Index: /issm/trunk-jpl/externalpackages/autotools/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/autotools/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/autotools/install.sh (revision 25860) @@ -9,12 +9,14 @@ LIBTOOL_VER="2.4.2" M4_VER="1.4.18" +PREFIX="${ISSM_DIR}/externalpackages/autotools/install" # Set to location where external package should be installed ## Environment # -export PATH="${ISSM_DIR}/externalpackages/autotools/install/bin:$PATH" +export PATH="${PREFIX}/bin:$PATH" # Cleanup -rm -rf install src -mkdir install +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} + # Install m4 @@ -25,5 +27,5 @@ cd src -./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" +./configure --prefix="${PREFIX}" make make install @@ -37,5 +39,5 @@ mv autoconf-${AUTOCONF_VER} src cd src -./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" +./configure --prefix="${PREFIX}" make make install @@ -49,5 +51,5 @@ mv automake-${AUTOMAKE_VER} src cd src -./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" +./configure --prefix="${PREFIX}" make make install @@ -62,5 +64,5 @@ mv libtool-${LIBTOOL_VER} src cd src -./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install" +./configure --prefix="${PREFIX}" make make install Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh (revision 25860) @@ -7,7 +7,5 @@ VER="1_73_0" -## Envrionment -# -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed # Download source @@ -18,9 +16,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source into 'src' directory -mv boost_${VER}/* src/ +mv boost_${VER}/* src rm -rf boost_${VER} @@ -28,5 +26,5 @@ cd src ./bootstrap.sh \ - --prefix="${BOOST_ROOT}/install" \ + --prefix=${PREFIX} \ --with-python=python2.7 Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh (revision 25860) @@ -7,7 +7,5 @@ VER="1_73_0" -## Envrionment -# -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed # Download source @@ -18,9 +16,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source into 'src' directory -mv boost_${VER}/* src/ +mv boost_${VER}/* src rm -rf boost_${VER} @@ -31,5 +29,5 @@ cd src ./bootstrap.sh \ - --prefix="${BOOST_ROOT}/install" \ + --prefix=${PREFIX} \ --with-python=python2.7 Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-linux.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-linux.sh (revision 25860) @@ -7,7 +7,5 @@ VER="1_73_0" -## Envrionment -# -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed # Download source @@ -18,9 +16,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source into 'src' directory -mv boost_${VER}/* src/ +mv boost_${VER}/* src rm -rf boost_${VER} @@ -28,5 +26,5 @@ cd src ./bootstrap.sh \ - --prefix="${BOOST_ROOT}/install" \ + --prefix=${PREFIX} \ --with-python=python2.7 Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh (revision 25860) @@ -7,7 +7,9 @@ VER="1_73_0" +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + ## Environment # -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" +export LDFLAGS="-Wl,-headerpad_max_install_names" # Download source @@ -18,9 +20,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source into 'src' directory -mv boost_${VER}/* src/ +mv boost_${VER}/* src rm -rf boost_${VER} @@ -28,5 +30,5 @@ cd src ./bootstrap.sh \ - --prefix="${BOOST_ROOT}/install" \ + --prefix=${PREFIX} \ --with-python=python2.7 @@ -41,3 +43,3 @@ # TODO: Reconfigure so that dynamic libraries are not compiled at all # -rm -f $(find ${BOOST_ROOT}/install/lib -name *.dylib) +rm -f $(find ${PREFIX}/lib -name *.dylib) Index: /issm/trunk-jpl/externalpackages/boost/install-1.7-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.7-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/boost/install-1.7-mac.sh (revision 25860) @@ -7,7 +7,8 @@ VER="1_73_0" +PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed + ## Environment # -export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost" export LDFLAGS="-Wl,-headerpad_max_install_names" @@ -19,9 +20,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source into 'src' directory -mv boost_${VER}/* src/ +mv boost_${VER}/* src rm -rf boost_${VER} @@ -29,5 +30,5 @@ cd src ./bootstrap.sh \ - --prefix=${BOOST_ROOT}/install \ + --prefix=${PREFIX} \ --with-python=python2.7 @@ -49,6 +50,6 @@ # patching it after the fact with install_name_tool is not necessary. # -cd ${BOOST_ROOT}/install/lib +cd ${PREFIX}/lib for name in *.dylib; do - install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name} 2>/dev/null + install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null done Index: /issm/trunk-jpl/externalpackages/chaco/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/chaco/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/chaco/install.sh (revision 25860) @@ -10,5 +10,5 @@ # Cleanup -rm -rf ${PREFIX} src Chaco-${VER} +rm -rf ${PREFIX} src mkdir -p ${PREFIX} src Index: /issm/trunk-jpl/externalpackages/cmake/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/cmake/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/cmake/install.sh (revision 25860) @@ -5,5 +5,7 @@ ## Constants # -VER="3.16.2" +VER="3.19.1" + +PREFIX="${ISSM_DIR}/externalpackages/cmake/install" # Set to location where external package should be installed # Download source @@ -14,15 +16,15 @@ # Cleanup -rm -rf install +rm -rf ${PREFIX} -# Move source into 'install' directory -mv cmake-${VER} install +# Move source into target directory +mv cmake-${VER} ${PREFIX} # Configure -cd install +cd ${PREFIX} #./bootstrap \ -# --prefix=${ISSM_DIR}/externalpackages/cmake/install # Breaks on ronne +# --prefix=${PREFIX} # Breaks on ronne ./configure \ - --prefix=${ISSM_DIR}/externalpackages/cmake/install + --prefix=${PREFIX} # Compile Index: /issm/trunk-jpl/externalpackages/curl/install-7-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7-linux-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/curl/install-7-linux-static.sh (revision 25860) @@ -7,22 +7,24 @@ VER="7.73.0" +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + # 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 +tar -zxvf curl-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER +mv curl-${VER}/* src +rm -rf curl-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --prefix="${PREFIX}" \ --disable-shared \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/curl/install-7-linux-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7-linux-with_tests.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/curl/install-7-linux-with_tests.sh (revision 25860) @@ -7,22 +7,24 @@ VER="7.73.0" +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + # 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 +tar -zxvf curl-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER +mv curl-${VER}/* src +rm -rf curl-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/curl/install-7-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7-linux.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/curl/install-7-linux.sh (revision 25860) @@ -7,22 +7,24 @@ VER="7.73.0" +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed + # 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 +tar -zxvf curl-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER +mv curl-${VER}/* src +rm -rf curl-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/curl/install-7-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7-mac-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/curl/install-7-mac-static.sh (revision 25860) @@ -6,4 +6,6 @@ # VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed ## Environment @@ -15,18 +17,18 @@ # Unpack source -tar -zxvf curl-$VER.tar.gz +tar -zxvf curl-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER +mv curl-${VER}/* src +rm -rf curl-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --prefix="${PREFIX}" \ --disable-shared \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/curl/install-7-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/curl/install-7-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/curl/install-7-mac.sh (revision 25860) @@ -6,4 +6,6 @@ # VER="7.73.0" + +PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed ## Environment @@ -15,18 +17,18 @@ # Unpack source -tar -zxvf curl-$VER.tar.gz +tar -zxvf curl-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv curl-$VER/* src -rm -rf curl-$VER +mv curl-${VER}/* src +rm -rf curl-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/curl/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh (revision 25860) @@ -3,23 +3,22 @@ -# Constants +## Constants # -DAK_ROOT=${ISSM_DIR}/externalpackages/dakota VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed ## Environment # -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it -export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version) -export DAK_BUILD=${DAK_ROOT}/build -export DAK_INSTALL=${DAK_ROOT}/install -export DAK_SRC=${DAK_ROOT}/src -export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup -rm -rf build install src -mkdir build install src +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} # Download source @@ -30,5 +29,5 @@ # Move source to 'src' directory -mv dakota-${VER}.0.src/* src +mv dakota-${VER}.0.src/* ${DAK_SRC} rm -rf dakota-${VER}.0.src Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh (revision 25860) @@ -3,24 +3,23 @@ -# Constants +## Constants # -DAK_ROOT=${ISSM_DIR}/externalpackages/dakota VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed ## Environment # -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it -export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version) #export CXXFLAGS='-std=c++11' -export DAK_BUILD=${DAK_ROOT}/build -export DAK_INSTALL=${DAK_ROOT}/install -export DAK_SRC=${DAK_ROOT}/src -export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup -rm -rf build install src -mkdir build install src +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} # Download source @@ -31,5 +30,5 @@ # Move source to 'src' directory -mv dakota-${VER}.0.src/* src +mv dakota-${VER}.0.src/* ${DAK_SRC} rm -rf dakota-${VER}.0.src Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac-static.sh (revision 25860) @@ -3,8 +3,9 @@ -# Constants +## Constants # -DAK_ROOT=${ISSM_DIR}/externalpackages/dakota VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed ## Environment @@ -17,6 +18,7 @@ # # TODO: -# - Test if -static-libgfortran flag will avoid all of this. -# - Otherwise, refactor this to work with other gfortran installations. +# - Move this to etc/environment.sh +# - Test if -static-libgfortran flag will avoid all of this +# - Otherwise, refactor this to work with other gfortran installations # LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) @@ -24,15 +26,13 @@ LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it -export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install -export DAK_BUILD=${DAK_ROOT}/build -export DAK_INSTALL=${DAK_ROOT}/install -export DAK_SRC=${DAK_ROOT}/src -export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup -rm -rf build install src -mkdir build install src +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} # Download source @@ -43,5 +43,5 @@ # Move source to 'src' directory -mv dakota-${VER}.0.src/* src +mv dakota-${VER}.0.src/* ${DAK_SRC} rm -rf dakota-${VER}.0.src Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-mac.sh (revision 25860) @@ -3,8 +3,9 @@ -# Constants +## Constants # -DAK_ROOT=${ISSM_DIR}/externalpackages/dakota VER="6.2" + +PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed ## Environment @@ -16,18 +17,19 @@ # returning one that is installed via package manager. # +# TODO: +# - Move this to etc/environment.sh +# LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1) LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*} -export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it -export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install -export DAK_BUILD=${DAK_ROOT}/build -export DAK_INSTALL=${DAK_ROOT}/install -export DAK_SRC=${DAK_ROOT}/src -export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install -export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it +export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS +export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS +export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS +export LAPACK_LIBS="-L${LAPACK_ROOT}/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it # Cleanup -rm -rf build install src -mkdir build install src +rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} +mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC} # Download source @@ -38,5 +40,5 @@ # Move source to 'src' directory -mv dakota-${VER}.0.src/* src +mv dakota-${VER}.0.src/* ${DAK_SRC} rm -rf dakota-${VER}.0.src Index: sm/trunk-jpl/externalpackages/gdal/install-3-netcdf-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-netcdf-static.sh (revision 25859) +++ (revision ) @@ -1,63 +1,0 @@ -#!/bin/bash -set -eu - - -# TODO -# - May want to supply path to Python instead of, effectively, using result of -# `which python` -# - -## Constants -# -VER="3.1.1" - -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -## Environment -# -export CC=mpicc -export CXX=mpicxx -export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time -export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time -export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) - -# 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="${PREFIX}" \ - --enable-fast-install \ - --disable-shared \ - --without-ld-shared \ - --enable-static \ - --with-pic \ - --with-libz="${ZLIB_ROOT}" \ - --with-hdf5="${HDF5_ROOT}" \ - --with-netcdf="${NETCDF_ROOT}" \ - --with-proj="${PROJ_ROOT}" \ - --with-pg=no - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk-jpl/externalpackages/gdal/install-3-netcdf.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-netcdf.sh (revision 25859) +++ (revision ) @@ -1,49 +1,0 @@ -#!/bin/bash -set -eu - - -# Constants -# -VER="3.1.1" - -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -## Environment -# -export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) - -# 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="${PREFIX}" \ - --enable-fast-install \ - --with-libz="${ZLIB_ROOT}" \ - --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 $1 install -fi Index: sm/trunk-jpl/externalpackages/gdal/install-3-python-netcdf-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-python-netcdf-static.sh (revision 25859) +++ (revision ) @@ -1,64 +1,0 @@ -#!/bin/bash -set -eu - - -# TODO -# - May want to supply path to Python instead of, effectively, using result of -# `which python` -# - -## Constants -# -VER="3.1.1" - -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -## Environment -# -export CC=mpicc -export CXX=mpicxx -export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time -export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time -export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) - -# Cleanup -rm -rf install src -mkdir install src - -# Download source -$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-$VER - -# Configure -cd src -./configure \ - --prefix="${PREFIX}" \ - --enable-fast-install \ - --disable-shared \ - --without-ld-shared \ - --enable-static \ - --with-pic \ - --with-python \ - --with-libz="${ZLIB_ROOT}" \ - --with-hdf5="${HDF5_ROOT}" \ - --with-netcdf="${NETCDF_ROOT}" \ - --with-proj="${PROJ_ROOT}" \ - --with-pg=no - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk-jpl/externalpackages/gdal/install-3-python-netcdf.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-python-netcdf.sh (revision 25859) +++ (revision ) @@ -1,54 +1,0 @@ -#!/bin/bash -set -eu - - -## TODO -# - May want to supply path to Python instead of, effectively, using result of `which python` -# - -## Constants -# -VER="3.1.1" - -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -## Environment -# -export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build) - -# 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="${PREFIX}" \ - --enable-fast-install \ - --with-python \ - --with-libz="${ZLIB_ROOT}" \ - --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 $1 install -fi Index: /issm/trunk-jpl/externalpackages/gdal/install-3-python-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-python-static.sh (revision 25860) +++ /issm/trunk-jpl/externalpackages/gdal/install-3-python-static.sh (revision 25860) @@ -0,0 +1,58 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.1.1" + +## Environment +# +export CC=mpicc +export CXX=mpicxx +export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$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-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --disable-shared \ + --without-ld-shared \ + --enable-static \ + --with-pic \ + --with-python \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" \ + --with-pg=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gdal/install-3-python.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-python.