvf proj-$VER.tar.gz + +# Move source into 'src' directory +mv proj-$VER/* src +rm -rf proj-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-shared + +# Compile and install +if [ $# -eq 0 ]; then + make + make check + make install +else + make -j $1 + make -j $1 check + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh (revision 24919) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh (revision 24919) @@ -0,0 +1,54 @@ +#!/bin/bash +set -eu + + +# Constants +# +VER="6.2.1" + +## Environnment +# +export CC=mpicc +export CXX=mpicxx +# NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently +# requires, +# +# SQLITE3_LIBS="-lsqlite3". +# +# On Ubuntu Linux, install the SQLite3 binary, libraries and headers +# with, +# +# `apt-get install sqlite3 libsqlite3-dev` +# +export SQLITE3_LIBS="-lsqlite3" + +# Cleanup +rm -rf install src +mkdir install src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "http://issm.jpl.nasa.gov/files/externalpackages/proj-${VER}.tar.gz" "proj-${VER}.tar.gz" + +# Unpack source +tar -zxvf proj-$VER.tar.gz + +# Move source into 'src' directory +mv proj-$VER/* src +rm -rf proj-$VER + +# Configure +cd src +./configure \ + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install \ + --disable-shared + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh (revision 24919) @@ -9,5 +9,6 @@ ## Environnment # - +export CC=mpicc +export CXX=mpicxx # NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently # requires, @@ -39,5 +40,7 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install # Compile and install Index: /issm/trunk-jpl/externalpackages/proj/install-6.2.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2.sh (revision 24918) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2.sh (revision 24919) @@ -9,5 +9,6 @@ ## Environnment # - +export CC=mpicc +export CXX=mpicxx # NOTE: On macOS, SQLite3 should be installed by default, but PROJ currently # requires, @@ -39,5 +40,7 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" + --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --disable-dependency-tracking \ + --enable-fast-install # Compile and install Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries (revision 24918) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries (revision 24919) @@ -63,5 +63,5 @@ # compilation. # -NUMCPUS_INSTALL=1 +NUMCPUS_INSTALL=8 # Number of CPUs used in the nightly runs Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-solid_earth (revision 24919) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-solid_earth (revision 24919) @@ -0,0 +1,85 @@ +#--------------------# +# ISSM Configuration # +#--------------------# + +MATLAB_PATH="/usr/local/MATLAB/R2019b" + +# NOTE: +# - We can disable dependency tracking in the Autotools because the binaries +# should always be a one-time build. +# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is +# copied by packaging script. +# +ISSM_CONFIG='\ + --prefix="${ISSM_DIR}" \ + --enable-standalone-executables \ + --enable-standalone-modules \ + --enable-standalone-libraries \ + --disable-dependency-tracking \ + --with-numthreads=4 \ + --with-pic \ + --with-matlab-dir=${MATLAB_PATH} \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/usr/local/lib/python2.7/dist-packages/numpy \ + --with-fortran-lib="-L${ISSM_DIR}/lib -lgfortran" \ + --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \ + --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ + --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \ +' + +#-------------------# +# External Packages # +#-------------------# + +EXTERNALPACKAGES=" + autotools install-debian-linux.sh + cmake install.sh + petsc install-3.12-linux-solid_earth-static.sh + boost install-1.72-linux-static.sh + triangle install-linux-static.sh + chaco install.sh + m1qn3 install.sh + semic install.sh + curl install-7.67-static.sh + netcdf install-4.7-parallel-static.sh + proj install-6.2-static.sh + gdal install-3.0-python-netcdf-static.sh + gshhg install.sh + gmt install-6.0-linux-static.sh + gmsh install-4-static.sh + shell2junit install.sh +" + +#---------# +# Testing # +#---------# + +# Test suites +MATLAB_TEST=0 +PYTHON_TEST=0 +JAVASCRIPT_TEST=0 +EXAMPLES_TEST=0 + +# Number of CPUs used in ISSM compilation +# +# NOTE: One is usually safer as some packages are very sensitive to parallel +# compilation. +# +NUMCPUS_INSTALL=8 + +# Number of CPUs used in the nightly runs +NUMCPUS_RUN=1 + +# Nightly run options +# +# See documentation in test/NightlyRun/runme.