Changeset 25860


Ignore:
Timestamp:
12/12/20 20:48:20 (4 years ago)
Author:
jdquinn
Message:

CHG: Simplification of installation script customization needs: should be able to simply set PREFIX in most cases

Location:
issm/trunk-jpl
Files:
1 added
13 deleted
69 edited
4 moved

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl/externalpackages/autotools/install.sh

    r24649 r25860  
    99LIBTOOL_VER="2.4.2"
    1010M4_VER="1.4.18"
     11PREFIX="${ISSM_DIR}/externalpackages/autotools/install" # Set to location where external package should be installed
    1112
    1213## Environment
    1314#
    14 export PATH="${ISSM_DIR}/externalpackages/autotools/install/bin:$PATH"
     15export PATH="${PREFIX}/bin:$PATH"
    1516
    1617# Cleanup
    17 rm -rf install src
    18 mkdir install
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX}
     20
    1921
    2022# Install m4
    … …  
    2527cd src
    2628
    27 ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
     29./configure --prefix="${PREFIX}"
    2830make
    2931make install
    … …  
    3739mv autoconf-${AUTOCONF_VER} src
    3840cd src
    39 ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
     41./configure --prefix="${PREFIX}"
    4042make
    4143make install
    … …  
    4951mv automake-${AUTOMAKE_VER} src
    5052cd src
    51 ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
     53./configure --prefix="${PREFIX}"
    5254make
    5355make install
    … …  
    6264mv libtool-${LIBTOOL_VER} src
    6365cd src
    64 ./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
     66./configure --prefix="${PREFIX}"
    6567make
    6668make install

  • issm/trunk-jpl/externalpackages/boost/install-1.7-linux-static.sh

    r25224 r25860  
    77VER="1_73_0"
    88
    9 ## Envrionment
    10 #
    11 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
     9PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed
    1210
    1311# Download source
    … …  
    1816
    1917# Cleanup
    20 rm -rf install src
    21 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    2220
    2321# Move source into 'src' directory
    24 mv boost_${VER}/* src/
     22mv boost_${VER}/* src
    2523rm -rf boost_${VER}
    2624
    … …  
    2826cd src
    2927./bootstrap.sh \
    30         --prefix="${BOOST_ROOT}/install" \
     28        --prefix=${PREFIX} \
    3129        --with-python=python2.7
    3230

  • issm/trunk-jpl/externalpackages/boost/install-1.7-linux-valgrind.sh

    r25706 r25860  
    77VER="1_73_0"
    88
    9 ## Envrionment
    10 #
    11 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
     9PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed
    1210
    1311# Download source
    … …  
    1816
    1917# Cleanup
    20 rm -rf install src
    21 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    2220
    2321# Move source into 'src' directory
    24 mv boost_${VER}/* src/
     22mv boost_${VER}/* src
    2523rm -rf boost_${VER}
    2624
    … …  
    3129cd src
    3230./bootstrap.sh \
    33         --prefix="${BOOST_ROOT}/install" \
     31        --prefix=${PREFIX} \
    3432        --with-python=python2.7
    3533

  • issm/trunk-jpl/externalpackages/boost/install-1.7-linux.sh

    r25224 r25860  
    77VER="1_73_0"
    88
    9 ## Envrionment
    10 #
    11 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
     9PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed
    1210
    1311# Download source
    … …  
    1816
    1917# Cleanup
    20 rm -rf install src
    21 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    2220
    2321# Move source into 'src' directory
    24 mv boost_${VER}/* src/
     22mv boost_${VER}/* src
    2523rm -rf boost_${VER}
    2624
    … …  
    2826cd src
    2927./bootstrap.sh \
    30         --prefix="${BOOST_ROOT}/install" \
     28        --prefix=${PREFIX} \
    3129        --with-python=python2.7
    3230

  • issm/trunk-jpl/externalpackages/boost/install-1.7-mac-static.sh

    r25224 r25860  
    77VER="1_73_0"
    88
     9PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed
     10
    911## Environment
    1012#
    11 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
     13export LDFLAGS="-Wl,-headerpad_max_install_names"
    1214
    1315# Download source
    … …  
    1820
    1921# Cleanup
    20 rm -rf install src
    21 mkdir install src
     22rm -rf ${PREFIX} src
     23mkdir -p ${PREFIX} src
    2224
    2325# Move source into 'src' directory
    24 mv boost_${VER}/* src/
     26mv boost_${VER}/* src
    2527rm -rf boost_${VER}
    2628
    … …  
    2830cd src
    2931./bootstrap.sh \
    30         --prefix="${BOOST_ROOT}/install" \
     32        --prefix=${PREFIX} \
    3133        --with-python=python2.7
    3234
    … …  
    4143# TODO: Reconfigure so that dynamic libraries are not compiled at all
    4244#
    43 rm -f $(find ${BOOST_ROOT}/install/lib -name *.dylib)
     45rm -f $(find ${PREFIX}/lib -name *.dylib)

  • issm/trunk-jpl/externalpackages/boost/install-1.7-mac.sh

    r25244 r25860  
    77VER="1_73_0"
    88
     9PREFIX="${ISSM_DIR}/externalpackages/boost/install" # Set to location where external package should be installed
     10
    911## Environment
    1012#
    11 export BOOST_ROOT="${ISSM_DIR}/externalpackages/boost"
    1213export LDFLAGS="-Wl,-headerpad_max_install_names"
    1314
    … …  
    1920
    2021# Cleanup
    21 rm -rf install src
    22 mkdir install src
     22rm -rf ${PREFIX} src
     23mkdir -p ${PREFIX} src
    2324
    2425# Move source into 'src' directory
    25 mv boost_${VER}/* src/
     26mv boost_${VER}/* src
    2627rm -rf boost_${VER}
    2728
    … …  
    2930cd src
    3031./bootstrap.sh \
    31         --prefix=${BOOST_ROOT}/install \
     32        --prefix=${PREFIX} \
    3233        --with-python=python2.7
    3334
    … …  
    4950#       patching it after the fact with install_name_tool is not necessary.
    5051#
    51 cd ${BOOST_ROOT}/install/lib
     52cd ${PREFIX}/lib
    5253for name in *.dylib; do
    53         install_name_tool -id ${BOOST_ROOT}/install/lib/${name} ${name} 2>/dev/null
     54        install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null
    5455done

  • issm/trunk-jpl/externalpackages/chaco/install.sh

    r25855 r25860  
    1010
    1111# Cleanup
    12 rm -rf ${PREFIX} src Chaco-${VER}
     12rm -rf ${PREFIX} src
    1313mkdir -p ${PREFIX} src
    1414

  • issm/trunk-jpl/externalpackages/cmake/install.sh

    r24593 r25860  
    55## Constants
    66#
    7 VER="3.16.2"
     7VER="3.19.1"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/cmake/install" # Set to location where external package should be installed
    810
    911# Download source
    … …  
    1416
    1517# Cleanup
    16 rm -rf install
     18rm -rf ${PREFIX}
    1719
    18 # Move source into 'install' directory
    19 mv cmake-${VER} install
     20# Move source into target directory
     21mv cmake-${VER} ${PREFIX}
    2022
    2123# Configure
    22 cd install
     24cd ${PREFIX}
    2325#./bootstrap \
    24 #       --prefix=${ISSM_DIR}/externalpackages/cmake/install # Breaks on ronne
     26#       --prefix=${PREFIX} # Breaks on ronne
    2527./configure \
    26         --prefix=${ISSM_DIR}/externalpackages/cmake/install
     28        --prefix=${PREFIX}
    2729
    2830# Compile

  • issm/trunk-jpl/externalpackages/curl/install-7-linux-static.sh

    r25799 r25860  
    77VER="7.73.0"
    88
     9PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed
     10
    911# Download source
    1012$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz"
    1113
    1214# Unpack source
    13 tar -zxvf curl-$VER.tar.gz
     15tar -zxvf curl-${VER}.tar.gz
    1416
    1517# Cleanup
    16 rm -rf install src
    17 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    1820
    1921# Move source to 'src' directory
    20 mv curl-$VER/* src
    21 rm -rf curl-$VER
     22mv curl-${VER}/* src
     23rm -rf curl-${VER}
    2224
    2325# Configure
    2426cd src
    2527./configure \
    26         --prefix="${ISSM_DIR}/externalpackages/curl/install" \
     28        --prefix="${PREFIX}" \
    2729        --disable-shared \
    2830        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/curl/install-7-linux-with_tests.sh

    r25799 r25860  
    77VER="7.73.0"
    88
     9PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed
     10
    911# Download source
    1012$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz"
    1113
    1214# Unpack source
    13 tar -zxvf curl-$VER.tar.gz
     15tar -zxvf curl-${VER}.tar.gz
    1416
    1517# Cleanup
    16 rm -rf install src
    17 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    1820
    1921# Move source to 'src' directory
    20 mv curl-$VER/* src
    21 rm -rf curl-$VER
     22mv curl-${VER}/* src
     23rm -rf curl-${VER}
    2224
    2325# Configure
    2426cd src
    2527./configure \
    26         --prefix="${ISSM_DIR}/externalpackages/curl/install" \
     28        --prefix="${PREFIX}" \
    2729        --disable-static \
    2830        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/curl/install-7-linux.sh