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gdal/install-3-python.sh (revision 25860) @@ -11,13 +11,11 @@ VER="3.1.1" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" - ## Environment # -export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build) +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -25,9 +23,9 @@ # Unpack source -tar -zxvf gdal-$VER.tar.gz +tar -zxvf gdal-${VER}.tar.gz # Move source into 'src' directory -mv gdal-$VER/* src -rm -rf gdal-$VER +mv gdal-${VER}/* src +rm -rf gdal-${VER} # Configure @@ -37,6 +35,7 @@ --enable-fast-install \ --with-python \ - --without-hdf5 \ - --without-netcdf \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ --with-proj="${PROJ_ROOT}" Index: /issm/trunk-jpl/externalpackages/gdal/install-3-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3-static.sh (revision 25860) +++ /issm/trunk-jpl/externalpackages/gdal/install-3-static.sh (revision 25860) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + + +## TODO +# - May want to supply path to Python instead of, effectively, using result of `which python` +# + +## Constants +# +VER="3.1.1" + +## Environment +# +export CC=mpicc +export CXX=mpicxx +export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$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-${VER} + +# Configure +cd src +./configure \ + --prefix="${PREFIX}" \ + --enable-fast-install \ + --disable-shared \ + --without-ld-shared \ + --enable-static \ + --with-pic \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ + --with-proj="${PROJ_ROOT}" \ + --with-pg=no + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gdal/install-3.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gdal/install-3.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gdal/install-3.sh (revision 25860) @@ -3,17 +3,15 @@ -# Constants +## Constants # VER="3.1.1" -PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install" - ## Environment # -export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build; do not need for this configuration, but including it for consistency) +export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # NOTE: Need to export this to properly set destination root for Python libraries on macOS (should not affect Linux build). Set to location where external package should be installed. # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -24,6 +22,6 @@ # Move source into 'src' directory -mv gdal-$VER/* src -rm -rf gdal-$VER +mv gdal-${VER}/* src +rm -rf gdal-${VER} # Configure @@ -32,6 +30,7 @@ --prefix="${PREFIX}" \ --enable-fast-install \ - --without-hdf5 \ - --without-netcdf \ + --with-libz="${ZLIB_ROOT}" \ + --with-hdf5="${HDF5_ROOT}" \ + --with-netcdf="${NETCDF_ROOT}" \ --with-proj="${PROJ_ROOT}" @@ -44,5 +43,2 @@ make -j $1 install fi - -# Return to initial directory -cd .. Index: sm/trunk-jpl/externalpackages/gmsh/install-4-linux-python-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-linux-python-static.sh (revision 25859) +++ (revision ) @@ -1,67 +1,0 @@ -#!/bin/bash -set -eu - - -# TODO: -# - Add support for, -# - BLAS_LAPACK -# - MUMPS -# - NUMPY -# - PETSC4PY -# - PETSC -# (see configs/4/linux/static/CMakeLists.txt) -# - -## Constants -# -VER="4.5.6" - -PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -# 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 - -# Copy customized source and config files to 'src' directory -cp configs/${VER}/static/CMakeLists.txt src - -# Configure -# -# NOTE: -# - Option -DENABLE_FLTK=0 is used because we do not need GUI. -# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG -# movies. -# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not -# importing STEP/IGES files. -# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we -# do not need to support Apple Touch bar. -# -cd install -cmake ../src \ - -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ - -DENABLE_BUILD_LIB=1 \ - -DENABLE_FLTK=0 \ - -DENABLE_MPEG_ENCODE=0 \ - -DENABLE_MPI=1 \ - -DENABLE_OCC=0 \ - -DMETIS_ROOT="${PETSC_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk-jpl/externalpackages/gmsh/install-4-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-linux-static.sh (revision 25859) +++ (revision ) @@ -1,63 +1,0 @@ -#!/bin/bash -set -eu - - -# TODO: -# - Add support for, -# - BLAS_LAPACK -# - MUMPS -# - PETSC -# (see configs/4/linux/static/CMakeLists.txt) -# - -## Constants -# -VER="4.5.6" - -PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -# 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 - -# Copy customized source and config files to 'src' directory -cp configs/${VER}/static/CMakeLists.txt src - -# Configure -# -# NOTE: -# - Option -DENABLE_FLTK=0 is used because we do not need GUI. -# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG -# movies. -# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not -# importing STEP/IGES files. -# -cd install -cmake ../src \ - -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ - -DENABLE_BUILD_LIB=1 \ - -DENABLE_FLTK=0 \ - -DENABLE_MPEG_ENCODE=0 \ - -DENABLE_MPI=1 \ - -DENABLE_OCC=0 \ - -DMETIS_ROOT="${PETSC_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk-jpl/externalpackages/gmsh/install-4-mac-python-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-mac-python-static.sh (revision 25859) +++ (revision ) @@ -1,68 +1,0 @@ -#!/bin/bash -set -eu - - -# TODO: -# - Add support for, -# - BLAS_LAPACK -# - MUMPS -# - NUMPY -# - PETSC4PY -# - PETSC -# (see configs/4/mac/static/CMakeLists.txt) -# - -## Constants -# -VER="4.5.6" - -PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -# 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 - -# Copy customized source and config files to 'src' directory -cp configs/${VER}/mac/static/CMakeLists.txt src - -# Configure -# -# NOTE: -# - Option -DENABLE_FLTK=0 is used because we do not need GUI. -# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG -# movies. -# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not -# importing STEP/IGES files. -# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we -# do not need to support Apple Touch bar. -# -cd install -cmake ../src \ - -DCMAKE_BUILD_TYPE=Release \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ - -DENABLE_BUILD_LIB=1 \ - -DENABLE_FLTK=0 \ - -DENABLE_MPEG_ENCODE=0 \ - -DENABLE_MPI=1 \ - -DENABLE_OCC=0 \ - -DENABLE_TOUCHBAR=0 \ - -DMETIS_ROOT="${PETSC_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: sm/trunk-jpl/externalpackages/gmsh/install-4-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-mac-static.sh (revision 25859) +++ (revision ) @@ -1,65 +1,0 @@ -#!/bin/bash -set -eu - - -# TODO: -# - Add support for, -# - BLAS_LAPACK -# - MUMPS -# - PETSC -# (see configs/4/mac/static/CMakeLists.txt) -# - -## Constants -# -VER="4.5.6" - -PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -# 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 - -# Copy customized source and config files to 'src' directory -cp configs/${VER}/mac/static/CMakeLists.txt src - -# Configure -# -# NOTE: -# - Option -DENABLE_FLTK=0 is used because we do not need GUI. -# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG -# movies. -# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not -# importing STEP/IGES files. -# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we -# do not need to support Apple Touch bar. -# -cd install -cmake ../src \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ - -DENABLE_BUILD_LIB=1 \ - -DENABLE_FLTK=0 \ - -DENABLE_MPEG_ENCODE=0 \ - -DENABLE_MPI=1 \ - -DENABLE_OCC=0 \ - -DENABLE_TOUCHBAR=0 \ - -DMETIS_ROOT="${PETSC_ROOT}" - -# Compile and install -if [ $# -eq 0 ]; then - make - make install -else - make -j $1 - make -j $1 install -fi Index: /issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh (revision 25860) +++ /issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh (revision 25860) @@ -0,0 +1,66 @@ +#!/bin/bash +set -eu + + +# TODO: +# - Add support for, +# - BLAS_LAPACK +# - MUMPS +# - PETSC +# (see configs/4/static/CMakeLists.txt) +# + +## Constants +# +VER="4.5.6" + +PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" + +# Unpack source +tar -xvzf gmsh-${VER}-source.tgz + +# Move source to 'src' directory +mv gmsh-${VER}-source/* src +rm -rf gmsh-${VER}-source + +# Copy customized source and config files to 'src' directory +cp configs/${VER}/static/CMakeLists.txt src + +# Configure +# +# NOTE: +# - Option -DENABLE_FLTK=0 is used because we do not need GUI. +# - Option -DENABLE_MPEG_ENCODE=0 is used because we do not need to record MPEG +# movies. +# - Option -DENABLE_OCC=0 is used because we do not need CAD kernel and are not +# importing STEP/IGES files. +# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we +# do not need to support Apple Touch bar (does not affect compilation on +# Linux). +# +cd src +cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DENABLE_BUILD_LIB=1 \ + -DENABLE_FLTK=0 \ + -DENABLE_MPEG_ENCODE=0 \ + -DENABLE_MPI=1 \ + -DENABLE_OCC=0 \ + -DENABLE_TOUCHBAR=0 \ + -DMETIS_ROOT="${METIS_ROOT}" + +# Compile and install +if [ $# -eq 0 ]; then + make + make install +else + make -j $1 + make -j $1 install +fi Index: /issm/trunk-jpl/externalpackages/gmsh/install-4.