* for more information. +# +MATLAB_NROPTIONS="" +PYTHON_NROPTIONS="" Index: /issm/trunk-jpl/jenkins/ross-debian_linux-gia =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-gia (revision 24918) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-gia (revision 24919) @@ -36,5 +36,5 @@ triangle install-linux.sh math77 install.sh - gmsh install.sh + gmsh install-4.sh shell2junit install.sh " Index: /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth (revision 24918) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth (revision 24919) @@ -20,4 +20,5 @@ --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \ + --with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \ --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \ @@ -44,5 +45,5 @@ gshhg install.sh gmt install-6.0-linux.sh - gmsh install.sh + gmsh install-4.sh shell2junit install.sh " Index: /issm/trunk-jpl/m4/issm_options.m4 =================================================================== --- /issm/trunk-jpl/m4/issm_options.m4 (revision 24918) +++ /issm/trunk-jpl/m4/issm_options.m4 (revision 24919) @@ -1122,4 +1122,43 @@ AM_CONDITIONAL([MEDIPACK], [test "x${HAVE_MEDIPACK}" == "xyes"]) dnl }}} + dnl HDF5 {{{ + AC_ARG_WITH( + [hdf5-dir], + AS_HELP_STRING([--with-hdf5-dir=DIR], [HDF5 root directory]), + [HDF5_ROOT=${withval}], + [HDF5_ROOT="no"] + ) + AC_MSG_CHECKING(for HDF5 libraries) + if test "x${HDF5_ROOT}" == "xno"; then + HAVE_HDF5=no + else + HAVE_HDF5=yes + if ! test -d "${HDF5_ROOT}"; then + AC_MSG_ERROR([HDF5 directory provided (${HDF5_ROOT}) does not exist!]); + fi + fi + AC_MSG_RESULT([${HAVE_HDF5}]) + + dnl HDF5 libraries and header files + dnl + dnl TODO: Add check for if we need to link to libhdf5_fortran and + dnl libhdf5hl_fortran, if and when necessary. + dnl + if test "x${HAVE_HDF5}" == "xyes"; then + case "${host_os}" in + *cygwin*) + HDF5LIB="-L`cygpath -m ${HDF5_ROOT}` -Wl,libhdf5.lib -Wl,libhdf5_hl.lib" + ;; + *linux*) + HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" + ;; + *darwin*) + HDF5LIB="-L${HDF5_ROOT}/lib -lhdf5 -lhdf5_hl" + ;; + esac + AC_DEFINE([_HAVE_HDF5_], [1], [with HDF5 in ISSM src]) + AC_SUBST([HDF5LIB]) + fi + dnl }}} dnl PETSc{{{ AC_ARG_WITH( @@ -1693,5 +1732,5 @@ HAVE_PLAPACK=no fi - elses + else HAVE_PLAPACK=no fi Index: /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh =================================================================== --- /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 24919) +++ /issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-solid_earth.sh (revision 24919) @@ -0,0 +1,139 @@ +#!/bin/bash + + +## Constants +# +LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself +LIBGFORTRAN_DIST="${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="'benchmark','slr'" +MATLAB_PATH="/usr/local/MATLAB/R2019b" +PACKAGE="ISSM-Solid_Earth" # Name of directory to copy distributable files to +PYTHON_NROPTIONS="--benchmark slr" +TARBALL_NAME="issm-linux-solid_earth" +TARBALL="${TARBALL_NAME}.tar.gz" + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd ${ISSM_DIR} +rm -rf ${PACKAGE} +mkdir ${PACKAGE} + +# Add/modify required binaries +cd ${ISSM_DIR}/bin + +echo "Modifying generic" +cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m +cat generic_static.py | sed -e "s/generic_static/generic/g" > generic.py + +echo "Moving MPICH binaries to bin/" +if [ -f ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/petsc/install/bin/hydra_pmi_proxy . +elif [ -f ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec ]; then + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/mpiexec . + cp ${ISSM_DIR}/externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "MPICH not found" + exit 1 +fi + +# Add/modify required libraries +echo "Moving libgfortran to lib/" +cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null + +# Run tests +echo "Running tests" +cd ${ISSM_DIR}/test/NightlyRun + +# Check that MATLAB tests run +echo "Running MATLAB tests" + +rm matlab.log 2> /dev/null + +# Run MATLAB tests redirecting output to logfile and suppressing output to console +${MATLAB_PATH}/bin/matlab -nojvm -nosplash -r "try, addpath ${ISSM_DIR}/bin ${ISSM_DIR}/lib; runme(${MATLAB_NROPTIONS}); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log &> /dev/null + +# Check that MATLAB did not exit in error +matlabExitCode=`echo $?` +matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab.log | wc -l` + +if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then + echo "----------MATLAB exited in error!----------" + cat matlab.log + echo "-----------End of matlab.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 +fi + +# Check that all MATLAB tests passed +numMatlabTestsFailed=`cat matlab.