    r25799 r25860  
    77VER="7.73.0"
    88
     9PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed
     10
    911# Download source
    1012$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/curl-${VER}.tar.gz" "curl-${VER}.tar.gz"
    1113
    1214# Unpack source
    13 tar -zxvf curl-$VER.tar.gz
     15tar -zxvf curl-${VER}.tar.gz
    1416
    1517# Cleanup
    16 rm -rf install src
    17 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    1820
    1921# Move source to 'src' directory
    20 mv curl-$VER/* src
    21 rm -rf curl-$VER
     22mv curl-${VER}/* src
     23rm -rf curl-${VER}
    2224
    2325# Configure
    2426cd src
    2527./configure \
    26         --prefix="${ISSM_DIR}/externalpackages/curl/install" \
     28        --prefix="${PREFIX}" \
    2729        --disable-static \
    2830        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/curl/install-7-mac-static.sh

    r25804 r25860  
    66#
    77VER="7.73.0"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed
    810
    911## Environment
    … …  
    1517
    1618# Unpack source
    17 tar -zxvf curl-$VER.tar.gz
     19tar -zxvf curl-${VER}.tar.gz
    1820
    1921# Cleanup
    20 rm -rf install src
    21 mkdir install src
     22rm -rf ${PREFIX} src
     23mkdir -p ${PREFIX} src
    2224
    2325# Move source to 'src' directory
    24 mv curl-$VER/* src
    25 rm -rf curl-$VER
     26mv curl-${VER}/* src
     27rm -rf curl-${VER}
    2628
    2729# Configure
    2830cd src
    2931./configure \
    30         --prefix="${ISSM_DIR}/externalpackages/curl/install" \
     32        --prefix="${PREFIX}" \
    3133        --disable-shared \
    3234        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/curl/install-7-mac.sh

    r25805 r25860  
    66#
    77VER="7.73.0"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/curl/install" # Set to location where external package should be installed
    810
    911## Environment
    … …  
    1517
    1618# Unpack source
    17 tar -zxvf curl-$VER.tar.gz
     19tar -zxvf curl-${VER}.tar.gz
    1820
    1921# Cleanup
    20 rm -rf install src
    21 mkdir install src
     22rm -rf ${PREFIX} src
     23mkdir -p ${PREFIX} src
    2224
    2325# Move source to 'src' directory
    24 mv curl-$VER/* src
    25 rm -rf curl-$VER
     26mv curl-${VER}/* src
     27rm -rf curl-${VER}
    2628
    2729# Configure
    2830cd src
    2931./configure \
    30         --prefix="${ISSM_DIR}/externalpackages/curl/install" \
     32        --prefix="${PREFIX}" \
    3133        --disable-static \
    3234        --disable-dependency-tracking \

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

    r25785 r25860  
    33
    44
    5 # Constants
     5## Constants
    66#
    7 DAK_ROOT=${ISSM_DIR}/externalpackages/dakota
    87VER="6.2"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
    910
    1011## Environment
    1112#
    12 export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    13 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
     13export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    1414export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
    15 export DAK_BUILD=${DAK_ROOT}/build
    16 export DAK_INSTALL=${DAK_ROOT}/install
    17 export DAK_SRC=${DAK_ROOT}/src
    18 export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install
    19 export LAPACK_LIBS="-L${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
     15export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
     16export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
     17export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
     18export LAPACK_LIBS="-L${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
    2019
    2120# Cleanup
    22 rm -rf build install src
    23 mkdir build install src
     21rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
     22mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
    2423
    2524# Download source
    … …  
    3029
    3130# Move source to 'src' directory
    32 mv dakota-${VER}.0.src/* src
     31mv dakota-${VER}.0.src/* ${DAK_SRC}
    3332rm -rf dakota-${VER}.0.src
    3433

  • issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh

    r24824 r25860  
    33
    44
    5 # Constants
     5## Constants
    66#
    7 DAK_ROOT=${ISSM_DIR}/externalpackages/dakota
    87VER="6.2"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
    910
    1011## Environment
    1112#
    12 export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    13 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
     13export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    1414export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
    1515#export CXXFLAGS='-std=c++11'
    16 export DAK_BUILD=${DAK_ROOT}/build
    17 export DAK_INSTALL=${DAK_ROOT}/install
    18 export DAK_SRC=${DAK_ROOT}/src
    19 export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install
    20 export LAPACK_LIBS="-L${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
     16export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
     17export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
     18export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
     19export LAPACK_LIBS="-L${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
    2120
    2221# Cleanup
    23 rm -rf build install src
    24 mkdir build install src
     22rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
     23mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
    2524
    2625# Download source
    … …  
    3130
    3231# Move source to 'src' directory
    33 mv dakota-${VER}.0.src/* src
     32mv dakota-${VER}.0.src/* ${DAK_SRC}
    3433rm -rf dakota-${VER}.0.src
    3534

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

    r25745 r25860  
    33
    44
    5 # Constants
     5## Constants
    66#
    7 DAK_ROOT=${ISSM_DIR}/externalpackages/dakota
    87VER="6.2"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
    910
    1011## Environment
    … …  
    1718#
    1819# TODO:
    19 # - Test if -static-libgfortran flag will avoid all of this.
    20 # - Otherwise, refactor this to work with other gfortran installations.
     20# - Move this to etc/environment.sh
     21# - Test if -static-libgfortran flag will avoid all of this
     22# - Otherwise, refactor this to work with other gfortran installations
    2123#
    2224LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
    … …  
    2426LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | grep -n libgcc.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
    2527
    26 export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    27 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
    28 export DAK_BUILD=${DAK_ROOT}/build
    29 export DAK_INSTALL=${DAK_ROOT}/install
    30 export DAK_SRC=${DAK_ROOT}/src
    31 export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install
    32 export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
     28export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
     29export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
     30export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
     31export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
     32export 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
    3333
    3434# Cleanup
    35 rm -rf build install src
    36 mkdir build install src
     35rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
     36mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
    3737
    3838# Download source
    … …  
    4343
    4444# Move source to 'src' directory
    45 mv dakota-${VER}.0.src/* src
     45mv dakota-${VER}.0.src/* ${DAK_SRC}
    4646rm -rf dakota-${VER}.0.src
    4747

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

    r25243 r25860  
    33
    44
    5 # Constants
     5## Constants
    66#
    7 DAK_ROOT=${ISSM_DIR}/externalpackages/dakota
    87VER="6.2"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
    910
    1011## Environment
    … …  
    1617# returning one that is installed via package manager.
    1718#
     19# TODO:
     20# - Move this to etc/environment.sh
     21#
    1822LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | grep -n libgfortran.a | grep -v i386 | sed "s/[0-9]*://g" | head -1)
    1923LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
    2024
    21 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
    22 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
    23 export DAK_BUILD=${DAK_ROOT}/build
    24 export DAK_INSTALL=${DAK_ROOT}/install
    25 export DAK_SRC=${DAK_ROOT}/src
    26 export GSL_HOME=${ISSM_DIR}/externalpackages/gsl/install
    27 export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
     25export BLAS_LIBS="-L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
     26export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
     27export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
     28export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
     29export 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
    2830
    2931# Cleanup
    30 rm -rf build install src
    31 mkdir build install src
     32rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
     33mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
    3234
    3335# Download source
    … …  
    3840
    3941# Move source to 'src' directory
    40 mv dakota-${VER}.0.src/* src
     42mv dakota-${VER}.0.src/* ${DAK_SRC}
    4143rm -rf dakota-${VER}.0.src
    4244

  • issm/trunk-jpl/externalpackages/gdal/install-3-python-static.sh

    r25859 r25860  
    33
    44
    5 # TODO
    6 # - May want to supply path to Python instead of, effectively, using result of
    7 #       `which python`
     5## TODO
     6#       - May want to supply path to Python instead of, effectively, using result of `which python`
    87#
    98
    … …  
    1110#
    1211VER="3.1.1"
    13 
    14 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    15 NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install"
    16 PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install"
    17 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    1812
    1913## Environment
    … …  
    2620
    2721# Cleanup
    28 rm -rf install src
    29 mkdir install src
     22rm -rf ${PREFIX} src
     23mkdir -p ${PREFIX} src
    3024
    3125# Download source
    … …  
    3327
    3428# Unpack source
    35 tar -zxvf gdal-$VER.tar.gz
     29tar -zxvf gdal-${VER}.tar.gz
    3630
    3731# Move source into 'src' directory
    38 mv gdal-$VER/* src
    39 rm -rf gdal-$VER
     32mv gdal-${VER}/* src
     33rm -rf gdal-${VER}
    4034
    4135# Configure

