Changeset 27202


Ignore:
Timestamp:
08/16/22 10:19:53 (3 years ago)
Author:
jdquinn
Message:

CHG: Varied clean up

Location:
issm/trunk-jpl
Files:
1 added
47 edited

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl/etc/environment.sh

    r27162 r27202  
    355355fi
    356356
     357QD_ROOT="${ISSM_EXT_DIR}/qd/install"
     358if [ -d "${QD_ROOT}" ]; then
     359        export QD_ROOT # Used in installation of MPLAPACK
     360        library_path_prepend "${QD_ROOT}/lib"
     361        ld_library_path_prepend "${QD_ROOT}/lib"
     362fi
     363
    357364SCALAPACK_ROOT="${ISSM_EXT_DIR}/scalapack/install"
    358365if [ -d "${SCALAPACK_ROOT}" ]; then
    … …  
    443450ld_library_path_append "${TAO_ROOT}/lib"
    444451
    445 DAKOTA_ROOT="${ISSM_EXT_DIR}/dakota/install"
    446 if [ -d "${DAKOTA_ROOT}" ]; then
    447         path_append "${DAKOTA_ROOT}/bin"
    448         ld_library_path_append "${DAKOTA_ROOT}/lib"
    449         dyld_library_path_prepend "${DAKOTA_ROOT}/lib"
    450 fi
    451 
    452 NCO_ROOT="${ISSM_EXT_DIR}/nco/install/bin"
    453 path_prepend "${NCO_ROOT}/bin"
    454 
    455 CPPCHECK_ROOT="${ISSM_EXT_DIR}/cppcheck/install"
    456 path_append "${CPPCHECK_ROOT}/bin"
    457 
    458 MERCURIAL_ROOT="${ISSM_EXT_DIR}/mercurial/install"
    459 if [ -d "${MERCURIAL_ROOT}" ]; then
    460         export PYTHONPATH="${PYTHONPATH}:${MERCURIAL_ROOT}/mercurial/pure/"
    461         path_append "${MERCURIAL_ROOT}"
    462 fi
    463 
    464452BOOST_ROOT="${ISSM_EXT_DIR}/boost/install"
    465453if [ -d "${BOOST_ROOT}" ]; then
    … …  
    467455        export BOOST_DIR=${BOOST_ROOT}
    468456        export BOOSTROOT=${BOOST_ROOT}
    469         library_path_append "${BOOST_ROOT}/lib"
    470         ld_library_path_append "${BOOST_ROOT}/lib"
    471         dyld_library_path_append "${BOOST_ROOT}/lib"
    472457        path_append "${BOOST_ROOT}/bin"
     458        library_path_prepend "${BOOST_ROOT}/lib"
     459        ld_library_path_prepend "${BOOST_ROOT}/lib"
     460        dyld_library_path_prepend "${BOOST_ROOT}/lib"
     461fi
     462
     463DAKOTA_ROOT="${ISSM_EXT_DIR}/dakota/install"
     464if [ -d "${DAKOTA_ROOT}" ]; then
     465        path_append "${DAKOTA_ROOT}/bin"
     466        ld_library_path_prepend "${DAKOTA_ROOT}/lib"
     467        dyld_library_path_prepend "${DAKOTA_ROOT}/lib"
     468fi
     469
     470NCO_ROOT="${ISSM_EXT_DIR}/nco/install/bin"
     471path_prepend "${NCO_ROOT}/bin"
     472
     473CPPCHECK_ROOT="${ISSM_EXT_DIR}/cppcheck/install"
     474path_append "${CPPCHECK_ROOT}/bin"
     475
     476MERCURIAL_ROOT="${ISSM_EXT_DIR}/mercurial/install"
     477if [ -d "${MERCURIAL_ROOT}" ]; then
     478        export PYTHONPATH="${PYTHONPATH}:${MERCURIAL_ROOT}/mercurial/pure/"
     479        path_append "${MERCURIAL_ROOT}"
    473480fi
    474481

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

    r26805 r27202  
    6060fi
    6161cd ..
     62
    6263# Install Automake
    6364echo " === INSTALLING AUTOMAKE ==="