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numMatlabTestsFailed} -ne 0 ]]; then + echo "One or more MATLAB tests FAILED" + exit 1; +else + echo "All MATLAB tests PASSED" +fi + +# Check that Python tests run +echo "Running Python tests" + +export PATH="${PATH}:${ISSM_DIR}/bin" +export PYTHONPATH="${ISSM_DIR}/src/m/dev" +export PYTHONSTARTUP="${PYTHONPATH}/devpath.py" +export PYTHONUNBUFFERED=1 # We don't want Python to buffer output, otherwise issm.exe output is not captured + +rm python.log 2> /dev/null +./runme.py ${PYTHON_NROPTIONS} &> python.log 2>&1 + +# Check that Python did not exit in error +pythonExitCode=`echo $?` +pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python.log | wc -l` + +if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then + echo "----------Python exited in error!----------" + cat python.log + echo "-----------End of python.log-----------" + + # Clean up execution directory + rm -rf ${ISSM_DIR}/execution/* + + exit 1 +fi + +# Check that all Python tests passed +numPythonTestsFailed=`cat python.log | grep -c -e "FAILED|ERROR"` + +if [[ ${numPythonTestsFailed} -ne 0 ]]; then + echo "One or more Python tests FAILED" + exit 1 +else + echo "All Python tests PASSED" +fi + +# Create tarball +cd ${ISSM_DIR} +rm -f ${TARBALL} +svn cleanup --remove-ignored --remove-unversioned test # Clean up test directory (before copying to package) +echo "Copying assets to package: ${PACKAGE}" +cp -rf bin examples lib scripts test ${PACKAGE}/ +echo "Cleaning up unneeded/unwanted files" +python -m compileall ${PACKAGE}/bin # Precompile all Python scripts to bytecode +rm -f ${PACKAGE}/bin/*.py # Remove all Python scripts +rm -f ${PACKAGE}/bin/generic_static.* # Remove static versions of generic cluster classes +rm -f ${PACKAGE}/lib/*.a # Remove static libraries from package +rm -f ${PACKAGE}/lib/*.la # Remove libtool libraries from package +echo "Creating tarball: ${TARBALL_NAME}" +tar -czf ${TARBALL} ${PACKAGE} +ls -lah ${ISSM_DIR}/${TARBALL} + +echo "Transferring binaries to ISSM Web site" +scp -i ~/.ssh/debian_linux-vm_to_ross ${TARBALL} jenkins@ross.ics.uci.edu:/var/www/html/${TARBALL} + +if [ $? -ne 0 ]; then + echo "FAILED: Manually check connection" + exit 1 +fi Index: /issm/trunk-jpl/src/c/Makefile.am =================================================================== --- /issm/trunk-jpl/src/c/Makefile.am (revision 24918) +++ /issm/trunk-jpl/src/c/Makefile.am (revision 24919) @@ -676,5 +676,5 @@ if !WINDOWS if !STANDALONE_LIBRARIES -libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) +libISSMCore_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) if FORTRAN libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) @@ -770,5 +770,5 @@ #External packages -LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) +LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) if FORTRAN Index: /issm/trunk-jpl/src/m/classes/mesh3dsurface.m =================================================================== --- /issm/trunk-jpl/src/m/classes/mesh3dsurface.m (revision 24918) +++ /issm/trunk-jpl/src/m/classes/mesh3dsurface.m (revision 24919) @@ -93,5 +93,5 @@ md = checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements 3]); if any(~ismember(1:md.mesh.numberofvertices,sort(unique(md.mesh.elements(:))))); - md = checkmessage(md,'orphan nodes have been found. Check the mesh outline'); + md = checkmessage(md,'orphan nodes have been found; check the mesh outline'); end md = checkfield(md,'fieldname','mesh.numberofelements','>',0); Index: /issm/trunk-jpl/src/m/classes/mesh3dsurface.py =================================================================== --- /issm/trunk-jpl/src/m/classes/mesh3dsurface.py (revision 24918) +++ /issm/trunk-jpl/src/m/classes/mesh3dsurface.py (revision 24919) @@ -122,5 +122,5 @@ md = checkfield(md, 'fieldname', 'mesh.elements', 'size', [md.mesh.numberofelements, 3]) if np.any(np.logical_not(np.in1d(np.arange(1, md.mesh.numberofvertices + 1), md.mesh.elements.flat))): - md = checkmessage(md, 'orphan nodes have been found. Check the mesh outline') + md = md.checkmessage('orphan nodes have been found; check the mesh outline') md = checkfield(md, 'fieldname', 'mesh.numberofelements', '>', 0) @@ -129,5 +129,5 @@ if (solution == 'ThermalSolution'): - md = checkmessage(md, 'thermal not supported for 2d mesh') + md = md.checkmessage('thermal not supported for 2d mesh') return md Index: /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m =================================================================== --- /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m (revision 24918) +++ /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m (revision 24919) @@ -1,4 +1,4 @@ function mesh=gmshplanet(varargin) -%GMSHPLANET - mesh generation for a sphere. Very specific code for gmsh. From demo/sphere.geo +%GMSHPLANET - mesh generation for a sphere. Very specific code for gmsh from $ISSM_DIR/src/demos/simple_geo/sphere.geo % % Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): @@ -14,4 +14,25 @@ % md.mesh=gmshplanet('radius',6000,'resolution',100); % md.mesh=gmshplanet('radius',6000,'resolution',100); + + % Get Gmsh version + % + % NOTE: + % - The output of `gmsh -version` does not follow a consistent format + % across major versions. + % - Under Gmsh 3.