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-4.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gmsh/install-4.sh (revision 25860) @@ -2,4 +2,12 @@ set -eu + +# TODO: +# - Add support for, +# - BLAS_LAPACK +# - MUMPS +# - PETSC +# (see configs/4/static/CMakeLists.txt) +# ## Constants @@ -7,14 +15,14 @@ VER="4.5.6" -PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz" -# Untar source +# Unpack source tar -xvzf gmsh-${VER}-source.tgz @@ -32,9 +40,10 @@ # importing STEP/IGES files. # - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we -# do not need to support Apple Touch bar. +# do not need to support Apple Touch bar (does not affect compilation on +# Linux). # -cd install -cmake ../src \ - -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \ +cd src +cmake \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ -DENABLE_BUILD_DYNAMIC=1 \ -DENABLE_BUILD_SHARED=1 \ @@ -44,5 +53,5 @@ -DENABLE_OCC=0 \ -DENABLE_TOUCHBAR=0 \ - -DMETIS_ROOT="${PETSC_ROOT}" + -DMETIS_ROOT="${METIS_ROOT}" # Compile and install Index: sm/trunk-jpl/externalpackages/gmsh/install-mac-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-mac-precompiled.sh (revision 25859) +++ (revision ) @@ -1,23 +1,0 @@ -#!/bin/bash -set -eu - -# Set gmsh version -GMSH_VER="3.0.5" - -# Set tarball name -GMSH_TARBALL_NAME="gmsh-${GMSH_VER}-mac-precompiled" - -# Clean up from previous installation -rm -f $GMSH_TARBALL_NAME.tar.gz -rm -rf install src - -# Download Mac precompiled gmsh from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/${GMSH_TARBALL_NAME}.tar.gz" "${GMSH_TARBALL_NAME}.tar.gz" - -# Untar gmsh -tar -xvzf $GMSH_TARBALL_NAME.tar.gz - -# Copy gmsh to path expected by packager -mkdir install -cp gmsh install -rm gmsh Index: sm/trunk-jpl/externalpackages/gmsh/install-win64-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmsh/install-win64-precompiled.sh (revision 25859) +++ (revision ) @@ -1,24 +1,0 @@ -#!/bin/bash -set -eu - -# Set gmsh version -VER="3.0.5" - -# Set tarball name -TARBALL_NAME="gmsh-${VER}-win64-precompiled" -TARBALL=${TARBALL_NAME}.tar.gz - -# Clean up from previous installation -rm -rf install - -# Download Windows 64-bit precompiled gmsh from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/${TARBALL}" "${TARBALL}" - -# Untar gmsh -tar -xvzf $TARBALL - -# Rename untarred dir -mv $TARBALL_NAME install - -# Clean up -rm -f $TARBALL Index: /issm/trunk-jpl/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake (revision 25859) +++ /issm/trunk-jpl/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake (revision 25860) @@ -39,5 +39,5 @@ # Installation path (usually defaults to /usr/local) [auto]: -set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install") +set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}") # Set install name suffix used for directories and gmt executables @@ -109,5 +109,5 @@ # Set path to GSHHG Shoreline Database [auto]: -set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install") +set (GSHHG_ROOT "$ENV{GSHHG_ROOT}") # Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]: @@ -136,9 +136,9 @@ # Set location of NetCDF (can be root directory, path to header file or path # to nc-config) [auto]: -set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install") +set (NETCDF_ROOT "$ENV{NETCDF_ROOT}") # Set location of GDAL (can be root directory, path to header file or path to # gdal-config) [auto]: -set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install") +set (GDAL_ROOT "$ENV{GDAL_ROOT}") # Set location of PCRE (can be root directory, path to header file or path to @@ -154,5 +154,5 @@ # Set location of ZLIB (can be root directory or path to header file) [auto]: -set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install") +set (ZLIB_ROOT "$ENV{ZLIB_ROOT}") # Set location of CURL (can be root directory or path to header file) [auto]: @@ -167,6 +167,6 @@ # Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically -set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack") -set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas") +set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack") +set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas") ## Index: /issm/trunk-jpl/externalpackages/gmt/install-6-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6-linux-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gmt/install-6-linux-static.sh (revision 25860) @@ -7,10 +7,4 @@ VER="6.0.0" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install" - -BLASLAPACK_ROOT="${PETSC_ROOT}" -HDF5_ROOT="${PETSC_ROOT}" - # Find libgfortran and libgcc so we do not have to hardcode them # @@ -18,4 +12,5 @@ # # TODO: +# - Move this to etc/environment.sh # - Figure out how to find and grep for single result like we do with mdfind # under macOS. @@ -25,6 +20,4 @@ LIBGCC="/usr/lib/gcc/x86_64-linux-gnu/8/libgcc.a" -CURL_INCLUDE_DIRS="${CURL_ROOT}/include" \ -CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a" \ GDAL_EXTRA_LIBS="-lstdc++" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs NETCDF_EXTRA_LIBS="-lm -ldl -lz" # `$NETCDF_ROOT/bin/nc-config --libs` does not report certain dependencies of certain static libraries (see also customized configuration file ./configs/6.0/static/cmake/modules/FindNETCDF.cmake) @@ -33,6 +26,7 @@ # export CC=mpicc -export CURL_INCLUDE_DIRS=${CURL_INCLUDE_DIRS} -export CURL_LIBRARIES=${CURL_LIBRARIES} +export CURL_INCLUDE_DIRS="${CURL_ROOT}/include" +export CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a" +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. # Download source @@ -43,6 +37,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory @@ -70,8 +64,8 @@ # cmake \ - -DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \ -DHDF5_ROOT="${HDF5_ROOT}" \ - -DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ + -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \ -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \ .. Index: /issm/trunk-jpl/externalpackages/gmt/install-6-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6-linux.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gmt/install-6-linux.sh (revision 25860) @@ -7,9 +7,8 @@ VER="6.0.0" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" - # Environment # export CC=mpicc +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. # Download source @@ -20,6 +19,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory Index: /issm/trunk-jpl/externalpackages/gmt/install-6-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-6-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gmt/install-6-mac.sh (revision 25860) @@ -7,9 +7,8 @@ VER="6.0.0" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" - # Environment # export CC=mpicc +export PREFIX="${ISSM_DIR}/externalpackages/gmt/install" # NOTE: Need to export this to be picked up by customized ConfigUser.cmake (see below). Set to location where external package should be installed. # Download source @@ -20,6 +19,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory Index: sm/trunk-jpl/externalpackages/gmt/install-mac-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-mac-precompiled.sh (revision 25859) +++ (revision ) @@ -1,24 +1,0 @@ -#!/bin/bash -set -eu - -# Set gmt version -VER="5.4.4" - -# Set tarball name -TARBALL_NAME="gmt-${VER}-mac-precompiled" -TARBALL=${TARBALL_NAME}.tar.gz - -# Clean up from previous installation -rm -rf install - -# Download Mac precompiled gmsh from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/${TARBALL}" "${TARBALL}" - -# Untar gmt -tar -xvzf $TARBALL - -# Rename untarred dir -mv $TARBALL_NAME install - -# Clean up -rm -f $TARBALL Index: sm/trunk-jpl/externalpackages/gmt/install-win64-precompiled.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gmt/install-win64-precompiled.sh (revision 25859) +++ (revision ) @@ -1,24 +1,0 @@ -#!