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

    r25860 r27202  
    5454        install_name_tool -id ${PREFIX}/lib/${name} ${name} 2>/dev/null
    5555done
     56
     57if [ "${VER}" == "1_79_0" ]; then
     58        ## Patch install names for certain libraries
     59        #
     60        # TODO: Figure out how to reconfigure source to apply these install names at compile time
     61        #
     62        install_name_tool -change @rpath/libboost_atomic.dylib ${PREFIX}/lib/libboost_atomic.dylib libboost_filesystem.dylib
     63fi

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

    r25860 r27202  
    88
    99PREFIX="${ISSM_DIR}/externalpackages/chaco/install" # Set to location where external package should be installed
     10
     11## Environment
     12#
     13export CFLAGS="-Wno-error=implicit-function-declaration"
    1014
    1115# Cleanup

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

    r27194 r27202  
    5353cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
    5454
     55# Disable requirement of Python 2 for TriBITS
     56sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
     57
    5558# Configure
    5659cd ${DAK_BUILD}

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

    r27187 r27202  
    4444cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
    4545
     46# Disable requirement of Python 2 for TriBITS
     47sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
     48
    4649# Configure
    4750cd ${DAK_BUILD}

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

    r27194 r27202  
    7171# cp configs/${VER}/mac/static/packages/nidr/nidr-scanner.c ${DAK_SRC}/packages/nidr
    7272
     73# Disable requirement of Python 2 for TriBITS
     74sed -i'' -e 's|SET(PythonInterp_FIND_VERSION|#SET(PythonInterp_FIND_VERSION|' ${DAK_SRC}/packages/teuchos/cmake/tribits/package_arch/TribitsFindPythonInterp.cmake
     75
    7376# Configure
    7477cd ${DAK_BUILD}

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

    r27194 r27202  
    55# TODO:
    66# - Add support for,
    7 #       - BLAS_LAPACK
    87#       - MUMPS
    9 #       - PETSC
    10 # (see configs/4/static/CMakeLists.txt)
     8#       - PETSc
     9#
     10# See Also:
     11# - configs/4/static/CMakeLists.txt
     12# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
    1113#
    1214
    1315## Constants
    1416#
    15 VER="4.5.6"
     17VER="4.10.5"
     18
     19PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    1620
    1721# Find libgfortran and libgcc so we do not have to hardcode them
    … …  
    2327LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
    2428LIBGCC=$(find ${LIBGFORTRAN_ROOT} -name libgcc* | egrep -n libgcc.a | sed "s/[0-9]*://g" | head -1)
    25 
    26 PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    2729
    2830# Cleanup
    … …  
    3941mv gmsh-${VER}-source/* src
    4042rm -rf gmsh-${VER}-source
    41 
    42 # Copy customized source and config files to 'src' directory
    43 cp configs/${VER}/static/CMakeLists.txt src
    4443
    4544# Configure
    … …  
    5958        -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
    6059        -DENABLE_BUILD_LIB=1 \
     60        -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \
     61        -DENABLE_BLAS_LAPACK=1 \
     62        -DENABLE_EIGEN=0 \
    6163        -DENABLE_FLTK=0 \
    6264        -DENABLE_MPEG_ENCODE=0 \
    … …  
    6466        -DENABLE_OCC=0 \
    6567        -DENABLE_TOUCHBAR=0 \
    66         -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \
    6768        -DMETIS_ROOT="${METIS_ROOT}"
    6869

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

    r27194 r27202  
    55# TODO:
    66# - Add support for,
    7 #       - BLAS_LAPACK
    87#       - MUMPS
    9 #       - PETSC
    10 # (see configs/4/static/CMakeLists.txt)
     8#       - PETSc
     9#
     10# See Also:
     11# - configs/4/static/CMakeLists.txt
     12# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
    1113#
    1214
    1315## Constants
    1416#
    15 VER="4.5.6"
     17VER="4.10.5"
    1618
    1719PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    … …  
    5658        -DENABLE_BUILD_DYNAMIC=1 \
    5759        -DENABLE_BUILD_SHARED=1 \
     60        -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \
     61        -DENABLE_BLAS_LAPACK=1 \
     62        -DENABLE_EIGEN=0 \
    5863        -DENABLE_FLTK=0 \
    5964        -DENABLE_MPEG_ENCODE=0 \
    … …  
    6166        -DENABLE_OCC=0 \
    6267        -DENABLE_TOUCHBAR=0 \
    63         -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \
    6468        -DMETIS_ROOT="${METIS_ROOT}"
    6569