*, output of `gmsh -info` needs to be explicitly + % redirected to console in order to be grep'ped. + % - May need to modify the regex supplied to `sed` for future Gmsh versions. + % + % TODO: + % - Move this so we can retrieve like we do with + % `IssmConfig(_DAKOTA_VERSION_)`. + % + [status,gmshmajorversion]=system('gmsh -info 2>&1 | grep "Version" | sed -e "s/Version[[:blank:]]*:[[:blank:]]//" | cut -d "." -f1'); + + gmshmajorversion=str2int(gmshmajorversion); + + if ~ismember([3,4],gmshmajorversion), + error(['gmshplanet: Gmsh major version ' gmshmajorversion ' not supported!']); + end %process options @@ -57,19 +78,26 @@ fprintf(fid,'Circle(11) = {4,1,6};\n'); fprintf(fid,'Circle(12) = {6,1,2};\n'); - fprintf(fid,'Line Loop(13) = {2,8,-10};\n'); + + if gmshmajorversion == 3, + curvename='Line Loop'; + elseif gmshmajorversion == 4, + curvename='Curve Loop'; + end + + fprintf(fid,'%s(13) = {2,8,-10};\n',curvename); fprintf(fid,'Surface(14) = {13};\n'); - fprintf(fid,'Line Loop(15) = {10,3,7};\n'); + fprintf(fid,'%s(15) = {10,3,7};\n',curvename); fprintf(fid,'Surface(16) = {15};\n'); - fprintf(fid,'Line Loop(17) = {-8,-9,1};\n'); + fprintf(fid,'%s(17) = {-8,-9,1};\n',curvename); fprintf(fid,'Surface(18) = {17};\n'); - fprintf(fid,'Line Loop(19) = {-11,-2,5};\n'); + fprintf(fid,'%s(19) = {-11,-2,5};\n',curvename); fprintf(fid,'Surface(20) = {19};\n'); - fprintf(fid,'Line Loop(21) = {-5,-12,-1};\n'); + fprintf(fid,'%s(21) = {-5,-12,-1};\n',curvename); fprintf(fid,'Surface(22) = {21};\n'); - fprintf(fid,'Line Loop(23) = {-3,11,6};\n'); + fprintf(fid,'%s(23) = {-3,11,6};\n',curvename); fprintf(fid,'Surface(24) = {23};\n'); - fprintf(fid,'Line Loop(25) = {-7,4,9};\n'); + fprintf(fid,'%s(25) = {-7,4,9};\n',curvename); fprintf(fid,'Surface(26) = {25};\n'); - fprintf(fid,'Line Loop(27) = {-4,12,-6};\n'); + fprintf(fid,'%s(27) = {-4,12,-6};\n',curvename); fprintf(fid,'Surface(28) = {27};\n'); fprintf(fid,'Surface Loop(29) = {28,26,16,14,20,24,22,18};\n'); @@ -115,9 +143,14 @@ end - %call gmsh + % Call gmsh + % + % NOTE: The default format in Gmsh 3 is "msh2". Rather than conditionally + % modifying our parsing scheme for Gmsh 4, for now, we simply set the + % "-format" option. + % if exist(options,'refine'), - system([gmshpath ' -tol 1e-8 -2 sphere.geo -bgm sphere.pos']); + system([gmshpath ' -tol 1e-8 -2 -format msh2 sphere.geo -bgm sphere.pos']); else - system([gmshpath ' -tol 1e-8 -2 sphere.geo']); + system([gmshpath ' -tol 1e-8 -2 -format msh2 sphere.geo']); end Index: /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py (revision 24918) +++ /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py (revision 24919) @@ -1,28 +1,51 @@ +import commands +import subprocess + +import numpy as np + from MatlabFuncs import * -import numpy as np -from numpy import * +from mesh3dsurface import * from pairoptions import * -from mesh3dsurface import * -import subprocess - - -def gmshplanet(* varargin): - #GMSHPLANET - mesh generation for a sphere. Very specific code for gmsh. From demo/sphere.geo - # - # Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): - # - # - radius: radius of the planet in km - # - resolution: resolution in km - # - refine: provide mesh - # - refinemetric: mesh quantity to specify resolution - # - # Returns 'mesh3dsurface' type mesh - # - # Examples: - # md.mesh = gmshplanet('radius', 6000, 'resolution', 100); - # md.mesh = gmshplanet('radius', 6000, 'resolution', 100); + + +def gmshplanet(*varargin): + ''' + GMSHPLANET - mesh generation for a sphere. Very specific code for gmsh from $ISSM_DIR/src/demos/simple_geo/sphere.geo + + Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): + - radius: radius of the planet in km + - resolution: resolution in km + - refine: provide mesh + - refinemetric: mesh quantity to specify resolution + + Returns 'mesh3dsurface' type mesh + + Examples: + md.mesh = gmshplanet('radius', 6000, 'resolution', 100); + md.mesh = gmshplanet('radius', 6000, 'resolution', 100); + ''' + + # Get Gmsh version + # + # NOTE: + # - The output of `gmsh -version` does not follow a consistent format + # across major versions. + # - Under Gmsh 3.