/bin/bash -set -eu - -# Set gmt version -VER="5.4.4" - -# Set tarball name -TARBALL_NAME="gmt-${VER}-win64-precompiled" -TARBALL=${TARBALL_NAME}.tar.gz - -# Clean up from previous installation -rm -rf install - -# Download Windows 64-bit precompiled gmsh from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/${TARBALL}" "${TARBALL}" - -# Untar gmt -tar -xvzf $TARBALL - -# Rename untarred dir -mv $TARBALL_NAME install - -# Clean up -rm -f $TARBALL Index: /issm/trunk-jpl/externalpackages/gshhg/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gshhg/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gshhg/install.sh (revision 25860) @@ -7,6 +7,9 @@ VER="2.3.4" +PREFIX="${ISSM_DIR}/externalpackages/gshhg/install" # Set to location where external package should be installed + # Cleanup -rm -rf install +rm -rf ${PREFIX} +mkdir -p ${PREFIX} # Download source @@ -17,3 +20,3 @@ # Install -mv gshhg-gmt-${VER} install +mv gshhg-gmt-${VER}/* ${PREFIX} Index: /issm/trunk-jpl/externalpackages/gsl/install-javascript.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gsl/install-javascript.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gsl/install-javascript.sh (revision 25860) @@ -3,10 +3,17 @@ -# TODO: +## TODO: # - Revisit enviroment variables (especially EMCC_CFLAGS) once support for # Fortran has been accomplished. # -# Environment +## Constants +# +VER="1.15" + +PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed + +## Environment +# export CC=emcc export CXX=em++ @@ -17,35 +24,35 @@ # Source Emscripten environment -source $ISSM_DIR/externalpackages/emscripten/install/emsdk_env.sh +source ${EMSCRIPTEN_ROOT}/emsdk_env.sh # Issue with variadic function signatures. #export CFLAGS=-DSTDC_HEADERS -# Cleanup from previous installation -rm -rf src-javascript install-javascript gsl-1.15 -mkdir src-javascript install-javascript +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz' +${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz" -#Untar -tar -zxvf gsl-1.15.tar.gz +# Unpack source +tar -zxvf gsl-${VER}.tar.gz -#Move gsl into src directory -mv gsl-1.15/* src-javascript -rm -rf gsl-1.15 +# Move source to 'src' directory +mv gsl-${VER}/* src +rm -rf gsl-${VER} -#Configure gsl -cd src-javascript - +# Configure +cd src ./configure \ - --prefix="$ISSM_DIR/externalpackages/gsl/install-javascript" \ - --disable-shared + --prefix="${PREFIX}" \ + --disable-shared \ #Compile gsl if [ $# -eq 0 ]; then make + make install else make -j $1 + make -j $1 install fi -make install Index: /issm/trunk-jpl/externalpackages/gsl/install-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gsl/install-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gsl/install-static.sh (revision 25860) @@ -3,12 +3,13 @@ -# Constants +## Constants # -GSL_ROOT=${ISSM_DIR}/externalpackages/gsl VER="1.15" -# Cleanup= -rm -rf install src -mkdir install src +PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -25,5 +26,5 @@ cd src ./configure \ - --prefix="${GSL_ROOT}/install" \ + --prefix="${PREFIX}" \ --disable-shared \ --with-pic Index: /issm/trunk-jpl/externalpackages/gsl/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/gsl/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/gsl/install.sh (revision 25860) @@ -5,10 +5,11 @@ # Constants # -GSL_ROOT=${ISSM_DIR}/externalpackages/gsl VER="1.15" -# Cleanup= -rm -rf install src -mkdir install src +PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -25,5 +26,5 @@ cd src ./configure \ - --prefix="${GSL_ROOT}/install" \ + --prefix="${PREFIX}" \ --disable-static Index: /issm/trunk-jpl/externalpackages/m1qn3/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/m1qn3/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/m1qn3/install.sh (revision 25860) @@ -2,14 +2,24 @@ set -eu -#Some cleanup -rm -rf install src m1qn3-3.3-distrib -mkdir install -#Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/m1qn3-3.3-distrib.tgz' 'm1qn3-3.3-distrib.tgz' +## Constants +# +VER=3.3 -#Untar -tar -xzf m1qn3-3.3-distrib.tgz -mv m1qn3-3.3-distrib src +PREFIX="${ISSM_DIR}/externalpackages/m1qn3/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src + +# Download source +$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m1qn3-${VER}-distrib.tgz" "m1qn3-${VER}-distrib.tgz" + +# Unpack source +tar -xzf m1qn3-${VER}-distrib.tgz + +# Move source to 'src' directory +mv m1qn3-${VER}-distrib/* src +rm -rf m1qn3-${VER}-distrib if which ifort >/dev/null; then @@ -22,5 +32,5 @@ fi -#Compile m1qn3 +# Compile and install cd src/src/ ( @@ -29,5 +39,5 @@ FC=$FC install: libm1qn3.\$(LIB_EXT) - cp libm1qn3.\$(LIB_EXT) ../../install/ + cp libm1qn3.\$(LIB_EXT) ${PREFIX} OBJECTS= m1qn3.o libm1qn3.\$(LIB_EXT): \$(OBJECTS) @@ -42,5 +52,4 @@ make -#compile ddot cd ../blas ( @@ -49,5 +58,5 @@ FC=$FC install: libddot.\$(LIB_EXT) - cp libddot.\$(LIB_EXT) ../../install/ + cp libddot.\$(LIB_EXT) ${PREFIX} OBJECTS= ddot.o libddot.\$(LIB_EXT): \$(OBJECTS) Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh (revision 25860) @@ -8,6 +8,4 @@ # - zlib (1.2.5 or later, for netCDF-4 compression) # - curl (7.18.0 or later, for DAP remote access client support) -# -# For most ISSM installations, only hdf5 will be necessary # # Sources: @@ -27,6 +25,5 @@ VER="4.7.2" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed # Environment @@ -42,18 +39,18 @@ # Unpack source -tar -zxvf netcdf-c-$VER.tar.gz +tar -zxvf netcdf-c-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv netcdf-c-$VER/* src/ -rm -rf netcdf-c-$VER +mv netcdf-c-${VER}/* src +rm -rf netcdf-c-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --prefix="${PREFIX}" \ --disable-shared \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh (revision 25860) @@ -8,6 +8,4 @@ # - zlib (1.2.5 or later, for netCDF-4 compression) # - curl (7.18.0 or later, for DAP remote access client support) -# -# For most ISSM installations, only hdf5 will be necessary # # Sources: @@ -27,6 +25,5 @@ VER="4.7.2" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed # Environment @@ -42,18 +39,18 @@ # Unpack source -tar -zxvf netcdf-c-$VER.tar.gz +tar -zxvf netcdf-c-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv netcdf-c-$VER/* src/ -rm -rf netcdf-c-$VER +mv netcdf-c-${VER}/* src +rm -rf netcdf-c-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --prefix="${PREFIX}" \ --disable-shared \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh (revision 25860) @@ -9,6 +9,4 @@ # - curl (7.18.0 or later, for DAP remote access client support) # -# For most ISSM installations, only hdf5 will be necessary -# # Sources: # - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building @@ -19,7 +17,5 @@ VER="4.7.2" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed # Environment @@ -33,18 +29,18 @@ # Unpack source -tar -zxvf netcdf-c-$VER.tar.gz +tar -zxvf netcdf-c-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv netcdf-c-$VER/* src/ -rm -rf netcdf-c-$VER +mv netcdf-c-${VER}/* src +rm -rf netcdf-c-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh (revision 25860) @@ -9,6 +9,4 @@ # - curl (7.18.0 or later, for DAP remote access client support) # -# For most ISSM installations, only hdf5 will be necessary -# # Sources: # - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building @@ -19,7 +17,5 @@ VER="4.7.2" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed # Environment @@ -33,18 +29,18 @@ # Unpack source -tar -zxvf netcdf-c-$VER.tar.gz +tar -zxvf netcdf-c-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv netcdf-c-$VER/* src/ -rm -rf netcdf-c-$VER +mv netcdf-c-${VER}/* src +rm -rf netcdf-c-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh (revision 25860) @@ -9,6 +9,4 @@ # - curl (7.18.0 or later, for DAP remote access client support) # -# For most ISSM installations, only hdf5 will be necessary -# # Sources: # - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building @@ -19,7 +17,5 @@ VER="4.7.2" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" +PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed # Environment @@ -32,18 +28,18 @@ # Unpack source -tar -zxvf netcdf-c-$VER.tar.gz +tar -zxvf netcdf-c-${VER}.tar.gz # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv netcdf-c-$VER/* src/ -rm -rf netcdf-c-$VER +mv netcdf-c-${VER}/* src +rm -rf netcdf-c-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: /issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh =================================================================== --- /issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh (revision 25860) @@ -9,6 +9,4 @@ # - curl (7.18.0 or later, for DAP remote access client support) # -# For most ISSM installations, only hdf5 will be necessary -# # Sources: # - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building @@ -18,7 +16,6 @@ # VER="4.7.2" -CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install" -HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install" -ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install" + +PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed # Environment @@ -34,9 +31,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Move source to 'src' directory -mv netcdf-c-${VER}/* src/ +mv netcdf-c-${VER}/* src rm -rf netcdf-c-${VER} @@ -44,5 +41,5 @@ cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \ + --prefix="${PREFIX}" \ --disable-static \ --disable-dependency-tracking \ Index: sm/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 25859) +++ (revision ) @@ -1,60 +1,0 @@ -#!