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

    r27191 r27202  
    55# TODO:
    66# - Add support for,
    7 #       - BLAS_LAPACK
    87#       - MUMPS
    9 #       - PETSC
    10 # (see configs/4/static/CMakeLists.txt)
     8#       - PETSc
     9#
     10# See Also:
     11# - configs/4/static/CMakeLists.txt
     12# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
    1113#
    1214
    1315## Constants
    1416#
    15 VER="4.5.6"
     17VER="4.10.5"
     18
     19PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
     20
    1621
    1722# Find libgfortran and libgcc so we do not have to hardcode them
    … …  
    2732LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
    2833LIBGCC=$(mdfind -onlyin ${LIBGFORTRAN_ROOT} -name libgcc | egrep -n libgcc.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
    29 
    30 PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    3134
    3235# Cleanup
    … …  
    6366        -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
    6467        -DENABLE_BUILD_LIB=1 \
     68        -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \
     69        -DENABLE_BLAS_LAPACK=1 \
     70        -DENABLE_EIGEN=0 \
    6571        -DENABLE_FLTK=0 \
    6672        -DENABLE_MPEG_ENCODE=0 \
    … …  
    6874        -DENABLE_OCC=0 \
    6975        -DENABLE_TOUCHBAR=0 \
    70         -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas ${LIBGFORTRAN_ROOT}/libgfortran.a ${LIBGFORTRAN_ROOT}/libquadmath.a ${LIBGCC}" \
    7176        -DMETIS_ROOT="${METIS_ROOT}"
    7277

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

    r27191 r27202  
    55# TODO:
    66# - Add support for,
    7 #       - BLAS_LAPACK
    87#       - MUMPS
    9 #       - PETSC
    10 # (see configs/4/static/CMakeLists.txt)
     8#       - PETSc
     9#
     10# See Also:
     11# - configs/4/static/CMakeLists.txt
     12# - http://gmsh.info/doc/texinfo/gmsh.html#Compiling-the-source-code
    1113#
    1214
    1315## Constants
    1416#
    15 VER="4.5.6"
     17VER="4.10.5"
    1618
    1719PREFIX="${ISSM_DIR}/externalpackages/gmsh/install" # Set to location where external package should be installed
    … …  
    5961        -DENABLE_BUILD_DYNAMIC=1 \
    6062        -DENABLE_BUILD_SHARED=1 \
     63        -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \
     64        -DENABLE_BLAS_LAPACK=1 \
     65        -DENABLE_EIGEN=0 \
    6166        -DENABLE_FLTK=0 \
    6267        -DENABLE_MPEG_ENCODE=0 \
    … …  
    6469        -DENABLE_OCC=0 \
    6570        -DENABLE_TOUCHBAR=0 \
    66         -DBLAS_LAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib -lflapack -L${BLAS_ROOT}/lib -lfblas -L${LIBGFORTRAN_ROOT} -lgfortran" \
    6771        -DMETIS_ROOT="${METIS_ROOT}"
    6872

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

    r27194 r27202  
    55## Constants
    66#
    7 VER="6.0.0"
     7VER="6.4.0"
    88
    99# Find libgfortran and libgcc so we do not have to hardcode them
    … …  
    6161cmake \
    6262        -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
     63        -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
     64        -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \
    6365        -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
    6466        -DHDF5_ROOT="${HDF5_ROOT}" \

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

    r26246 r27202  
    55## Constants
    66#
    7 VER="6.0.0"
     7VER="6.4.0"
     8
     9# Find libgfortran so that we do not have to hardcode it.
     10#
     11# TODO:
     12# - Move this to etc/environment.sh
     13#
     14LIBGFORTRAN=$(find /usr -name libgfortran* | egrep -n libgfortran.a | sed "s/[0-9]*://g" | head -1)
     15LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
    816
    917# Environment
    … …  
    4250#
    4351cmake \
    44         -DCURL_LIBRARY="${CURL_ROOT}/lib" \
     52        -DBLAS_LIBRARIES="-L${BLAS_ROOT}/lib;-lfblas;-L${LIBGFORTRAN_ROOT};-lgfortran" \
    4553        -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
     54        -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \
     55        -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \
    4656        ..
    4757