*, output of `gmsh -info` needs to be explicitly + # redirected to console in order to be grep'ped. + # - May need to modify the regex supplied to `sed` for future Gmsh versions. + # + # TODO: + # - Move this so we can retrieve like we do with + # `IssmConfig(_DAKOTA_VERSION_)`. + # + gmshmajorversion = commands.getoutput('gmsh -info 2>&1 | grep "Version" | sed -e "s/Version[[:blank:]]*:[[:blank:]]//" | cut -d "." -f1') + + gmshmajorversion = int(gmshmajorversion) + + if gmshmajorversion not in [3, 4]: + raise RuntimeError('gmshplanet: Gmsh major version %s not supported!' % gmshmajorversion) #process options - options = pairoptions(* varargin) + options = pairoptions(*varargin) #options = deleteduplicates(options, 1) @@ -49,5 +72,5 @@ fid.write('Point(3) = {0, radius, 0.0, resolution};\n') fid.write('Circle(1) = {2, 1, 3};\n') - fid.write('Point(4) = { -radius, 0, 0.0, resolution};\n') + fid.write('Point(4) = {-radius, 0, 0.0, resolution};\n') fid.write('Point(5) = {0, -radius, 0.0, resolution};\n') fid.write('Circle(2) = {3, 1, 4};\n') @@ -64,19 +87,25 @@ fid.write('Circle(11) = {4, 1, 6};\n') fid.write('Circle(12) = {6, 1, 2};\n') - fid.write('Line Loop(13) = {2, 8, -10};\n') + + if gmshmajorversion == 3: + curvename = 'Line Loop' + elif gmshmajorversion == 4: + curvename = 'Curve Loop' + + fid.write('%s(13) = {2, 8, -10};\n' % curvename) fid.write('Surface(14) = {13};\n') - fid.write('Line Loop(15) = {10, 3, 7};\n') + fid.write('%s(15) = {10, 3, 7};\n' % curvename) fid.write('Surface(16) = {15};\n') - fid.write('Line Loop(17) = { -8, -9, 1};\n') + fid.write('%s(17) = {-8, -9, 1};\n' % curvename) fid.write('Surface(18) = {17};\n') - fid.write('Line Loop(19) = { -11, -2, 5};\n') + fid.write('%s(19) = {-11, -2, 5};\n' % curvename) fid.write('Surface(20) = {19};\n') - fid.write('Line Loop(21) = { -5, -12, -1};\n') + fid.write('%s(21) = {-5, -12, -1};\n' % curvename) fid.write('Surface(22) = {21};\n') - fid.write('Line Loop(23) = { -3, 11, 6};\n') + fid.write('%s(23) = {-3, 11, 6};\n' % curvename) fid.write('Surface(24) = {23};\n') - fid.write('Line Loop(25) = { -7, 4, 9};\n') + fid.write('%s(25) = {-7, 4, 9};\n' % curvename) fid.write('Surface(26) = {25};\n') - fid.write('Line Loop(27) = { -4, 12, -6};\n') + fid.write('%s(27) = {-4, 12, -6};\n' % curvename) fid.write('Surface(28) = {27};\n') fid.write('Surface Loop(29) = {28, 26, 16, 14, 20, 24, 22, 18};\n') @@ -105,10 +134,14 @@ # }}} - #call gmsh + # Call gmsh + # + # NOTE: The default format in Gmsh 3 is "msh2". Rather than conditionally + # modifying our parsing scheme for Gmsh 4, for now, we simply set the + # "-format" option. + # if options.exist('refine'): - subprocess.call('gmsh -tol 1e-8 -2 sphere.geo -bgm sphere.pos', shell=True) + subprocess.call('gmsh -tol 1e-8 -2 -format msh2 sphere.geo -bgm sphere.pos', shell=True) else: - #call gmsh - subprocess.call('gmsh -tol 1e-8 -2 sphere.geo', shell=True) + subprocess.call('gmsh -tol 1e-8 -2 -format msh2 sphere.geo', shell=True) #import mesh: {{{ @@ -117,15 +150,15 @@ #Get Mesh format A = fid.readline().strip() - if not strcmp(A, '$MeshFormat'): + if A != '$MeshFormat': raise RuntimeError(['Expecting $MeshFormat (', A, ')']) A = fid.readline().split() A = fid.readline().strip() - if not strcmp(A, '$EndMeshFormat'): + if A != '$EndMeshFormat': raise RuntimeError(['Expecting $EndMeshFormat (', A, ')']) #Nodes A = fid.readline().strip() - if not strcmp(A, '$Nodes'): + if A != '$Nodes': raise RuntimeError(['Expecting $Nodes (', A, ')']) @@ -141,10 +174,10 @@ A = fid.readline().strip() - if not strcmp(A, '$EndNodes'): + if A != '$EndNodes': raise RuntimeError(['Expecting $EndNodes (', A, ')']) #Elements A = fid.readline().strip() - if not strcmp(A, '$Elements'): + if A != '$Elements': raise RuntimeError(['Expecting $Elements (', A, ')']) mesh.numberofelements = int(fid.readline().strip()) @@ -155,5 +188,5 @@ mesh.elements = mesh.elements.astype(int) A = fid.readline().strip() - if not strcmp(A, '$EndElements'): + if A != '$EndElements': raise RuntimeError(['Expecting $EndElements (', A, ')']) fid.close() Index: /issm/trunk-jpl/src/wrappers/matlab/Makefile.am =================================================================== --- /issm/trunk-jpl/src/wrappers/matlab/Makefile.am (revision 24918) +++ /issm/trunk-jpl/src/wrappers/matlab/Makefile.am (revision 24919) @@ -130,5 +130,5 @@ # Module sources and dependencies {{{ if !WINDOWS -libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB) +libISSMMatlab_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB) endif @@ -136,123 +136,123 @@ libISSMMatlab_la_LDFLAGS = -static libISSMApi_la_LDFLAGS = -static -deps += $(PETSCLIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) -endif - -if !WINDOWS -libISSMApi_la_LIBADD = $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB) +deps += $(PETSCLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) +endif + +if !WINDOWS +libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MATHLIB) $(MEXLIB) endif BamgConvertMesh_matlab_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp BamgConvertMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgConvertMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +BamgConvertMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) BamgMesher_matlab_la_SOURCES = ../BamgMesher/BamgMesher.cpp BamgMesher_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgMesher_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +BamgMesher_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) BamgTriangulate_matlab_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp BamgTriangulate_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgTriangulate_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +BamgTriangulate_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) if CHACO Chaco_matlab_la_SOURCES = ../Chaco/Chaco.cpp Chaco_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Chaco_matlab_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +Chaco_matlab_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) endif ContourToMesh_matlab_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp ContourToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ContourToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +ContourToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) ContourToNodes_matlab_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp ContourToNodes_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ContourToNodes_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +ContourToNodes_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) CoordTransform_matlab_la_SOURCES = ../CoordTransform/CoordTransform.cpp CoordTransform_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -CoordTransform_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +CoordTransform_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) DistanceToMaskBoundary_matlab_la_SOURCES = ../DistanceToMaskBoundary/DistanceToMaskBoundary.cpp DistanceToMaskBoundary_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +DistanceToMaskBoundary_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) ElementConnectivity_matlab_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp ElementConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ElementConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +ElementConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) ExpToLevelSet_matlab_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp ExpToLevelSet_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ExpToLevelSet_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +ExpToLevelSet_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) ExpSimplify_matlab_la_SOURCES = ../ExpSimplify/ExpSimplify.cpp ExpSimplify_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ExpSimplify_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(NEOPZLIB) +ExpSimplify_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(NEOPZLIB) InterpFromGridToMesh_matlab_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp InterpFromGridToMesh_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +InterpFromGridToMesh_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) InterpFromMesh2d_matlab_la_SOURCES = ../InterpFromMesh2d/InterpFromMesh2d.cpp InterpFromMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +InterpFromMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) InterpFromMeshToGrid_matlab_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp InterpFromMeshToGrid_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +InterpFromMeshToGrid_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) InterpFromMeshToMesh2d_matlab_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp InterpFromMeshToMesh2d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +InterpFromMeshToMesh2d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) InterpFromMeshToMesh3d_matlab_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp InterpFromMeshToMesh3d_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +InterpFromMeshToMesh3d_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) IssmConfig_matlab_la_SOURCES = ../IssmConfig/IssmConfig.cpp IssmConfig_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -IssmConfig_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(MPILIB) $(NEOPZLIB) +IssmConfig_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) Kriging_matlab_la_SOURCES = ../Kriging/Kriging.cpp Kriging_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Kriging_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJLIB) +Kriging_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJLIB) M1qn3_matlab_la_SOURCES = ../M1qn3/M1qn3.cpp