/bin/bash -set -eu - - -# NOTE: There is a single difference between the Linux and macOS -# configurations, which is the addition of the -static-libgfortran -# option to FFLAGS on the macOS static configurations. For the sake of -# consistency, we maintain separate files for each, respective Linux and -# macOS configuration. - -## 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/petsc/install-3.12-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-static.sh (revision 25860) @@ -3,13 +3,10 @@ -# NOTE: There is a single difference between the Linux and macOS -# configurations, which is the addition of the -static-libgfortran -# option to FFLAGS on the macOS static configurations. For the sake of -# consistency, we maintain separate files for each, respective Linux and -# macOS configuration. - ## Constants # VER="3.12.3" + +PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed # Download source @@ -20,14 +17,14 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PREFIX} ${PETSC_DIR} -# Move source to 'src' directory -mv petsc-${VER}/* src/ +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} rm -rf petsc-${VER} # Configure # -# NOTE: +# NOTE: # - Cannot use --with-fpic option when compiling static libs, # @@ -36,8 +33,15 @@ # compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS # -cd src +# - Added -fallow-argument-mismatch to FFLAGS in order to clear, +# +# error: The Fortran compiler gfortran will not compile files that call +# the same routine with arguments of different types. +# +# for gfortran 10 or later (may need to remove it for earlier versions). +# +cd ${PETSC_DIR} ./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ --with-shared-libraries=0 \ --CFLAGS="-fPIC" \ Index: /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.12-linux.sh (revision 25860) @@ -7,4 +7,7 @@ VER="3.12.3" +PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + # Download source $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" @@ -14,16 +17,16 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PREFIX} ${PETSC_DIR} -# Move source to 'src' directory -mv petsc-${VER}/* src/ +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} rm -rf petsc-${VER} # Configure -cd src +cd ${PETSC_DIR} ./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ --with-debugging=0 \ --with-valgrind=0 \ Index: /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac-static.sh (revision 25860) @@ -7,4 +7,7 @@ VER="3.12.3" +PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + # Download source $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" @@ -14,14 +17,14 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PREFIX} ${PETSC_DIR} -# Move source to 'src' directory -mv petsc-${VER}/* src/ +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} rm -rf petsc-${VER} # Configure # -# NOTE: +# NOTE: # - Cannot use --with-fpic option when compiling static libs, # @@ -41,8 +44,8 @@ # work out of the box on Linux. # -cd src +cd ${PETSC_DIR} ./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ --with-shared-libraries=0 \ --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \ Index: /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.12-mac.sh (revision 25860) @@ -7,4 +7,7 @@ VER="3.12.3" +PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS +PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed + # Download source $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz" @@ -14,9 +17,9 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} ${PETSC_DIR} +mkdir -p ${PREFIX} ${PETSC_DIR} -# Move source to 'src' directory -mv petsc-${VER}/* src/ +# Move source to $PETSC_DIR +mv petsc-${VER}/* ${PETSC_DIR} rm -rf petsc-${VER} @@ -24,4 +27,6 @@ # # NOTE: +# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. +# (may need to remove it for earlier versions not using the C99 standard). # - Added -fallow-argument-mismatch to FFLAGS in order to clear, # @@ -30,11 +35,9 @@ # # for gfortran 10 or later (may need to remove it for earlier versions). -# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12. -# (may need to remove it for earlier versions not using the C99 standard). # -cd src +cd ${PETSC_DIR} ./config/configure.py \ - --prefix="${ISSM_DIR}/externalpackages/petsc/install" \ - --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \ + --prefix="${PREFIX}" \ + --PETSC_DIR="${PETSC_DIR}" \ --CFLAGS="-Wno-error=implicit-function-declaration" \ --FFLAGS="-fallow-argument-mismatch" \ Index: /issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh (revision 25860) @@ -7,5 +7,7 @@ VER="6.2.1" -## Environnment +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed + +## Environment # export CC=mpicc @@ -24,6 +26,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -31,14 +33,14 @@ # Unpack source -tar -zxvf proj-$VER.tar.gz +tar -zxvf proj-${VER}.tar.gz # Move source into 'src' directory -mv proj-$VER/* src -rm -rf proj-$VER +mv proj-${VER}/* src +rm -rf proj-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --prefix="${PREFIX}" \ --disable-dependency-tracking \ --enable-fast-install \ @@ -52,5 +54,6 @@ else make -j $1 - make -j $1 check + mack -j $1 check make -j $1 install fi + Index: /issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh (revision 25860) @@ -6,4 +6,6 @@ # VER="6.2.1" + +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed ## Environment @@ -24,6 +26,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -31,14 +33,14 @@ # Unpack source -tar -zxvf proj-$VER.tar.gz +tar -zxvf proj-${VER}.tar.gz # Move source into 'src' directory -mv proj-$VER/* src -rm -rf proj-$VER +mv proj-${VER}/* src +rm -rf proj-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --prefix="${PREFIX}" \ --disable-dependency-tracking \ --enable-fast-install \ Index: /issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh (revision 25860) @@ -7,5 +7,7 @@ VER="6.2.1" -## Environnment +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed + +## Environment # export CC=mpicc @@ -24,6 +26,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -31,14 +33,14 @@ # Unpack source -tar -zxvf proj-$VER.tar.gz +tar -zxvf proj-${VER}.tar.gz # Move source into 'src' directory -mv proj-$VER/* src -rm -rf proj-$VER +mv proj-${VER}/* src +rm -rf proj-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --prefix="${PREFIX}" \ --disable-dependency-tracking \ --enable-fast-install @@ -51,5 +53,5 @@ else make -j $1 - make -j $1 check + mack -j $1 check make -j $1 install fi Index: /issm/trunk-jpl/externalpackages/proj/install-6.2.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install-6.2.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/proj/install-6.2.sh (revision 25860) @@ -7,5 +7,7 @@ VER="6.2.1" -## Environnment +PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed + +## Environment # export CC=mpicc @@ -24,6 +26,6 @@ # Cleanup -rm -rf install src -mkdir install src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} src # Download source @@ -31,14 +33,14 @@ # Unpack source -tar -zxvf proj-$VER.tar.gz +tar -zxvf proj-${VER}.tar.gz # Move source into 'src' directory -mv proj-$VER/* src -rm -rf proj-$VER +mv proj-${VER}/* src +rm -rf proj-${VER} # Configure cd src ./configure \ - --prefix="${ISSM_DIR}/externalpackages/proj/install" \ + --prefix="${PREFIX}" \ --disable-dependency-tracking \ --enable-fast-install Index: sm/trunk-jpl/externalpackages/proj/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/proj/install.sh (revision 25859) +++ (revision ) @@ -1,15 +1,0 @@ -#!