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

    r27191 r27202  
    55## Constants
    66#
    7 VER="6.0.0"
     7VER="6.4.0"
    88
    99# Find libgfortran and libgcc so we do not have to hardcode them
    … …  
    6565cmake \
    6666        -DBLAS_LIBRARIES="${BLAS_ROOT}/lib/libfblas.a;${LIBGFORTRAN_ROOT}/libgfortran.a;${LIBGFORTRAN_ROOT}/libquadmath.a;${LIBGCC}" \
     67        -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
     68        -DCURL_LIBRARY="${CURL_ROOT}/lib/libcurl.a" \
    6769        -DGDAL_EXTRA_LIBS="${GDAL_EXTRA_LIBS}" \
    6870        -DHDF5_ROOT="${HDF5_ROOT}" \

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

    r26246 r27202  
    55## Constants
    66#
    7 VER="6.0.0"
     7VER="6.4.0"
     8
     9# Find libgfortran so that we do not have to hardcode it.
     10#
     11# Should retrieve a copy of gfortran that is compiled from source before
     12# returning one that is installed via package manager.
     13#
     14# TODO:
     15# - Move this to etc/environment.sh
     16#
     17LIBGFORTRAN=$(mdfind -onlyin /usr -name libgfortran | egrep -n libgfortran.a | egrep -v i386 | sed "s/[0-9]*://g" | head -1)
     18LIBGFORTRAN_ROOT=${LIBGFORTRAN%/*}
    819
    920# Environment
    … …  
    4253#
    4354cmake \
    44         -DCURL_LIBRARY="${CURL_ROOT}/lib" \
     55        -DBLAS_LIBRARIES="-L${BLAS_ROOT}/lib;-lfblas;-L${LIBGFORTRAN_ROOT};-lgfortran" \
    4556        -DCURL_INCLUDE_DIR="${CURL_ROOT}/include" \
     57        -DCURL_LIBRARY="-L${CURL_ROOT}/lib;-lcurl" \
     58        -DLAPACK_LIBRARIES="-L${LAPACK_ROOT}/lib;-lflapack;-L${LIBGFORTRAN_ROOT};-lgfortran" \
    4659        ..
    4760

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

    r27048 r27202  
    33
    44
    5 # Constants
     5## Constants
    66#
    77VER="2.7"

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

    r26239 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

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

    r25899 r27202  
    11#!/bin/bash
    22set -eu
     3
    34
    45## Constants
    56#
    67VER="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
    711
    812# Download source
    … …  
    1317
    1418# Cleanup
    15 rm -rf install src
    16 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    1721
    18 # Move source to 'src' directory
    19 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2024rm -rf petsc-${VER}
    2125
    22 #configure
    23 cd src
     26# Configure
     27cd ${PETSC_DIR}
    2428./config/configure.py \
    25         --prefix="$ISSM_DIR/externalpackages/petsc/install" \
    26         --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
     29        --prefix="${PREFIX}" \
     30        --PETSC_DIR="${PETSC_DIR}" \
    2731        --with-mpi-dir="/opt/cray/pe/mpt/7.7.3/gni/mpich-intel/16.0/" \
    2832        --with-blas-lapack-dir="$TACC_MKL_LIB" \

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

    r25959 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.12-win-msys2-gcc-msmpi.sh

    r26034 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.13-pleiades.sh

    r26406 r27202  
    2020# Cleanup
    2121rm -rf ${PREFIX} ${PETSC_DIR}
    22 mkdir ${PETSC_DIR}
     22mkdir -p ${PETSC_DIR}
    2323
    2424# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-discover.sh

    r27000 r27202  
    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 
    11 # Constants
     5## Constants
     6#
    127VER="3.14.6"
    138
     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
    1412# Download source
    15 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    1614
    1715# Unpack source
    … …  
    1917
    2018# Cleanup
    21 rm -rf install src
    22 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2321
    24 # Move source to 'src' directory
    25 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2624rm -rf petsc-${VER}
    2725
    2826# Configure
    29 cd src
     27cd ${PETSC_DIR}
    3028./config/configure.py \
    3129        COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
    32         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    33         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     30        --prefix="${PREFIX}" \
     31        --PETSC_DIR="${PETSC_DIR}" \
    3432        --with-debugging=0 \
    3533        --with-valgrind=0 \