  • issm/trunk-jpl/externalpackages/gdal/install-3-python.sh

    r25205 r25860  
    1111VER="3.1.1"
    1212
    13 PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install"
    14 
    1513## Environment
    1614#
    17 export PREFIX="${ISSM_DIR}/externalpackages/gdal/install" # Need this to properly set destination root for Python libraries on macOS (should not affect Linux build)
     15export 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.
    1816
    1917# Cleanup
    20 rm -rf install src
    21 mkdir install src
     18rm -rf ${PREFIX} src
     19mkdir -p ${PREFIX} src
    2220
    2321# Download source
    … …  
    2523
    2624# Unpack source
    27 tar -zxvf gdal-$VER.tar.gz
     25tar -zxvf gdal-${VER}.tar.gz
    2826
    2927# Move source into 'src' directory
    30 mv gdal-$VER/* src
    31 rm -rf gdal-$VER
     28mv gdal-${VER}/* src
     29rm -rf gdal-${VER}
    3230
    3331# Configure
    … …  
    3735        --enable-fast-install \
    3836        --with-python \
    39         --without-hdf5 \
    40         --without-netcdf \
     37        --with-libz="${ZLIB_ROOT}" \
     38        --with-hdf5="${HDF5_ROOT}" \
     39        --with-netcdf="${NETCDF_ROOT}" \
    4140        --with-proj="${PROJ_ROOT}"
    4241

  • issm/trunk-jpl/externalpackages/gdal/install-3-static.sh

    r25859 r25860  
    33
    44
    5 # TODO
    6 # - May want to supply path to Python instead of, effectively, using result of
    7 #       `which python`
     5## TODO
     6#       - May want to supply path to Python instead of, effectively, using result of `which python`
    87#
    98
    … …  
    1110#
    1211VER="3.1.1"
    13 
    14 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    15 NETCDF_ROOT="${ISSM_DIR}/externalpackages/netcdf/install"
    16 PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install"
    17 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    1812
    1913## Environment
    … …  
    2317export LDFLAGS="-L${HDF5_ROOT}/lib" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time
    2418export LIBS="-lhdf5_hl -lhdf5" # Need to do this so HDF5 symbols referenced in NETCDF library are found at link time
    25 export PREFIX="${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)
     19export 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.
    2620
    2721# Cleanup
    28 rm -rf install src
    29 mkdir install src
     22rm -rf ${PREFIX} src
     23mkdir -p ${PREFIX} src
    3024
    3125# Download source
    … …  
    3327
    3428# Unpack source
    35 tar -zxvf gdal-$VER.tar.gz
     29tar -zxvf gdal-${VER}.tar.gz
    3630
    3731# Move source into 'src' directory
    38 mv gdal-$VER/* src
    39 rm -rf gdal-$VER
     32mv gdal-${VER}/* src
     33rm -rf gdal-${VER}
    4034
    4135# Configure

  • issm/trunk-jpl/externalpackages/gdal/install-3.sh

    r25205 r25860  
    33
    44
    5 # Constants
     5## Constants
    66#
    77VER="3.1.1"
    88
    9 PROJ_ROOT="${ISSM_DIR}/externalpackages/proj/install"
    10 
    119## Environment
    1210#
    13 export PREFIX="${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)
     11export 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.
    1412
    1513# Cleanup
    16 rm -rf install src
    17 mkdir install src
     14rm -rf ${PREFIX} src
     15mkdir -p ${PREFIX} src
    1816
    1917# Download source
    … …  
    2422
    2523# Move source into 'src' directory
    26 mv gdal-$VER/* src
    27 rm -rf gdal-$VER
     24mv gdal-${VER}/* src
     25rm -rf gdal-${VER}
    2826
    2927# Configure
    … …  
    3230        --prefix="${PREFIX}" \
    3331        --enable-fast-install \
    34         --without-hdf5 \
    35         --without-netcdf \
     32        --with-libz="${ZLIB_ROOT}" \
     33        --with-hdf5="${HDF5_ROOT}" \
     34        --with-netcdf="${NETCDF_ROOT}" \
    3635        --with-proj="${PROJ_ROOT}"
    3736
    … …  
    4443        make -j $1 install
    4544fi
    46 
    47 # Return to initial directory
    48 cd ..

  • issm/trunk-jpl/externalpackages/gmsh/install-4-static.sh

    r25854 r25860  
    88#       - MUMPS
    99#       - PETSC
    10 # (see configs/4/mac/static/CMakeLists.txt)
     10# (see configs/4/static/CMakeLists.txt)
    1111#
    1212
    … …  
    1515VER="4.5.6"
    1616
    17 PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     17PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    1818
    1919# Cleanup
    20 rm -rf install src
    21 mkdir install src
     20rm -rf ${PREFIX} src
     21mkdir -p ${PREFIX} src
    2222
    2323# Download source
    2424$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
    2525
    26 # Untar source
     26# Unpack source
    2727tar -xvzf gmsh-${VER}-source.tgz
    2828
    … …  
    3232
    3333# Copy customized source and config files to 'src' directory
    34 cp configs/${VER}/mac/static/CMakeLists.txt src
     34cp configs/${VER}/static/CMakeLists.txt src
    3535
    3636# Configure
    … …  
    4343#       importing STEP/IGES files.
    4444# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
    45 #       do not need to support Apple Touch bar.
     45#       do not need to support Apple Touch bar (does not affect compilation on
     46#       Linux).
    4647#
    47 cd install
    48 cmake ../src \
    49         -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \
     48cd src
     49cmake \
     50        -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
    5051        -DENABLE_BUILD_LIB=1 \
    5152        -DENABLE_FLTK=0 \
    … …  
    5455        -DENABLE_OCC=0 \
    5556        -DENABLE_TOUCHBAR=0 \
    56         -DMETIS_ROOT="${PETSC_ROOT}"
     57        -DMETIS_ROOT="${METIS_ROOT}"
    5758
    5859# Compile and install

  • issm/trunk-jpl/externalpackages/gmsh/install-4.sh

    r25767 r25860  
    22set -eu
    33
     4
     5# TODO:
     6# - Add support for,
     7#       - BLAS_LAPACK
     8#       - MUMPS
     9#       - PETSC
     10# (see configs/4/static/CMakeLists.txt)
     11#
    412
    513## Constants
    … …  
    715VER="4.5.6"
    816
    9 PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     17PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    1018
    1119# Cleanup
    12 rm -rf install src
    13 mkdir install src
     20rm -rf ${PREFIX} src
     21mkdir -p ${PREFIX} src
    1422
    1523# Download source
    1624$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gmsh-${VER}-source.tgz" "gmsh-${VER}-source.tgz"
    1725
    18 # Untar source
     26# Unpack source
    1927tar -xvzf gmsh-${VER}-source.tgz
    2028
    … …  
    3240#       importing STEP/IGES files.
    3341# - Option -DENABLE_TOUCHBAR=0 is used because we do not have GUI, therefore we
    34 #       do not need to support Apple Touch bar.
     42#       do not need to support Apple Touch bar (does not affect compilation on
     43#       Linux).
    3544#
    36 cd install
    37 cmake ../src \
    38         -DCMAKE_INSTALL_PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" \
     45cd src
     46cmake \
     47        -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
    3948        -DENABLE_BUILD_DYNAMIC=1 \
    4049        -DENABLE_BUILD_SHARED=1 \
    … …  
    4453        -DENABLE_OCC=0 \
    4554        -DENABLE_TOUCHBAR=0 \
    46         -DMETIS_ROOT="${PETSC_ROOT}"
     55        -DMETIS_ROOT="${METIS_ROOT}"
    4756
    4857# Compile and install

  • issm/trunk-jpl/externalpackages/gmt/configs/6/cmake/ConfigUser.cmake

    r25745 r25860  
    3939
    4040# Installation path (usually defaults to /usr/local) [auto]:
    41 set (CMAKE_INSTALL_PREFIX "$ENV{ISSM_DIR}/externalpackages/gmt/install")
     41set (CMAKE_INSTALL_PREFIX "$ENV{PREFIX}")
    4242
    4343# Set install name suffix used for directories and gmt executables
    … …  
    109109
    110110# Set path to GSHHG Shoreline Database [auto]:
    111 set (GSHHG_ROOT "$ENV{ISSM_DIR}/externalpackages/gshhg/install")
     111set (GSHHG_ROOT "$ENV{GSHHG_ROOT}")
    112112
    113113# Copy GSHHG files to ${GMT_DATADIR}/coast [FALSE]:
    … …  
    136136# Set location of NetCDF (can be root directory, path to header file or path
    137137# to nc-config) [auto]:
    138 set (NETCDF_ROOT "$ENV{ISSM_DIR}/externalpackages/netcdf/install")
     138set (NETCDF_ROOT "$ENV{NETCDF_ROOT}")
    139139
    140140# Set location of GDAL (can be root directory, path to header file or path to
    141141# gdal-config) [auto]:
    142 set (GDAL_ROOT "$ENV{ISSM_DIR}/externalpackages/gdal/install")
     142set (GDAL_ROOT "$ENV{GDAL_ROOT}")
    143143
    144144# Set location of PCRE (can be root directory, path to header file or path to
    … …  
    154154
    155155# Set location of ZLIB (can be root directory or path to header file) [auto]:
    156 set (ZLIB_ROOT "$ENV{ISSM_DIR}/externalpackages/petsc/install")
     156set (ZLIB_ROOT "$ENV{ZLIB_ROOT}")
    157157
    158158# Set location of CURL (can be root directory or path to header file) [auto]:
    … …  
    167167
    168168# Set LAPACK location. Use this when want to link with LAPACK and it's not found automatically
    169 set (LAPACK_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lflapack")
    170 set (BLAS_LIBRARY "-L$ENV{ISSM_DIR}/externalpackages/petsc/install/lib -lfblas")
     169set (LAPACK_LIBRARY "-L$ENV{LAPACK_ROOT} -lflapack")
     170set (BLAS_LIBRARY "-L$ENV{BLAS_ROOT} -lfblas")
    171171
    172172##