/bin/bash -set -eu - -#Some cleanup -rm -rf install - -#Download trunk -svn checkout http://svn.osgeo.org/metacrs/proj/trunk/proj install - -#compile -cd install -./configure --prefix="$ISSM_DIR/externalpackages/proj/install" -make -make install -cd .. Index: /issm/trunk-jpl/externalpackages/semic/configs/surface_physics.f90.patch =================================================================== --- /issm/trunk-jpl/externalpackages/semic/configs/surface_physics.f90.patch (revision 25860) +++ /issm/trunk-jpl/externalpackages/semic/configs/surface_physics.f90.patch (revision 25860) @@ -0,0 +1,15 @@ +--- surface_physics.f90 2018-12-10 08:27:55.000000000 +0100 ++++ my_surface_physics.f90 2018-12-10 08:58:14.000000000 +0100 +@@ -775,9 +775,9 @@ + n_ksub = par%n_ksub + + ! Read parameters from input namelist file +- open(7,file=trim(filename)) +- read(7,nml=surface_physics) +- close(7) ++ !open(7,file=trim(filename)) ++ !read(7,nml=surface_physics) ++ !close(7) + ! write(*,nml=surface_physics) + + ! Store local parameter values in output object Index: /issm/trunk-jpl/externalpackages/semic/install.sh =================================================================== --- /issm/trunk-jpl/externalpackages/semic/install.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/semic/install.sh (revision 25860) @@ -2,9 +2,14 @@ set -eu -#Some cleanup -rm -rf install src -mkdir install -#Download latest version +## Constants +# +PREFIX="${ISSM_DIR}/externalpackages/semic/install" # Set to location where external package should be installed + +# Cleanup +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} + +# Download source git clone https://github.com/mkrapp/semic.git src @@ -22,5 +27,5 @@ fi -#Compile semic module utils.f90 +# Compile and install semic module utils.f90 cd src/ ( @@ -30,6 +35,6 @@ FFLAGS=$FFLAGS install: libutils.\$(LIB_EXT) - cp libutils.\$(LIB_EXT) ../install/ - cp utils.mod ../install/ + cp libutils.\$(LIB_EXT) ${PREFIX} + cp utils.mod ${PREFIX} OBJECTS= utils.o libutils.\$(LIB_EXT): \$(OBJECTS) @@ -44,8 +49,8 @@ make -# patch surface_physics -patch surface_physics.f90 < ../surface_physics.f90.patch +# Apply patch surface_physics +patch surface_physics.f90 < ../configs/surface_physics.f90.patch -#Compile semic module surface_physics.f90 +# Compile semic module surface_physics.f90 ( cat << EOF @@ -54,6 +59,6 @@ FFLAGS=$FFLAGS install: libsurface_physics.\$(LIB_EXT) - cp libsurface_physics.\$(LIB_EXT) ../install/ - cp surface_physics.mod ../install/ + cp libsurface_physics.\$(LIB_EXT) ${PREFIX} + cp surface_physics.mod ${PREFIX} OBJECTS= surface_physics.o libsurface_physics.\$(LIB_EXT): \$(OBJECTS) Index: sm/trunk-jpl/externalpackages/semic/surface_physics.f90.patch =================================================================== --- /issm/trunk-jpl/externalpackages/semic/surface_physics.f90.patch (revision 25859) +++ (revision ) @@ -1,15 +1,0 @@ ---- surface_physics.f90 2018-12-10 08:27:55.000000000 +0100 -+++ my_surface_physics.f90 2018-12-10 08:58:14.000000000 +0100 -@@ -775,9 +775,9 @@ - n_ksub = par%n_ksub - - ! Read parameters from input namelist file -- open(7,file=trim(filename)) -- read(7,nml=surface_physics) -- close(7) -+ !open(7,file=trim(filename)) -+ !read(7,nml=surface_physics) -+ !close(7) - ! write(*,nml=surface_physics) - - ! Store local parameter values in output object Index: /issm/trunk-jpl/externalpackages/triangle/install-linux-javascript.sh =================================================================== --- /issm/trunk-jpl/externalpackages/triangle/install-linux-javascript.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/triangle/install-linux-javascript.sh (revision 25860) @@ -10,5 +10,5 @@ # Constants # -INSTALL_DIR="install-javascript" +export PREFIX="${ISSM_DIR}/triangle/install" # Set to location where external package should be installed # Environment @@ -22,5 +22,5 @@ # Source Emscripten environment -source ${ISSM_DIR}/externalpackages/emscripten/install/emsdk_env.sh +source ${EMSCRIPTEN_ROOT}/emsdk_env.sh # Cleanup Index: /issm/trunk-jpl/externalpackages/triangle/install-linux-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/triangle/install-linux-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/triangle/install-linux-static.sh (revision 25860) @@ -5,9 +5,9 @@ # Constants # -INSTALL_DIR="install" +export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed # Cleanup -rm -rf ${INSTALL_DIR} src -mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src # Download source @@ -20,5 +20,5 @@ cp configs/makefile src cp configs/triangle.h src -cp configs/linux/configure.make src +cp configs/mac/configure.make src # Compile @@ -28,6 +28,6 @@ # Install cd .. -cp src/libtriangle.* ${INSTALL_DIR}/lib -cp src/triangle.h ${INSTALL_DIR}/include +cp src/libtriangle.* ${PREFIX}/lib +cp src/triangle.h ${PREFIX}/include # Cleanup Index: /issm/trunk-jpl/externalpackages/triangle/install-linux.sh =================================================================== --- /issm/trunk-jpl/externalpackages/triangle/install-linux.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/triangle/install-linux.sh (revision 25860) @@ -5,9 +5,9 @@ # Constants # -INSTALL_DIR="install" +export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed # Cleanup -rm -rf ${INSTALL_DIR} src -mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src # Download source @@ -20,5 +20,5 @@ cp configs/makefile src cp configs/triangle.h src -cp configs/linux/configure.make src +cp configs/mac/configure.make src # Compile @@ -28,6 +28,6 @@ # Install cd .. -cp src/libtriangle.* ${INSTALL_DIR}/lib -cp src/triangle.h ${INSTALL_DIR}/include +cp src/libtriangle.* ${PREFIX}/lib +cp src/triangle.h ${PREFIX}/include # Cleanup Index: /issm/trunk-jpl/externalpackages/triangle/install-mac-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/triangle/install-mac-static.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/triangle/install-mac-static.sh (revision 25860) @@ -5,9 +5,9 @@ # Constants # -INSTALL_DIR="install" +export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed # Cleanup -rm -rf ${INSTALL_DIR} src -mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src # Download source @@ -28,6 +28,6 @@ # Install cd .. -cp src/libtriangle.* ${INSTALL_DIR}/lib -cp src/triangle.h ${INSTALL_DIR}/include +cp src/libtriangle.* ${PREFIX}/lib +cp src/triangle.h ${PREFIX}/include # Cleanup Index: /issm/trunk-jpl/externalpackages/triangle/install-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/triangle/install-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/triangle/install-mac.sh (revision 25860) @@ -5,9 +5,9 @@ # Constants # -export INSTALL_DIR="${ISSM_DIR}/externalpackages/triangle/install" +export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed # Cleanup -rm -rf ${INSTALL_DIR} src -mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src +rm -rf ${PREFIX} src +mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src # Download source @@ -28,6 +28,6 @@ # Install cd .. -cp src/libtriangle.* ${INSTALL_DIR}/lib -cp src/triangle.h ${INSTALL_DIR}/include +cp src/libtriangle.* ${PREFIX}/lib +cp src/triangle.h ${PREFIX}/include # Cleanup Index: /issm/trunk-jpl/externalpackages/triangle/makefile =================================================================== --- /issm/trunk-jpl/externalpackages/triangle/makefile (revision 25859) +++ /issm/trunk-jpl/externalpackages/triangle/makefile (revision 25860) @@ -35,5 +35,5 @@ libtriangle.dylib: $(OBJECTS) - $(CC) $(CSWITCHES) $(TRILIBDEFS) -dynamiclib -install_name $(PREFIX)/$@ -o $@ triangle.c + $(CC) $(CSWITCHES) $(TRILIBDEFS) -dynamiclib -install_name ${PREFIX}/lib/$@ -o $@ triangle.c libtriangle.lib: $(OBJECTS) Index: /issm/trunk-jpl/externalpackages/valgrind/install-mac.sh =================================================================== --- /issm/trunk-jpl/externalpackages/valgrind/install-mac.sh (revision 25859) +++ /issm/trunk-jpl/externalpackages/valgrind/install-mac.sh (revision 25860) @@ -3,10 +3,14 @@ +## Constants +# +PREFIX="${ISSM_DIR}/externalpackages/valgrind/install" # Set to location where external package should be installed + # Clean up -rm -rf install +rm -rf ${PREFIX} # Download development version (the current release never supports the latest # OS X releases) -git clone git://sourceware.org/git/valgrind.git install +git clone git://sourceware.org/git/valgrind.git ${PREFIX} # Configure @@ -14,5 +18,5 @@ ./autogen.sh ./configure \ - --prefix="$ISSM_DIR/externalpackages/valgrind/install" \ + --prefix="${PREFIX}" \ --enable-only64bit @@ -25,3 +29,2 @@ make install -j $1 fi - Index: /issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth (revision 25859) +++ /issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth (revision 25860) @@ -42,5 +42,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-linux.