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-greenplanet.sh

    r25635 r27202  
    22set -eu
    33
    4 #WARNING: make sure you have the right mpi
    54
    6 #Some cleanup
    7 rm -rf install petsc-3.14.0 src
    8 mkdir install src
     5# WARNING: Make sure you have the right MPI
    96
    10 #Download from ISSM server
    11 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.14.0.tar.gz' 'petsc-3.14.0.tar.gz'
     7## Constants
     8#
     9VER="3.14.0"
    1210
    13 #Untar and move petsc to install directory
    14 tar -zxvf  petsc-3.14.0.tar.gz
    15 mv petsc-3.14.0/* src/
    16 rm -rf petsc-3.14.0
     11PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
     12PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
     13
     14# Download source
     15$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     16
     17# Unpack source
     18tar -zxvf petsc-${VER}.tar.gz
     19
     20# Cleanup
     21rm -rf ${PREFIX} ${PETSC_DIR}
     22mkdir -p ${PETSC_DIR}
     23
     24# Move source to $PETSC_DIR
     25mv petsc-${VER}/* ${PETSC_DIR}
     26rm -rf petsc-${VER}
    1727
    1828#configure
    19 cd src
     29cd ${PETSC_DIR}
    2030./config/configure.py \
    2131        COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
    22         --prefix="$ISSM_DIR/externalpackages/petsc/install" \
    23         --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
     32        --prefix="${PREFIX}" \
     33        --PETSC_DIR="${PETSC_DIR}" \
    2434        --with-blas-lapack-dir="/sopt/INTEL/compilers_and_libraries_2018.3.222/linux/mkl/" \
    2535        --with-mpi-dir="/sopt/OpenMPI/3.1.2/intel-2018.3-slim/" \

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-linux.sh

    r27000 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-mac-nohdf5.sh

    r27000 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-mac.sh

    r27000 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-pleiades.sh

    r27000 r27202  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-tetralith.sh

    r27000 r27202  
    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.
     5## Constants
     6#
     7VER="3.14.6"
    108
    11 # Constants
    12 VER="3.14.6"
     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
    1311
    1412# Download source
    … …  
    1917
    2018# Cleanup
    21 rm -rf install src
    22 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2321
    24 # Move source to 'src' directory
    25 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2624rm -rf petsc-${VER}
    2725
    2826# Configure
    29 cd src
     27cd ${PETSC_DIR}
    3028./config/configure.py \
    3129        COPTFLAGS="-g -O2" CXXOPTFLAGS="-g -O2" FOPTFLAGS="-g -O2" \
    32         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    33         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     30        --prefix="${PREFIX}" \
     31        --PETSC_DIR="${PETSC_DIR}" \
    3432        --with-debugging=0 \
    3533        --with-valgrind=0 \

  • issm/trunk-jpl/externalpackages/petsc/install-3.14-win-msys2-mingw-msmpi.sh

    r27000 r27202  
    3232# Cleanup
    3333rm -rf ${PREFIX} ${PETSC_DIR}
    34 mkdir ${PETSC_DIR}
     34mkdir -p ${PETSC_DIR}
    3535
    3636# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.15-babylon.sh

    r26413 r27202  
    1111
    1212# Download source
    13 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    1414
    1515# Unpack source
    … …  
    1818# Cleanup
    1919rm -rf ${PREFIX} ${PETSC_DIR}
    20 mkdir ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR

  • issm/trunk-jpl/externalpackages/petsc/install-3.15-discovery.sh

    r26993 r27202  
    33
    44## Constants
     5#
    56VER="3.15.3"
    67
     8PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" # DO NOT CHANGE THIS
     9PREFIX="${ISSM_DIR}/externalpackages/petsc/install" # Set to location where external package should be installed
     10
    711# Download source
    8 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     12$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    913
    1014# Unpack source
    … …  
    1216
    1317# Cleanup
    14 rm -rf install src
    15 mkdir install src
     18rm -rf ${PREFIX} ${PETSC_DIR}
     19mkdir -p ${PETSC_DIR}
    1620
    17 # Move source to 'src' directory
    18 mv petsc-${VER}/* src/
     21# Move source to $PETSC_DIR
     22mv petsc-${VER}/* ${PETSC_DIR}
    1923rm -rf petsc-${VER}
    2024
    21 cd src
     25# Configure
     26cd ${PETSC_DIR}
    2227./config/configure.py \
    2328        COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
    24         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    25         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     29        --prefix="${PREFIX}" \
     30        --PETSC_DIR="${PETSC_DIR}" \
    2631        --with-make-np=20 \
    2732        --with-blas-lapack-dir=$MKL_ROOT \