  • issm/trunk-jpl/externalpackages/gmt/install-6-linux-static.sh

    r25785 r25860  
    77VER="6.0.0"
    88
    9 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    10 PETSC_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    11 
    12 BLASLAPACK_ROOT="${PETSC_ROOT}"
    13 HDF5_ROOT="${PETSC_ROOT}"
    14 
    159# Find libgfortran and libgcc so we do not have to hardcode them
    1610#
    … …  
    1812#
    1913# TODO:
     14# - Move this to etc/environment.sh
    2015# - Figure out how to find and grep for single result like we do with mdfind
    2116#       under macOS.
    … …  
    2520LIBGCC="/usr/lib/gcc/x86_64-linux-gnu/8/libgcc.a"
    2621
    27 CURL_INCLUDE_DIRS="${CURL_ROOT}/include" \
    28 CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a" \
    2922GDAL_EXTRA_LIBS="-lstdc++" # Determined by running `$GDAL_ROOT/bin/gdal-config --dep-libs` then removing duplicate libs
    3023NETCDF_EXTRA_LIBS="-lm -ldl -lz" # `$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)
    … …  
    3326#
    3427export CC=mpicc
    35 export CURL_INCLUDE_DIRS=${CURL_INCLUDE_DIRS}
    36 export CURL_LIBRARIES=${CURL_LIBRARIES}
     28export CURL_INCLUDE_DIRS="${CURL_ROOT}/include"
     29export CURL_LIBRARIES="${CURL_ROOT}/lib/libcurl.a;/usr/lib/x86_64-linux-gnu/libssl.a;/usr/lib/x86_64-linux-gnu/libcrypto.a"
     30export 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.
    3731
    3832# Download source
    … …  
    4337
    4438# Cleanup
    45 rm -rf install src
    46 mkdir install src
     39rm -rf ${PREFIX} src
     40mkdir -p ${PREFIX} src
    4741
    4842# Move source to 'src' directory
    … …  
    7064#
    7165cmake \
    72         -DBLAS_LIBRARIES="${BLASLAPACK_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
     66        -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
    7367        -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
    7468        -DHDF5_ROOT="${HDF5_ROOT}" \
    75         -DLAPACK_LIBRARIES="${BLASLAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
     69        -DLAPACK_LIBRARIES="${LAPACK_ROOT}/lib/libflapack.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
    7670        -DNETCDF_EXTRA_LIBS="${NETCDF_EXTRA_LIBS}" \
    7771        ..

  • issm/trunk-jpl/externalpackages/gmt/install-6-linux.sh

    r25745 r25860  
    77VER="6.0.0"
    88
    9 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    10 
    119# Environment
    1210#
    1311export CC=mpicc
     12export PREFIX="${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.
    1413
    1514# Download source
    … …  
    2019
    2120# Cleanup
    22 rm -rf install src
    23 mkdir install src
     21rm -rf ${PREFIX} src
     22mkdir -p ${PREFIX} src
    2423
    2524# Move source to 'src' directory

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

    r25745 r25860  
    77VER="6.0.0"
    88
    9 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    10 
    119# Environment
    1210#
    1311export CC=mpicc
     12export PREFIX="${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.
    1413
    1514# Download source
    … …  
    2019
    2120# Cleanup
    22 rm -rf install src
    23 mkdir install src
     21rm -rf ${PREFIX} src
     22mkdir -p ${PREFIX} src
    2423
    2524# Move source to 'src' directory

  • issm/trunk-jpl/externalpackages/gshhg/install.sh

    r24321 r25860  
    77VER="2.3.4"
    88
     9PREFIX="${ISSM_DIR}/externalpackages/gshhg/install" # Set to location where external package should be installed
     10
    911# Cleanup
    10 rm -rf install
     12rm -rf ${PREFIX}
     13mkdir -p ${PREFIX}
    1114
    1215# Download source
    … …  
    1720
    1821# Install
    19 mv gshhg-gmt-${VER} install
     22mv gshhg-gmt-${VER}/* ${PREFIX}

  • issm/trunk-jpl/externalpackages/gsl/install-javascript.sh

    r24317 r25860  
    33
    44
    5 # TODO:
     5## TODO:
    66# - Revisit enviroment variables (especially EMCC_CFLAGS) once support for
    77#       Fortran has been accomplished.
    88#
    99
    10 # Environment
     10## Constants
     11#
     12VER="1.15"
     13
     14PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed
     15
     16## Environment
     17#
    1118export CC=emcc
    1219export CXX=em++
    … …  
    1724
    1825# Source Emscripten environment
    19 source $ISSM_DIR/externalpackages/emscripten/install/emsdk_env.sh
     26source ${EMSCRIPTEN_ROOT}/emsdk_env.sh
    2027
    2128# Issue with variadic function signatures.
    2229#export CFLAGS=-DSTDC_HEADERS
    2330
    24 # Cleanup from previous installation
    25 rm -rf src-javascript install-javascript gsl-1.15
    26 mkdir src-javascript install-javascript
     31# Cleanup
     32rm -rf ${PREFIX} src
     33mkdir -p ${PREFIX} src
    2734
    2835# Download source
    29 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/gsl-1.15.tar.gz' 'gsl-1.15.tar.gz'
     36${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/gsl-${VER}.tar.gz" "gsl-${VER}.tar.gz"
    3037
    31 #Untar
    32 tar -zxvf  gsl-1.15.tar.gz
     38# Unpack source
     39tar -zxvf gsl-${VER}.tar.gz
    3340
    34 #Move gsl into src directory
    35 mv gsl-1.15/* src-javascript
    36 rm -rf gsl-1.15
     41# Move source to 'src' directory
     42mv gsl-${VER}/* src
     43rm -rf gsl-${VER}
    3744
    38 #Configure gsl
    39 cd src-javascript
    40 
     45# Configure
     46cd src
    4147./configure \
    42         --prefix="$ISSM_DIR/externalpackages/gsl/install-javascript" \
    43         --disable-shared
     48        --prefix="${PREFIX}" \
     49        --disable-shared \
    4450
    4551#Compile gsl
    4652if [ $# -eq 0 ]; then
    4753        make
     54        make install
    4855else
    4956        make -j $1
     57        make -j $1 install
    5058fi
    51 make install

  • issm/trunk-jpl/externalpackages/gsl/install-static.sh

    r24826 r25860  
    33
    44
    5 # Constants
     5## Constants
    66#
    7 GSL_ROOT=${ISSM_DIR}/externalpackages/gsl
    87VER="1.15"
    98
    10 # Cleanup=
    11 rm -rf install src
    12 mkdir install src
     9PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed
     10
     11# Cleanup
     12rm -rf ${PREFIX} src
     13mkdir -p ${PREFIX} src
    1314
    1415# Download source
    … …  
    2526cd src
    2627./configure \
    27         --prefix="${GSL_ROOT}/install" \
     28        --prefix="${PREFIX}" \
    2829        --disable-shared \
    2930        --with-pic

  • issm/trunk-jpl/externalpackages/gsl/install.sh

    r24824 r25860  
    55# Constants
    66#
    7 GSL_ROOT=${ISSM_DIR}/externalpackages/gsl
    87VER="1.15"
    98
    10 # Cleanup=
    11 rm -rf install src
    12 mkdir install src
     9PREFIX="${ISSM_DIR}/externalpackages/gsl/install" # Set to location where external package should be installed
     10
     11# Cleanup
     12rm -rf ${PREFIX} src
     13mkdir -p ${PREFIX} src
    1314
    1415# Download source
    … …  
    2526cd src
    2627./configure \
    27         --prefix="${GSL_ROOT}/install" \
     28        --prefix="${PREFIX}" \
    2829        --disable-static
    2930