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-matlab (revision 25860) @@ -51,8 +51,8 @@ netcdf install-4.7-parallel-static.sh proj install-6.2-static.sh - gdal install-3-netcdf-static.sh + gdal install-3-static.sh gshhg install.sh gmt install-6-mac-static.sh - gmsh install-4-mac-static.sh + gmsh install-4-static.sh triangle install-mac-static.sh chaco install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-binaries-python (revision 25860) @@ -52,5 +52,5 @@ gshhg install.sh gmt install-6-mac-static.sh - gmsh install-4-mac-python-static.sh + gmsh install-4-static.sh triangle install-mac-static.sh chaco install.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-dakota =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-dakota (revision 25860) @@ -47,5 +47,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-mac.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-full =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-full (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-full (revision 25860) @@ -49,5 +49,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-mac.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind (revision 25860) @@ -49,5 +49,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-mac.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-python =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-python (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-python (revision 25860) @@ -44,5 +44,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-mac.sh Index: /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth (revision 25859) +++ /issm/trunk-jpl/jenkins/pine_island-mac-solid_earth (revision 25860) @@ -47,5 +47,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-mac.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab (revision 25860) @@ -50,8 +50,8 @@ netcdf install-4.7-parallel-static.sh proj install-6.2-static.sh - gdal install-3-netcdf-static.sh + gdal install-3-static.sh gshhg install.sh gmt install-6-linux-static.sh - gmsh install-4-linux-static.sh + gmsh install-4-static.sh triangle install-linux-static.sh chaco install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python (revision 25860) @@ -52,5 +52,5 @@ gshhg install.sh gmt install-6-linux-static.sh - gmsh install-4-linux-static.sh + gmsh install-4-static.sh triangle install-linux-static.sh chaco install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-dakota =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-dakota (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-dakota (revision 25860) @@ -49,5 +49,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-linux.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-full =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-full (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-full (revision 25860) @@ -49,5 +49,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-linux.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind (revision 25860) @@ -49,5 +49,5 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-linux.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-python =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-python (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-python (revision 25860) @@ -43,8 +43,8 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-linux.sh - gmsh install-4.sh + gmsh install-4-linux.sh triangle install-linux.sh chaco install.sh Index: /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth =================================================================== --- /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth (revision 25859) +++ /issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth (revision 25860) @@ -47,8 +47,8 @@ netcdf install-4.7-parallel.sh proj install-6.2.sh - gdal install-3-python-netcdf.sh + gdal install-3-python.sh gshhg install.sh gmt install-6-linux.sh - gmsh install-4.sh + gmsh install-4-linux.sh triangle install-linux.sh chaco install.sh Index: /issm/trunk-jpl/src/m/coordsystems/gmtmask.m =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gmtmask.m (revision 25859) +++ /issm/trunk-jpl/src/m/coordsystems/gmtmask.m (revision 25860) @@ -35,35 +35,10 @@ dlmwrite(filename_all,[long lat (1:nv)'],'delimiter','\t','precision',10); - %Avoid bypassing of the ld library path by Matlab (:() - % - % TODO: Do we really need this (we can/already set it in etc/environment.sh)? - if ismac, - dyld_library_path_old=getenv('DYLD_LIBRARY_PATH'); - setenv('DYLD_LIBRARY_PATH',[ issmdir '/externalpackages/curl/install/lib:' issmdir '/externalpackages/hdf5/install/lib:' issmdir '/externalpackages/netcdf/install/lib' ]); - end - - %Find path to gmt, list all possible known paths to gmt (you may need to add yours to the list) - gmtpaths = {[issmdir '/bin/gmt'],[issmdir '/externalpackages/gmt/install/bin/gmt'],'/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt'}; - gmtpath = ''; - for i=gmtpaths - if exist(i{1},'file'), - gmtpath = i{1}; - break; - end - end - if isempty(gmtpath), - error('gmt not found! Make sure it is properly installed, or add its path to this file.'); - end - %figure out which vertices are on the ocean, which one on the continent: - [status,result] = system([gmtpath ' gmtselect ./' filename_all ' -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./' filename_oce]); + [status,result] = system(['gmtselect ./' filename_all ' -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./' filename_oce]); if status~=0, error(result); end - %reset DYLD_LIBRARY_PATH to what it was: - if ismac, - setenv('DYLD_LIBRARY_PATH',dyld_library_path_old); - end %read the con_vertices.txt file and flag our mesh vertices on the continent fid=fopen(['./' filename_oce],'r'); Index: /issm/trunk-jpl/src/m/coordsystems/gmtmask.py =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gmtmask.py (revision 25859) +++ /issm/trunk-jpl/src/m/coordsystems/gmtmask.py (revision 25860) @@ -44,41 +44,6 @@ np.savetxt('./all_vertices.txt', np.transpose([long, lat, np.arange(1, nv + 1)]), delimiter='\t', fmt='%.10f') - #Avoid bypassing of the ld library path by Matlab (:() - issm_dir = issmdir() - - try: - ismac - except NameError: - ismac = False - - # TODO: Do we really need this (we can/already set it in etc/environment.sh)? - if ismac: - dyld_library_path_old = os.getenv('DYLD_LIBRARY_PATH') - os.putenv('DYLD_LIBRARY_PATH', issm_dir + '/externalpackages/curl/install/lib:' + issm_dir + '/externalpackages/hdf5/install/lib:' + issm_dir + '/externalpackages/netcdf/install/lib') - - #Find path to gmt (you may need to add yours to the list). - # - # NOTE: Assumes gmtselect is also in this directory. - # - gmtpaths = [ - issm_dir + '/bin/gmt', - issm_dir + '/externalpackages/gmt/install/bin/gmt', - '/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt' - ] - gmtpath = '' - for i in range(len(gmtpaths)): - if os.path.isfile(gmtpaths[i]): - gmtpath = gmtpaths[i] - break - - if gmtpath == '': - raise Exception('gmt not found! Make sure it is properly installed, or add its path to this file.') - #figure out which vertices are on the ocean, which one on the continent: - subprocess.call(gmtpath + ' gmtselect ./ all_vertices.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt', shell=True) - - #reset DYLD_LIBRARY_PATH to what it was: - if ismac: - os.putenv('DYLD_LIBRARY_PATH', dyld_library_path_old) + subprocess.call('gmtselect ./ all_vertices.txt -h0 -Df -R0/360/-90/90 -A0 -JQ180/200 -Nk/s/s/k/s > ./oce_vertices.txt', shell=True) #read the con_vertices.txt file and flag our mesh vertices on the continent Index: /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m =================================================================== --- /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m (revision 25859) +++ /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m (revision 25860) @@ -15,23 +15,6 @@ % md.mesh=gmshplanet('radius',6000,'resolution',100); - %Find path to gmsh - paths = {... - [issmdir() 'bin/gmsh'],... - [issmdir() 'externalpackages/gmsh/install/gmsh']... - }; - disp(paths{1}) - gmshpath = ''; - for i=paths - if exist(i{1},'file'), - gmshpath = i{1}; - break; - end - end - if isempty(gmshpath), - error('gmsh not found, make sure it is properly installed'); - end - % Get Gmsh version - [s,r]=system([gmshpath ' -info 2>&1 | command grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']); + [s,r]=system(['gmsh -info 2>&1 | command grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']); if s~=0, error(r); @@ -143,7 +126,7 @@ % if exist(options,'refine'), - system([gmshpath ' -tol 1e-8 -2 -format msh2 sphere.geo -bgm sphere.pos']); + system(['gmsh -tol 1e-8 -2 -format msh2 sphere.geo -bgm sphere.pos']); else - system([gmshpath ' -tol 1e-8 -2 -format msh2 sphere.geo']); + system(['gmsh -tol 1e-8 -2 -format msh2 sphere.geo']); end