M1qn3_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -M1qn3_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(M1QN3LIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +M1qn3_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(M1QN3LIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) MeshPartition_matlab_la_SOURCES = ../MeshPartition/MeshPartition.cpp MeshPartition_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -MeshPartition_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +MeshPartition_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(METISLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) MeshProfileIntersection_matlab_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp MeshProfileIntersection_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +MeshProfileIntersection_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) NodeConnectivity_matlab_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp NodeConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -NodeConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +NodeConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) PointCloudFindNeighbors_matlab_la_SOURCES = ../PointCloudFindNeighbors/PointCloudFindNeighbors.cpp PointCloudFindNeighbors_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +PointCloudFindNeighbors_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) PropagateFlagsFromConnectivity_matlab_la_SOURCES = ../PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.cpp PropagateFlagsFromConnectivity_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +PropagateFlagsFromConnectivity_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) Scotch_matlab_la_SOURCES = ../Scotch/Scotch.cpp Scotch_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Scotch_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(BLASLAPACKLIB) +Scotch_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(BLASLAPACKLIB) ShpRead_matlab_la_SOURCES = ../ShpRead/ShpRead.cpp ShpRead_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +ShpRead_matlab_la_LIBADD = ${deps} $(SHAPELIBLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) Triangle_matlab_la_SOURCES = ../Triangle/Triangle.cpp Triangle_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -Triangle_matlab_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +Triangle_matlab_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) ProcessRifts_matlab_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp ProcessRifts_matlab_la_CXXFLAGS = ${AM_CXXFLAGS} -ProcessRifts_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) -#}}} +ProcessRifts_matlab_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJLIB) +#}}} Index: /issm/trunk-jpl/src/wrappers/python/Makefile.am =================================================================== --- /issm/trunk-jpl/src/wrappers/python/Makefile.am (revision 24918) +++ /issm/trunk-jpl/src/wrappers/python/Makefile.am (revision 24919) @@ -100,86 +100,86 @@ #}}} # Module sources and dependencies {{{ -libISSMPython_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) +libISSMPython_la_LIBADD = ./../../c/libISSMCore.la ./../../c/libISSMModules.la $(PETSCLIB) $(HDF5LIB) $(MPILIB) $(NEOPZLIB) $(MKLLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) if STANDALONE_LIBRARIES libISSMPython_la_LDFLAGS = -static libISSMApi_la_LDFLAGS = -static -deps += $(DAKOTALIB) $(PETSCLIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) +deps += $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(TAOLIB) $(NEOPZLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(TRIANGLELIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) endif -libISSMApi_la_LIBADD = $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) +libISSMApi_la_LIBADD = $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) $(MATHLIB) BamgConvertMesh_python_la_SOURCES = ../BamgConvertMesh/BamgConvertMesh.cpp BamgConvertMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgConvertMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +BamgConvertMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) BamgMesher_python_la_SOURCES = ../BamgMesher/BamgMesher.cpp BamgMesher_python_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgMesher_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +BamgMesher_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) BamgTriangulate_python_la_SOURCES = ../BamgTriangulate/BamgTriangulate.cpp BamgTriangulate_python_la_CXXFLAGS = ${AM_CXXFLAGS} -BamgTriangulate_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +BamgTriangulate_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) if CHACO Chaco_python_la_SOURCES = ../Chaco/Chaco.cpp Chaco_python_la_CXXFLAGS = ${AM_CXXFLAGS} -Chaco_python_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +Chaco_python_la_LIBADD = ${deps} $(CHACOLIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) endif ContourToMesh_python_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp ContourToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS} -ContourToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +ContourToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) ContourToNodes_python_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp ContourToNodes_python_la_CXXFLAGS = ${AM_CXXFLAGS} -ContourToNodes_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +ContourToNodes_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) ElementConnectivity_python_la_SOURCES = ../ElementConnectivity/ElementConnectivity.cpp ElementConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS} -ElementConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +ElementConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) ExpToLevelSet_python_la_SOURCES = ../ExpToLevelSet/ExpToLevelSet.cpp ExpToLevelSet_python_la_CXXFLAGS = ${AM_CXXFLAGS} -ExpToLevelSet_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) $(NEOPZLIB) +ExpToLevelSet_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) $(NEOPZLIB) InterpFromGridToMesh_python_la_SOURCES = ../InterpFromGridToMesh/InterpFromGridToMesh.cpp InterpFromGridToMesh_python_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromGridToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromGridToMesh_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMeshToGrid_python_la_SOURCES = ../InterpFromMeshToGrid/InterpFromMeshToGrid.cpp InterpFromMeshToGrid_python_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMeshToGrid_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMeshToMesh2d_python_la_SOURCES = ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp InterpFromMeshToMesh2d_python_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMeshToMesh2d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) InterpFromMeshToMesh3d_python_la_SOURCES = ../InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.cpp InterpFromMeshToMesh3d_python_la_CXXFLAGS = ${AM_CXXFLAGS} -InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) +InterpFromMeshToMesh3d_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(MULTITHREADINGLIB) $(GSLLIB) $(PROJ4LIB) IssmConfig_python_la_SOURCES = ../IssmConfig/IssmConfig.cpp IssmConfig_python_la_CXXFLAGS = ${AM_CXXFLAGS} -IssmConfig_python_la_LIBADD = ${deps} $(DAKOTALIB) $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) +IssmConfig_python_la_LIBADD = ${deps} $(DAKOTALIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) MeshPartition_python_la_SOURCES = ../MeshPartition/MeshPartition.cpp MeshPartition_python_la_CXXFLAGS = ${AM_CXXFLAGS} -MeshPartition_python_la_LIBADD = ${deps} $(PETSCLIB) $(METISLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +MeshPartition_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(METISLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) MeshProfileIntersection_python_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp MeshProfileIntersection_python_la_CXXFLAGS = ${AM_CXXFLAGS} -MeshProfileIntersection_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +MeshProfileIntersection_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) NodeConnectivity_python_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp NodeConnectivity_python_la_CXXFLAGS = ${AM_CXXFLAGS} -NodeConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +NodeConnectivity_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) Triangle_python_la_SOURCES = ../Triangle/Triangle.cpp Triangle_python_la_CXXFLAGS = ${AM_CXXFLAGS} -Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +Triangle_python_la_LIBADD = ${deps} $(TRIANGLELIB) $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) ProcessRifts_python_la_SOURCES = ../ProcessRifts/ProcessRifts.cpp ProcessRifts_python_la_CXXFLAGS = ${AM_CXXFLAGS} -ProcessRifts_python_la_LIBADD = ${deps} $(PETSCLIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) +ProcessRifts_python_la_LIBADD = ${deps} $(PETSCLIB) $(HDF5LIB) $(BLASLAPACKLIB) $(MPILIB) $(NEOPZLIB) $(GSLLIB) $(PROJ4LIB) #}}} Index: /issm/trunk-jpl/test/NightlyRun/test2003.py =================================================================== --- /issm/trunk-jpl/test/NightlyRun/test2003.py (revision 24918) +++ /issm/trunk-jpl/test/NightlyRun/test2003.py (revision 24919) @@ -19,5 +19,5 @@ md.dsl.global_average_thermosteric_sea_level_change=np.zeros((2, )) md.dsl.sea_surface_height_change_above_geoid=np.zeros((md.mesh.numberofvertices+1, )) -md.dsl.sea_water_pressure_change_at_sea_floor=zeros((md.mesh.numberofvertices+1, )) +md.dsl.sea_water_pressure_change_at_sea_floor=np.zeros((md.mesh.numberofvertices+1, ))