  • issm/trunk-jpl/externalpackages/m1qn3/install.sh

    r23435 r25860  
    22set -eu
    33
    4 #Some cleanup
    5 rm -rf install src m1qn3-3.3-distrib
    6 mkdir install
    74
    8 #Download from ISSM server
    9 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/m1qn3-3.3-distrib.tgz' 'm1qn3-3.3-distrib.tgz'
     5## Constants
     6#
     7VER=3.3
    108
    11 #Untar
    12 tar -xzf m1qn3-3.3-distrib.tgz
    13 mv m1qn3-3.3-distrib src
     9PREFIX="${ISSM_DIR}/externalpackages/m1qn3/install" # Set to location where external package should be installed
     10
     11# Cleanup
     12rm -rf ${PREFIX} src
     13mkdir -p ${PREFIX} src
     14
     15# Download source
     16$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m1qn3-${VER}-distrib.tgz" "m1qn3-${VER}-distrib.tgz"
     17
     18# Unpack source
     19tar -xzf m1qn3-${VER}-distrib.tgz
     20
     21# Move source to 'src' directory
     22mv m1qn3-${VER}-distrib/* src
     23rm -rf m1qn3-${VER}-distrib
    1424
    1525if which ifort >/dev/null; then
    … …  
    2232fi
    2333
    24 #Compile m1qn3
     34# Compile and install
    2535cd src/src/
    2636(
    … …  
    2939FC=$FC
    3040install: libm1qn3.\$(LIB_EXT)
    31         cp libm1qn3.\$(LIB_EXT) ../../install/
     41        cp libm1qn3.\$(LIB_EXT) ${PREFIX}
    3242OBJECTS= m1qn3.o
    3343libm1qn3.\$(LIB_EXT): \$(OBJECTS)
    … …  
    4252make
    4353
    44 #compile ddot
    4554cd ../blas
    4655(
    … …  
    4958FC=$FC
    5059install: libddot.\$(LIB_EXT)
    51         cp libddot.\$(LIB_EXT) ../../install/
     60        cp libddot.\$(LIB_EXT) ${PREFIX}
    5261OBJECTS= ddot.o
    5362libddot.\$(LIB_EXT): \$(OBJECTS)

  • issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static-with_tests.sh

    r25846 r25860  
    88# - zlib (1.2.5 or later, for netCDF-4 compression)
    99# - curl (7.18.0 or later, for DAP remote access client support)
    10 #
    11 # For most ISSM installations, only hdf5 will be necessary
    1210#
    1311# Sources:
    … …  
    2725VER="4.7.2"
    2826
    29 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    30 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     27PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed
    3128
    3229# Environment
    … …  
    4239
    4340# Unpack source
    44 tar -zxvf netcdf-c-$VER.tar.gz
     41tar -zxvf netcdf-c-${VER}.tar.gz
    4542
    4643# Cleanup
    47 rm -rf install src
    48 mkdir install src
     44rm -rf ${PREFIX} src
     45mkdir -p ${PREFIX} src
    4946
    5047# Move source to 'src' directory
    51 mv netcdf-c-$VER/* src/
    52 rm -rf netcdf-c-$VER
     48mv netcdf-c-${VER}/* src
     49rm -rf netcdf-c-${VER}
    5350
    5451# Configure
    5552cd src
    5653./configure \
    57         --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
     54        --prefix="${PREFIX}" \
    5855        --disable-shared \
    5956        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-static.sh

    r25846 r25860  
    88# - zlib (1.2.5 or later, for netCDF-4 compression)
    99# - curl (7.18.0 or later, for DAP remote access client support)
    10 #
    11 # For most ISSM installations, only hdf5 will be necessary
    1210#
    1311# Sources:
    … …  
    2725VER="4.7.2"
    2826
    29 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    30 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     27PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed
    3128
    3229# Environment
    … …  
    4239
    4340# Unpack source
    44 tar -zxvf netcdf-c-$VER.tar.gz
     41tar -zxvf netcdf-c-${VER}.tar.gz
    4542
    4643# Cleanup
    47 rm -rf install src
    48 mkdir install src
     44rm -rf ${PREFIX} src
     45mkdir -p ${PREFIX} src
    4946
    5047# Move source to 'src' directory
    51 mv netcdf-c-$VER/* src/
    52 rm -rf netcdf-c-$VER
     48mv netcdf-c-${VER}/* src
     49rm -rf netcdf-c-${VER}
    5350
    5451# Configure
    5552cd src
    5653./configure \
    57         --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
     54        --prefix="${PREFIX}" \
    5855        --disable-shared \
    5956        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel-with_tests.sh

    r25846 r25860  
    99# - curl (7.18.0 or later, for DAP remote access client support)
    1010#
    11 # For most ISSM installations, only hdf5 will be necessary
    12 #
    1311# Sources:
    1412# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building
    … …  
    1917VER="4.7.2"
    2018
    21 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    22 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    23 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     19PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed
    2420
    2521# Environment
    … …  
    3329
    3430# Unpack source
    35 tar -zxvf netcdf-c-$VER.tar.gz
     31tar -zxvf netcdf-c-${VER}.tar.gz
    3632
    3733# Cleanup
    38 rm -rf install src
    39 mkdir install src
     34rm -rf ${PREFIX} src
     35mkdir -p ${PREFIX} src
    4036
    4137# Move source to 'src' directory
    42 mv netcdf-c-$VER/* src/
    43 rm -rf netcdf-c-$VER
     38mv netcdf-c-${VER}/* src
     39rm -rf netcdf-c-${VER}
    4440
    4541# Configure
    4642cd src
    4743./configure \
    48         --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
     44        --prefix="${PREFIX}" \
    4945        --disable-static \
    5046        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/netcdf/install-4.7-parallel.sh

    r25846 r25860  
    99# - curl (7.18.0 or later, for DAP remote access client support)
    1010#
    11 # For most ISSM installations, only hdf5 will be necessary
    12 #
    1311# Sources:
    1412# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building
    … …  
    1917VER="4.7.2"
    2018
    21 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    22 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    23 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     19PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed
    2420
    2521# Environment
    … …  
    3329
    3430# Unpack source
    35 tar -zxvf netcdf-c-$VER.tar.gz
     31tar -zxvf netcdf-c-${VER}.tar.gz
    3632
    3733# Cleanup
    38 rm -rf install src
    39 mkdir install src
     34rm -rf ${PREFIX} src
     35mkdir -p ${PREFIX} src
    4036
    4137# Move source to 'src' directory
    42 mv netcdf-c-$VER/* src/
    43 rm -rf netcdf-c-$VER
     38mv netcdf-c-${VER}/* src
     39rm -rf netcdf-c-${VER}
    4440
    4541# Configure
    4642cd src
    4743./configure \
    48         --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
     44        --prefix="${PREFIX}" \
    4945        --disable-static \
    5046        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/netcdf/install-4.7-with_tests.sh

    r25846 r25860  
    99# - curl (7.18.0 or later, for DAP remote access client support)
    1010#
    11 # For most ISSM installations, only hdf5 will be necessary
    12 #
    1311# Sources:
    1412# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building
    … …  
    1917VER="4.7.2"
    2018
    21 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    22 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    23 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     19PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed
    2420
    2521# Environment
    … …  
    3228
    3329# Unpack source
    34 tar -zxvf netcdf-c-$VER.tar.gz
     30tar -zxvf netcdf-c-${VER}.tar.gz
    3531
    3632# Cleanup
    37 rm -rf install src
    38 mkdir install src
     33rm -rf ${PREFIX} src
     34mkdir -p ${PREFIX} src
    3935
    4036# Move source to 'src' directory
    41 mv netcdf-c-$VER/* src/
    42 rm -rf netcdf-c-$VER
     37mv netcdf-c-${VER}/* src
     38rm -rf netcdf-c-${VER}
    4339
    4440# Configure
    4541cd src
    4642./configure \
    47         --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
     43        --prefix="${PREFIX}" \
    4844        --disable-static \
    4945        --disable-dependency-tracking \

  • issm/trunk-jpl/externalpackages/netcdf/install-4.7.sh

    r25125 r25860  
    99# - curl (7.18.0 or later, for DAP remote access client support)
    1010#
    11 # For most ISSM installations, only hdf5 will be necessary
    12 #
    1311# Sources:
    1412# - https://www.unidata.ucar.edu/software/netcdf/documentation/NUG/getting_and_building_netcdf.html#building
    … …  
    1816#
    1917VER="4.7.2"
    20 CURL_ROOT="${ISSM_DIR}/externalpackages/curl/install"
    21 HDF5_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
    22 ZLIB_ROOT="${ISSM_DIR}/externalpackages/petsc/install"
     18
     19PREFIX="${ISSM_DIR}/externalpackages/netcdf/install" # Set to location where external package should be installed
    2320
    2421# Environment
    … …  
    3431
    3532# Cleanup
    36 rm -rf install src
    37 mkdir install src
     33rm -rf ${PREFIX} src
     34mkdir -p ${PREFIX} src
    3835
    3936# Move source to 'src' directory
    40 mv netcdf-c-${VER}/* src/
     37mv netcdf-c-${VER}/* src
    4138rm -rf netcdf-c-${VER}
    4239
    … …  
    4441cd src
    4542./configure \
    46         --prefix="${ISSM_DIR}/externalpackages/netcdf/install" \
     43        --prefix="${PREFIX}" \
    4744        --disable-static \
    4845        --disable-dependency-tracking \