  • issm/trunk-jpl/externalpackages/petsc/install-3.15-pleiades.sh

    r26950 r27202  
    1414
    1515# Unpack source
    16 tar -zxvf petsc-3.15.0.tar.gz
     16tar -zxvf petsc-${VER}.tar.gz
    1717
    1818# Cleanup
    19 rm -rf install src
    20 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR
    23 mv petsc-3.15.0/* src/
    24 rm -rf petsc-3.15.0
    25 
     23mv petsc-${VER}/* ${PETSC_DIR}
     24rm -rf petsc-${VER}
    2625
    2726# Configure
    2827#
    29 # NOTE: Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables; look for CONFIGURE_OPTIONS
     28# NOTE:
     29# - Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables (look
     30#       for CONFIGURE_OPTIONS)
    3031#
    31 cd src
     32cd ${PETSC_DIR}
    3233./config/configure.py \
    3334        --prefix="${PREFIX}" \

  • issm/trunk-jpl/externalpackages/petsc/install-3.16-linux.sh

    r26496 r27202  
    33
    44## Constants
     5#
    56VER="3.16.0"
    67
    … …  
    910
    1011# Download source
    11 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     12$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    1213
    1314# Unpack source
    … …  
    1516
    1617# Cleanup
    17 rm -rf install src
    18 mkdir install src
     18rm -rf ${PREFIX} ${PETSC_DIR}
     19mkdir -p ${PETSC_DIR}
    1920
    2021# Move source to $PETSC_DIR
    21 mv petsc-${VER}/* src/
     22mv petsc-${VER}/* ${PETSC_DIR}
    2223rm -rf petsc-${VER}
    2324
    2425# Configure
    25 cd src
     26cd ${PETSC_DIR}
    2627./config/configure.py \
    27         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    28         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     28        --prefix="${PREFIX}" \
     29        --PETSC_DIR="${PETSC_DIR}" \
    2930        -COPTFLAGS="-g -O2" -CXXOPTFLAGS="-g -O2" -FOPTFLAGS="-g -O2" \
    3031        --with-debugging=0 \

  • issm/trunk-jpl/externalpackages/petsc/install-3.16-pleiades.sh

    r26950 r27202  
    1717
    1818# Cleanup
    19 rm -rf install src
    20 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    2121
    2222# Move source to $PETSC_DIR
    23 mv petsc-${VER}/* src/
     23mv petsc-${VER}/* ${PETSC_DIR}
    2424rm -rf petsc-${VER}
    2525
    … …  
    2727# Configure
    2828#
    29 # NOTE: Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables; look for CONFIGURE_OPTIONS
     29# NOTE:
     30# - Based on /nasa/petsc/3.7.5/intel_mpt/lib/petsc/conf/petscvariables (look
     31#       for CONFIGURE_OPTIONS)
    3032#
    31 cd src
     33cd ${PETSC_DIR}
    3234./config/configure.py \
    3335        --prefix="${PREFIX}" \

  • issm/trunk-jpl/externalpackages/petsc/install-3.17-mac-intel.sh

    r27041 r27202  
    22set -eu
    33
     4
    45## Constants
    5 VER="3.17.1"
     6#
     7VER="3.17.4"
     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
    611
    712# Download source
    8 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    914
    1015# Unpack source
    … …  
    1217
    1318# Cleanup
    14 rm -rf install src
    15 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    1621
    17 # Move source to 'src' directory
    18 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    1924rm -rf petsc-${VER}
    2025
    21 cd src
     26# Configure
     27cd ${PETSC_DIR}
    2228./configure \
    23         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    24         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     29        --prefix="${PREFIX}" \
     30        --PETSC_DIR="${PETSC_DIR}" \
    2531        --with-debugging=0 \
    2632        --with-valgrind=0 \
    … …  
    3440        --download-scalapack=1 \
    3541        --download-mumps=1 \
    36         --download-zlib=1
     42        --download-zlib=1 \
     43        --download-hdf5=1
    3744
    3845# Compile and install
    3946make
    4047make install
     48