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

    r25785 r25860  
    33
    44
    5 # NOTE: There is a single difference between the Linux and macOS
    6 #               configurations, which is the addition of the -static-libgfortran
    7 #               option to FFLAGS on the macOS static configurations. For the sake of
    8 #               consistency, we maintain separate files for each, respective Linux and
    9 #               macOS configuration.
    10 
    115## Constants
    126#
    137VER="3.12.3"
     8
     9PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS
     10PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
    1411
    1512# Download source
    … …  
    2017
    2118# Cleanup
    22 rm -rf install src
    23 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PREFIX} ${PETSC_DIR}
    2421
    25 # Move source to 'src' directory
    26 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2724rm -rf petsc-${VER}
    2825
    2926# Configure
    3027#
    31 # NOTE: 
     28# NOTE:
    3229# - Cannot use --with-fpic option when compiling static libs,
    3330#
    … …  
    3633#               compiler PIC flag via CFLAGS, CXXXFLAGS, and FCFLAGS
    3734#
    38 cd src
     35# - Added -fallow-argument-mismatch to FFLAGS in order to clear,
     36#
     37#               error: The Fortran compiler gfortran will not compile files that call
     38#               the same routine with arguments of different types.
     39#
     40#       for gfortran 10 or later (may need to remove it for earlier versions).
     41#
     42cd ${PETSC_DIR}
    3943./config/configure.py \
    40         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    41         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     44        --prefix="${PREFIX}" \
     45        --PETSC_DIR="${PETSC_DIR}" \
    4246        --with-shared-libraries=0 \
    4347        --CFLAGS="-fPIC" \

  • issm/trunk-jpl/externalpackages/petsc/install-3.12-linux.sh

    r25659 r25860  
    77VER="3.12.3"
    88
     9PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS
     10PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
     11
    912# Download source
    1013$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    … …  
    1417
    1518# Cleanup
    16 rm -rf install src
    17 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PREFIX} ${PETSC_DIR}
    1821
    19 # Move source to 'src' directory
    20 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2124rm -rf petsc-${VER}
    2225
    2326# Configure
    24 cd src
     27cd ${PETSC_DIR}
    2528./config/configure.py \
    26         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    27         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     29        --prefix="${PREFIX}" \
     30        --PETSC_DIR="${PETSC_DIR}" \
    2831        --with-debugging=0 \
    2932        --with-valgrind=0 \

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

    r25800 r25860  
    77VER="3.12.3"
    88
     9PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS
     10PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
     11
    912# Download source
    1013$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    … …  
    1417
    1518# Cleanup
    16 rm -rf install src
    17 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PREFIX} ${PETSC_DIR}
    1821
    19 # Move source to 'src' directory
    20 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2124rm -rf petsc-${VER}
    2225
    2326# Configure
    2427#
    25 # NOTE: 
     28# NOTE:
    2629# - Cannot use --with-fpic option when compiling static libs,
    2730#
    … …  
    4144#       work out of the box on Linux.
    4245#
    43 cd src
     46cd ${PETSC_DIR}
    4447./config/configure.py \
    45         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    46         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     48        --prefix="${PREFIX}" \
     49        --PETSC_DIR="${PETSC_DIR}" \
    4750        --with-shared-libraries=0 \
    4851        --CFLAGS="-fPIC -Wno-error=implicit-function-declaration" \

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

    r25800 r25860  
    77VER="3.12.3"
    88
     9PETSC_DIR=${ISSM_DIR}/externalpackages/petsc/src # DO NOT CHANGE THIS
     10PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
     11
    912# Download source
    1013$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    … …  
    1417
    1518# Cleanup
    16 rm -rf install src
    17 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PREFIX} ${PETSC_DIR}
    1821
    19 # Move source to 'src' directory
    20 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2124rm -rf petsc-${VER}
    2225
    … …  
    2427#
    2528# NOTE:
     29# - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12.
     30#       (may need to remove it for earlier versions not using the C99 standard).
    2631# - Added -fallow-argument-mismatch to FFLAGS in order to clear,
    2732#
    … …  
    3035#
    3136#       for gfortran 10 or later (may need to remove it for earlier versions).
    32 # - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12.
    33 #       (may need to remove it for earlier versions not using the C99 standard).
    3437#
    35 cd src
     38cd ${PETSC_DIR}
    3639./config/configure.py \
    37         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    38         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     40        --prefix="${PREFIX}" \
     41        --PETSC_DIR="${PETSC_DIR}" \
    3942        --CFLAGS="-Wno-error=implicit-function-declaration" \
    4043        --FFLAGS="-fallow-argument-mismatch" \

  • issm/trunk-jpl/externalpackages/proj/install-6.2-static-with_tests.sh

    r24919 r25860  
    77VER="6.2.1"
    88
    9 ## Environnment
     9PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed
     10
     11## Environment
    1012#
    1113export CC=mpicc
    … …  
    2426
    2527# Cleanup
    26 rm -rf install src
    27 mkdir install src
     28rm -rf ${PREFIX} src
     29mkdir -p ${PREFIX} src
    2830
    2931# Download source
    … …  
    3133
    3234# Unpack source
    33 tar -zxvf proj-$VER.tar.gz
     35tar -zxvf proj-${VER}.tar.gz
    3436
    3537# Move source into 'src' directory
    36 mv proj-$VER/* src
    37 rm -rf proj-$VER
     38mv proj-${VER}/* src
     39rm -rf proj-${VER}
    3840
    3941# Configure
    4042cd src
    4143./configure \
    42         --prefix="${ISSM_DIR}/externalpackages/proj/install" \
     44        --prefix="${PREFIX}" \
    4345        --disable-dependency-tracking \
    4446        --enable-fast-install \
    … …  
    5254else
    5355        make -j $1
    54         make -j $1 check
     56        mack -j $1 check
    5557        make -j $1 install
    5658fi
     59

  • issm/trunk-jpl/externalpackages/proj/install-6.2-static.sh

    r25745 r25860  
    66#
    77VER="6.2.1"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed
    810
    911## Environment
    … …  
    2426
    2527# Cleanup
    26 rm -rf install src
    27 mkdir install src
     28rm -rf ${PREFIX} src
     29mkdir -p ${PREFIX} src
    2830
    2931# Download source
    … …  
    3133
    3234# Unpack source
    33 tar -zxvf proj-$VER.tar.gz
     35tar -zxvf proj-${VER}.tar.gz
    3436
    3537# Move source into 'src' directory
    36 mv proj-$VER/* src
    37 rm -rf proj-$VER
     38mv proj-${VER}/* src
     39rm -rf proj-${VER}
    3840
    3941# Configure
    4042cd src
    4143./configure \
    42         --prefix="${ISSM_DIR}/externalpackages/proj/install" \
     44        --prefix="${PREFIX}" \
    4345        --disable-dependency-tracking \
    4446        --enable-fast-install \

  • issm/trunk-jpl/externalpackages/proj/install-6.2-with_tests.sh

    r24919 r25860  
    77VER="6.2.1"
    88
    9 ## Environnment
     9PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed
     10
     11## Environment
    1012#
    1113export CC=mpicc
    … …  
    2426
    2527# Cleanup
    26 rm -rf install src
    27 mkdir install src
     28rm -rf ${PREFIX} src
     29mkdir -p ${PREFIX} src
    2830
    2931# Download source
    … …  
    3133
    3234# Unpack source
    33 tar -zxvf proj-$VER.tar.gz
     35tar -zxvf proj-${VER}.tar.gz
    3436
    3537# Move source into 'src' directory
    36 mv proj-$VER/* src
    37 rm -rf proj-$VER
     38mv proj-${VER}/* src
     39rm -rf proj-${VER}
    3840
    3941# Configure
    4042cd src
    4143./configure \
    42         --prefix="${ISSM_DIR}/externalpackages/proj/install" \
     44        --prefix="${PREFIX}" \
    4345        --disable-dependency-tracking \
    4446        --enable-fast-install
    … …  
    5153else
    5254        make -j $1
    53         make -j $1 check
     55        mack -j $1 check
    5456        make -j $1 install
    5557fi

  • issm/trunk-jpl/externalpackages/proj/install-6.2.sh

    r24919 r25860  
    77VER="6.2.1"
    88
    9 ## Environnment
     9PREFIX="${ISSM_DIR}/externalpackages/proj/install" # Set to location where external package should be installed
     10
     11## Environment
    1012#
    1113export CC=mpicc
    … …  
    2426
    2527# Cleanup
    26 rm -rf install src
    27 mkdir install src
     28rm -rf ${PREFIX} src
     29mkdir -p ${PREFIX} src
    2830
    2931# Download source
    … …  
    3133
    3234# Unpack source
    33 tar -zxvf proj-$VER.tar.gz
     35tar -zxvf proj-${VER}.tar.gz
    3436
    3537# Move source into 'src' directory
    36 mv proj-$VER/* src
    37 rm -rf proj-$VER
     38mv proj-${VER}/* src
     39rm -rf proj-${VER}
    3840
    3941# Configure
    4042cd src
    4143./configure \
    42         --prefix="${ISSM_DIR}/externalpackages/proj/install" \
     44        --prefix="${PREFIX}" \
    4345        --disable-dependency-tracking \
    4446        --enable-fast-install