  • issm/trunk-jpl/externalpackages/petsc/install-3.17-mac-m1-static.sh

    r27042 r27202  
    22set -eu
    33
     4
    45## Constants
    5 VER="3.17.1"
     6#
     7VER="3.17.4"
     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
    611
    712# Download source
    8 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    914
    1015# Unpack source
    … …  
    1217
    1318# Cleanup
    14 rm -rf install src
    15 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    1621
    17 # Move source to 'src' directory
    18 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    1924rm -rf petsc-${VER}
    2025
    … …  
    3439#
    3540#       for gfortran 10 or later (may need to remove it for earlier versions).
    36 cd src
    37 ./configure \
    38         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    39         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     41cd ${PETSC_DIR}
     42./config/configure.py \
     43        --prefix="${PREFIX}" \
     44        --PETSC_DIR="${PETSC_DIR}" \
    4045        --LDFLAGS="-Wl,-no_compact_unwind" \
    4146        --with-shared-libraries=0 \

  • issm/trunk-jpl/externalpackages/petsc/install-3.17-mac-m1.sh

    r27043 r27202  
    44
    55## Constants
    6 VER="3.17.0"
     6#
     7VER="3.17.4"
     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
    711
    812# Download source
    9 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    1014
    1115# Unpack source
    … …  
    1317
    1418# Cleanup
    15 rm -rf install src
    16 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    1721
    18 # Move source to 'src' directory
    19 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2024rm -rf petsc-${VER}
    2125
    22 cd src
    23 ./configure \
    24         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    25         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     26# Configure
     27cd ${PETSC_DIR}
     28./config/configure.py \
     29        --prefix="${PREFIX}" \
     30        --PETSC_DIR="${PETSC_DIR}" \
    2631        --LDFLAGS="-Wl,-no_compact_unwind" \
    2732        --with-debugging=0 \

  • issm/trunk-jpl/externalpackages/petsc/install-3.17-pleiades.sh

    r27192 r27202  
    22set -eu
    33
     4
    45## Constants
     6#
    57VER="3.17.4"
    68
     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
    712# Download source
    8 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    914
    1015# Unpack source
    … …  
    1217
    1318# Cleanup
    14 rm -rf install src
    15 mkdir install src
     19rm -rf ${PREFIX} ${PETSC_DIR}
     20mkdir -p ${PETSC_DIR}
    1621
    17 # Move source to 'src' directory
    18 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    1924rm -rf petsc-${VER}
    2025
    21 #options from cat /nasa/petsc/3.14.5_toss3/lib/petsc/conf/petscvariables | grep CONF
    22 cd src
     26# Configure
     27#
     28# NOTE:
     29# - Options from,
     30#
     31#               cat /nasa/petsc/3.14.5_toss3/lib/petsc/conf/petscvariables | grep CONF
     32#
     33cd ${PETSC_DIR}
    2334./configure \
    24         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    25         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     35        --prefix="${PREFIX}" \
     36        --PETSC_DIR="${PETSC_DIR}" \
    2637        --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \
    2738        --with-scalapack-include="/nasa/intel/Compiler/2018.3.222/mkl/include" \

  • issm/trunk-jpl/jenkins/examples_tests.sh

    r26162 r27202  
    4040for dir in ./* ; do
    4141        if [ -d "${dir}" ]; then
     42                # # Temporary short circuit to check single example
     43                # example="./AMR"
     44                # if [ "${dir}" != "${example}" ]; then
     45                #       continue
     46                # fi
     47
    4248                # Some of the examples are incomplete (on purpose). As such, we will
    4349                # have to populate the missing steps in order to make sure that
    … …  
    4551
    4652                cd ${dir}
    47 
    4853                if [ "${dir}" == "./AMR" ]; then
    4954                        sed -i.bak -e '1 s|^.*$|try\n\n&|' $RUNME_FILE