  • issm/trunk-jpl/externalpackages/semic/install.sh

    r23550 r25860  
    22set -eu
    33
    4 #Some cleanup
    5 rm -rf install src
    6 mkdir install
    74
    8 #Download latest version
     5## Constants
     6#
     7PREFIX="${ISSM_DIR}/externalpackages/semic/install" # Set to location where external package should be installed
     8
     9# Cleanup
     10rm -rf ${PREFIX} src
     11mkdir -p ${PREFIX}
     12
     13# Download source
    914git clone https://github.com/mkrapp/semic.git src
    1015
    … …  
    2227fi
    2328
    24 #Compile semic module utils.f90
     29# Compile and install semic module utils.f90
    2530cd src/
    2631(
    … …  
    3035FFLAGS=$FFLAGS
    3136install: libutils.\$(LIB_EXT)
    32         cp libutils.\$(LIB_EXT) ../install/
    33         cp utils.mod ../install/
     37        cp libutils.\$(LIB_EXT) ${PREFIX}
     38        cp utils.mod ${PREFIX}
    3439OBJECTS= utils.o
    3540libutils.\$(LIB_EXT): \$(OBJECTS)
    … …  
    4449make
    4550
    46 # patch surface_physics
    47 patch surface_physics.f90 < ../surface_physics.f90.patch
     51# Apply patch surface_physics
     52patch surface_physics.f90 < ../configs/surface_physics.f90.patch
    4853
    49 #Compile semic module surface_physics.f90
     54# Compile semic module surface_physics.f90
    5055(
    5156cat << EOF
    … …  
    5459FFLAGS=$FFLAGS
    5560install: libsurface_physics.\$(LIB_EXT)
    56         cp libsurface_physics.\$(LIB_EXT) ../install/
    57         cp surface_physics.mod ../install/
     61        cp libsurface_physics.\$(LIB_EXT) ${PREFIX}
     62        cp surface_physics.mod ${PREFIX}
    5863OBJECTS= surface_physics.o
    5964libsurface_physics.\$(LIB_EXT): \$(OBJECTS)

  • issm/trunk-jpl/externalpackages/triangle/install-linux-javascript.sh

    r24593 r25860  
    1010# Constants
    1111#
    12 INSTALL_DIR="install-javascript"
     12export PREFIX="${ISSM_DIR}/triangle/install" # Set to location where external package should be installed
    1313
    1414# Environment
    … …  
    2222
    2323# Source Emscripten environment
    24 source ${ISSM_DIR}/externalpackages/emscripten/install/emsdk_env.sh
     24source ${EMSCRIPTEN_ROOT}/emsdk_env.sh
    2525
    2626# Cleanup

  • issm/trunk-jpl/externalpackages/triangle/install-linux-static.sh

    r24617 r25860  
    55# Constants
    66#
    7 INSTALL_DIR="install"
     7export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed
    88
    99# Cleanup
    10 rm -rf ${INSTALL_DIR} src
    11 mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src
     10rm -rf ${PREFIX} src
     11mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src
    1212
    1313# Download source
    … …  
    2020cp configs/makefile src
    2121cp configs/triangle.h src
    22 cp configs/linux/configure.make src
     22cp configs/mac/configure.make src
    2323
    2424# Compile
    … …  
    2828# Install
    2929cd ..
    30 cp src/libtriangle.* ${INSTALL_DIR}/lib
    31 cp src/triangle.h ${INSTALL_DIR}/include
     30cp src/libtriangle.* ${PREFIX}/lib
     31cp src/triangle.h ${PREFIX}/include
    3232
    3333# Cleanup

  • issm/trunk-jpl/externalpackages/triangle/install-linux.sh

    r24598 r25860  
    55# Constants
    66#
    7 INSTALL_DIR="install"
     7export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed
    88
    99# Cleanup
    10 rm -rf ${INSTALL_DIR} src
    11 mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src
     10rm -rf ${PREFIX} src
     11mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src
    1212
    1313# Download source
    … …  
    2020cp configs/makefile src
    2121cp configs/triangle.h src
    22 cp configs/linux/configure.make src
     22cp configs/mac/configure.make src
    2323
    2424# Compile
    … …  
    2828# Install
    2929cd ..
    30 cp src/libtriangle.* ${INSTALL_DIR}/lib
    31 cp src/triangle.h ${INSTALL_DIR}/include
     30cp src/libtriangle.* ${PREFIX}/lib
     31cp src/triangle.h ${PREFIX}/include
    3232
    3333# Cleanup

  • issm/trunk-jpl/externalpackages/triangle/install-mac-static.sh

    r24617 r25860  
    55# Constants
    66#
    7 INSTALL_DIR="install"
     7export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed
    88
    99# Cleanup
    10 rm -rf ${INSTALL_DIR} src
    11 mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src
     10rm -rf ${PREFIX} src
     11mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src
    1212
    1313# Download source
    … …  
    2828# Install
    2929cd ..
    30 cp src/libtriangle.* ${INSTALL_DIR}/lib
    31 cp src/triangle.h ${INSTALL_DIR}/include
     30cp src/libtriangle.* ${PREFIX}/lib
     31cp src/triangle.h ${PREFIX}/include
    3232
    3333# Cleanup

  • issm/trunk-jpl/externalpackages/triangle/install-mac.sh

    r24612 r25860  
    55# Constants
    66#
    7 export INSTALL_DIR="${ISSM_DIR}/externalpackages/triangle/install"
     7export PREFIX="${ISSM_DIR}/externalpackages/triangle/install" # Set to location where external package should be installed
    88
    99# Cleanup
    10 rm -rf ${INSTALL_DIR} src
    11 mkdir ${INSTALL_DIR} ${INSTALL_DIR}/include ${INSTALL_DIR}/lib src
     10rm -rf ${PREFIX} src
     11mkdir -p ${PREFIX} ${PREFIX}/include ${PREFIX}/lib src
    1212
    1313# Download source
    … …  
    2828# Install
    2929cd ..
    30 cp src/libtriangle.* ${INSTALL_DIR}/lib
    31 cp src/triangle.h ${INSTALL_DIR}/include
     30cp src/libtriangle.* ${PREFIX}/lib
     31cp src/triangle.h ${PREFIX}/include
    3232
    3333# Cleanup

  • issm/trunk-jpl/externalpackages/triangle/makefile

    r24616 r25860  
    3535
    3636libtriangle.dylib: $(OBJECTS)
    37         $(CC) $(CSWITCHES) $(TRILIBDEFS) -dynamiclib -install_name $(PREFIX)/$@ -o $@ triangle.c
     37        $(CC) $(CSWITCHES) $(TRILIBDEFS) -dynamiclib -install_name ${PREFIX}/lib/$@ -o $@ triangle.c
    3838
    3939libtriangle.lib: $(OBJECTS)

  • issm/trunk-jpl/externalpackages/valgrind/install-mac.sh

    r25706 r25860  
    33
    44
     5## Constants
     6#
     7PREFIX="${ISSM_DIR}/externalpackages/valgrind/install" # Set to location where external package should be installed
     8
    59# Clean up
    6 rm -rf install
     10rm -rf ${PREFIX}
    711
    812# Download development version (the current release never supports the latest
    913# OS X releases)
    10 git clone git://sourceware.org/git/valgrind.git install
     14git clone git://sourceware.org/git/valgrind.git ${PREFIX}
    1115
    1216# Configure
    … …  
    1418./autogen.sh
    1519./configure \
    16         --prefix="$ISSM_DIR/externalpackages/valgrind/install" \
     20        --prefix="${PREFIX}" \
    1721        --enable-only64bit
    1822
    … …  
    2529        make install -j $1
    2630fi
    27 

  • issm/trunk-jpl/jenkins/aws-amazon_linux-solid_earth

    r25829 r25860  
    4242        netcdf                  install-4.7-parallel.sh
    4343        proj                    install-6.2.sh
    44         gdal                    install-3-python-netcdf.sh
     44        gdal                    install-3-python.sh
    4545        gshhg                   install.sh
    4646        gmt                             install-6-linux.sh

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

    r25803 r25860  
    5151        netcdf          install-4.7-parallel-static.sh
    5252        proj            install-6.2-static.sh
    53         gdal            install-3-netcdf-static.sh
     53        gdal            install-3-static.sh
    5454        gshhg           install.sh
    5555        gmt                     install-6-mac-static.sh
    56         gmsh            install-4-mac-static.sh
     56        gmsh            install-4-static.sh
    5757        triangle        install-mac-static.sh
    5858        chaco           install.sh

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

    r25803 r25860  
    5252        gshhg           install.sh
    5353        gmt                     install-6-mac-static.sh
    54         gmsh            install-4-mac-python-static.sh
     54        gmsh            install-4-static.sh
    5555        triangle        install-mac-static.sh
    5656        chaco           install.sh

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

    r25790 r25860  
    4747        netcdf                  install-4.7-parallel.sh
    4848        proj                    install-6.2.sh
    49         gdal                    install-3-python-netcdf.sh
     49        gdal                    install-3-python.sh
    5050        gshhg                   install.sh
    5151        gmt                             install-6-mac.sh

  • issm/trunk-jpl/jenkins/pine_island-mac-full

    r25849 r25860  
    4949        netcdf          install-4.7-parallel.sh
    5050        proj            install-6.2.sh
    51         gdal            install-3-python-netcdf.sh
     51        gdal            install-3-python.sh
    5252        gshhg           install.sh
    5353        gmt                     install-6-mac.sh

  • issm/trunk-jpl/jenkins/pine_island-mac-full-valgrind

    r25849 r25860  
    4949        netcdf          install-4.7-parallel.sh
    5050        proj            install-6.2.sh
    51         gdal            install-3-python-netcdf.sh
     51        gdal            install-3-python.sh
    5252        gshhg           install.sh
    5353        gmt                     install-6-mac.sh

  • issm/trunk-jpl/jenkins/pine_island-mac-python

    r25790 r25860  
    4444        netcdf          install-4.7-parallel.sh
    4545        proj            install-6.2.sh
    46         gdal            install-3-python-netcdf.sh
     46        gdal            install-3-python.sh
    4747        gshhg           install.sh
    4848        gmt                     install-6-mac.sh

  • issm/trunk-jpl/jenkins/pine_island-mac-solid_earth

    r25790 r25860  
    4747        netcdf                  install-4.7-parallel.sh
    4848        proj                    install-6.2.sh
    49         gdal                    install-3-python-netcdf.sh
     49        gdal                    install-3-python.sh
    5050        gshhg                   install.sh
    5151        gmt                             install-6-mac.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-binaries-matlab

    r25803 r25860  
    5050        netcdf          install-4.7-parallel-static.sh
    5151        proj            install-6.2-static.sh
    52         gdal            install-3-netcdf-static.sh
     52        gdal            install-3-static.sh
    5353        gshhg           install.sh
    5454        gmt                     install-6-linux-static.sh
    55         gmsh            install-4-linux-static.sh
     55        gmsh            install-4-static.sh
    5656        triangle        install-linux-static.sh
    5757        chaco           install.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-binaries-python

    r25815 r25860  
    5252        gshhg           install.sh
    5353        gmt                     install-6-linux-static.sh
    54         gmsh            install-4-linux-static.sh
     54        gmsh            install-4-static.sh
    5555        triangle        install-linux-static.sh
    5656        chaco           install.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-dakota

    r25824 r25860  
    4949        netcdf                  install-4.7-parallel.sh
    5050        proj                    install-6.2.sh
    51         gdal                    install-3-python-netcdf.sh
     51        gdal                    install-3-python.sh
    5252        gshhg                   install.sh
    5353        gmt                             install-6-linux.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-full

    r25820 r25860  
    4949        netcdf          install-4.7-parallel.sh
    5050        proj            install-6.2.sh
    51         gdal            install-3-python-netcdf.sh
     51        gdal            install-3-python.sh
    5252        gshhg           install.sh
    5353        gmt                     install-6-linux.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-full-valgrind

    r25820 r25860  
    4949        netcdf          install-4.7-parallel.sh
    5050        proj            install-6.2.sh
    51         gdal            install-3-python-netcdf.sh
     51        gdal            install-3-python.sh
    5252        gshhg           install.sh
    5353        gmt                     install-6-linux.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-python

    r25790 r25860  
    4343        netcdf          install-4.7-parallel.sh
    4444        proj            install-6.2.sh
    45         gdal            install-3-python-netcdf.sh
     45        gdal            install-3-python.sh
    4646        gshhg           install.sh
    4747        gmt                     install-6-linux.sh
    48         gmsh            install-4.sh
     48        gmsh            install-4-linux.sh
    4949        triangle        install-linux.sh
    5050        chaco           install.sh

  • issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth

    r25790 r25860  
    4747        netcdf                  install-4.7-parallel.sh
    4848        proj                    install-6.2.sh
    49         gdal                    install-3-python-netcdf.sh
     49        gdal                    install-3-python.sh
    5050        gshhg                   install.sh
    5151        gmt                             install-6-linux.sh
    52         gmsh                    install-4.sh
     52        gmsh                    install-4-linux.sh
    5353        triangle                install-linux.sh
    5454        chaco                   install.sh

  • issm/trunk-jpl/src/m/coordsystems/gmtmask.m

    r25196 r25860  
    3535        dlmwrite(filename_all,[long lat (1:nv)'],'delimiter','\t','precision',10);
    3636
    37         %Avoid bypassing of the ld library path by Matlab (:()
    38         %
    39         % TODO: Do we really need this (we can/already set it in etc/environment.sh)?
    40         if ismac,
    41                 dyld_library_path_old=getenv('DYLD_LIBRARY_PATH');
    42                 setenv('DYLD_LIBRARY_PATH',[ issmdir '/externalpackages/curl/install/lib:' issmdir '/externalpackages/hdf5/install/lib:' issmdir '/externalpackages/netcdf/install/lib' ]);
    43         end
    44 
    45         %Find path to gmt, list all possible known paths to gmt (you may need to add yours to the list)
    46    gmtpaths = {[issmdir '/bin/gmt'],[issmdir '/externalpackages/gmt/install/bin/gmt'],'/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt'};
    47    gmtpath = '';
    48    for i=gmtpaths
    49       if exist(i{1},'file'),
    50          gmtpath = i{1};
    51                         break;
    52       end
    53    end
    54    if isempty(gmtpath),
    55       error('gmt not found! Make sure it is properly installed, or add its path to this file.');
    56    end
    57    
    5837        %figure out which vertices are on the ocean, which one on the continent:
    59         [status,result] = system([gmtpath ' gmtselect ./' filename_all ' -h0 -Df -R0/360/-90/90  -A0 -JQ180/200 -Nk/s/s/k/s > ./' filename_oce]);
     38        [status,result] = system(['gmtselect ./' filename_all ' -h0 -Df -R0/360/-90/90  -A0 -JQ180/200 -Nk/s/s/k/s > ./' filename_oce]);
    6039        if status~=0,
    6140                error(result);
    6241        end
    6342
    64         %reset DYLD_LIBRARY_PATH to what it was:
    65         if ismac,
    66                 setenv('DYLD_LIBRARY_PATH',dyld_library_path_old);
    67         end
    6843        %read the con_vertices.txt file and flag our mesh vertices on the continent
    6944        fid=fopen(['./' filename_oce],'r');

  • issm/trunk-jpl/src/m/coordsystems/gmtmask.py

    r25196 r25860  
    4444    np.savetxt('./all_vertices.txt', np.transpose([long, lat, np.arange(1, nv + 1)]), delimiter='\t', fmt='%.10f')
    4545
    46     #Avoid bypassing of the ld library path by Matlab (:()
    47     issm_dir = issmdir()
    48 
    49     try:
    50         ismac
    51     except NameError:
    52         ismac = False
    53 
    54     # TODO: Do we really need this (we can/already set it in etc/environment.sh)?
    55     if ismac:
    56         dyld_library_path_old = os.getenv('DYLD_LIBRARY_PATH')
    57         os.putenv('DYLD_LIBRARY_PATH', issm_dir + '/externalpackages/curl/install/lib:' + issm_dir + '/externalpackages/hdf5/install/lib:' + issm_dir + '/externalpackages/netcdf/install/lib')
    58 
    59     #Find path to gmt (you may need to add yours to the list).
    60     #
    61     # NOTE: Assumes gmtselect is also in this directory.
    62     #
    63     gmtpaths = [
    64         issm_dir + '/bin/gmt',
    65         issm_dir + '/externalpackages/gmt/install/bin/gmt',
    66         '/Applications/GMT-5.4.3.app/Contents/Resources/bin/gmt'
    67     ]
    68     gmtpath = ''
    69     for i in range(len(gmtpaths)):
    70         if os.path.isfile(gmtpaths[i]):
    71             gmtpath = gmtpaths[i]
    72             break
    73 
    74     if gmtpath == '':
    75         raise Exception('gmt not found! Make sure it is properly installed, or add its path to this file.')
    76 
    7746    #figure out which vertices are on the ocean, which one on the continent:
    78     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)
    79 
    80     #reset DYLD_LIBRARY_PATH to what it was:
    81     if ismac:
    82         os.putenv('DYLD_LIBRARY_PATH', dyld_library_path_old)
     47    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)
    8348
    8449    #read the con_vertices.txt file and flag our mesh vertices on the continent

  • issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m

    r25747 r25860  
    1515%      md.mesh=gmshplanet('radius',6000,'resolution',100);
    1616
    17         %Find path to gmsh
    18         paths = {...
    19                 [issmdir() 'bin/gmsh'],...
    20                 [issmdir() 'externalpackages/gmsh/install/gmsh']...
    21         };
    22         disp(paths{1})
    23         gmshpath = '';
    24         for i=paths
    25                 if exist(i{1},'file'),
    26                         gmshpath = i{1};
    27                         break;
    28                 end
    29         end
    30         if isempty(gmshpath),
    31                 error('gmsh not found, make sure it is properly installed');
    32         end
    33 
    3417        % Get Gmsh version
    35         [s,r]=system([gmshpath ' -info 2>&1 | command grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']);
     18        [s,r]=system(['gmsh -info 2>&1 | command grep ''Version'' | sed -e ''s/Version[[:blank:]]*:[[:blank:]]//'' | cut -d ''.'' -f1']);
    3619        if s~=0,
    3720                error(r);
    … …  
    143126        %
    144127        if  exist(options,'refine'),
    145                 system([gmshpath ' -tol 1e-8 -2 -format msh2 sphere.geo -bgm sphere.pos']);
     128                system(['gmsh -tol 1e-8 -2 -format msh2 sphere.geo -bgm sphere.pos']);
    146129        else
    147                 system([gmshpath ' -tol 1e-8 -2 -format msh2 sphere.geo']);
     130                system(['gmsh -tol 1e-8 -2 -format msh2 sphere.geo']);
    148131        end
    149132
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