  • issm/trunk-jpl/jenkins/jenkins.sh

    r26817 r27202  
    178178                cd ${ISSM_DIR}/externalpackages/$PACKAGENAME
    179179
    180                 echo "======================================================";
    181                 echo "       Installing $PACKAGENAME                        ";
    182                 echo "======================================================";
    183 
    184                 ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log
    185                 if [ $? -ne 0 ] && [ "${PACKAGENAME}" != "boost" ]; then
    186                         cat compil.log
     180                # Do not install package if it already exists
     181                #
     182                # NOTE: Assumes PREFIX is defined in package installation script
     183                #
     184                PREFIX=$(egrep "PREFIX=" ./$PACKAGEINST | cut -d'"' -f 2 | envsubst)
     185                if [ ! -d "${PREFIX}" ]; then
    187186                        echo "======================================================";
    188                         echo "    ERROR: installation of $PACKAGENAME failed        ";
     187                        echo "       Installing $PACKAGENAME                        ";
    189188                        echo "======================================================";
    190                         echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\">" >> $EXTERNAL_TEST_FILE
    191                         echo '<failure message="failure">External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
    192                         cat compil.log >> $EXTERNAL_TEST_FILE
    193                         echo '</failure>' >> $EXTERNAL_TEST_FILE
    194                         echo '</testcase>' >> $EXTERNAL_TEST_FILE
    195                         EXTERNALPACKAGES_FAILED=1;
     189
     190                        ./$PACKAGEINST $NUMCPUS_INSTALL &> compil.log
     191                        if [ $? -ne 0 ] && [ "${PACKAGENAME}" != "boost" ]; then
     192                                cat compil.log
     193                                echo "======================================================";
     194                                echo "    ERROR: installation of $PACKAGENAME failed        ";
     195                                echo "======================================================";
     196                                echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\">" >> $EXTERNAL_TEST_FILE
     197                                echo '<failure message="failure">External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
     198                                cat compil.log >> $EXTERNAL_TEST_FILE
     199                                echo '</failure>' >> $EXTERNAL_TEST_FILE
     200                                echo '</testcase>' >> $EXTERNAL_TEST_FILE
     201                                EXTERNALPACKAGES_FAILED=1;
     202                        else
     203                                echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\"/>" >> $EXTERNAL_TEST_FILE
     204                        fi
     205                        source ${ISSM_DIR}/etc/environment.sh
     206
     207                        #If external package is rebuilt, we also need to recompile
     208                        ISSM_RECONFIGURE="yes"
     209                        ISSM_COMPILATION="yes"
    196210                else
     211                        echo "======================================================";
     212                        echo "       Skipping $PACKAGENAME                          ";
     213                        echo "======================================================";
    197214                        echo "<testcase classname=\"externalpackages\" name=\"$PACKAGENAME\"/>" >> $EXTERNAL_TEST_FILE
    198215                fi
    199                 source ${ISSM_DIR}/etc/environment.sh
    200 
    201                 #If external package is rebuilt, we also need to recompile
    202                 ISSM_RECONFIGURE="yes"
    203                 ISSM_COMPILATION="yes"
    204216        else
    205217                echo "======================================================";

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

    r27191 r27202  
    4444        autotools       install-mac.sh
    4545        cmake           install.sh
    46         petsc           install-3.16-mac.sh
     46        petsc           install-3.17-mac-intel.sh
    4747        gsl                     install.sh
    4848        boost           install-1.7-mac.sh

  • issm/trunk-jpl/m4/issm_options.m4

    r27158 r27202  
    648648                dnl TODO:
    649649                dnl - Should we also be checking if HAVE_BOOST before adding boost libs?
     650                dnl - Clean up the following conditionals
    650651                dnl
    651652                case "${host_os}" in
    … …  
    672673                                elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
    673674                                        if test "${BOOST_VERSION_MAJOR}" == "1"; then
    674                                                 DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
     675                                                DAKOTAFLAGS="-DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
    675676                                                DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
    676677                                                DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"
    … …  
    685686                                                        DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -L$BOOST_ROOT/lib -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system ${BLASLAPACKLIB}"
    686687                                                elif test "${BOOST_VERSION_MINOR}" == "72"; then
    687                                                         DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
     688                                                        DAKOTAFLAGS="-DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
    688689                                                        DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchosremainder -lteuchosnumerics -lteuchoscomm -lteuchosparameterlist -lteuchosparser -lteuchoscore -lpecos_util -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lapproxnn -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system ${BLASLAPACKLIB}"
    689690                                                fi
    … …  
    705706                                elif test "${DAKOTA_VERSION}" == "6.1" || test "${DAKOTA_VERSION}" == "6.2"; then
    706707                                        if test "${BOOST_VERSION_MAJOR}" == "1"; then
    707                                                 DAKOTAFLAGS="-DHAVE_CONFIG_H -DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
     708                                                DAKOTAFLAGS="-DHAVE_CONFIG_H -DDISABLE_DAKOTA_CONFIG_H -DBOOST_DISABLE_ASSERTS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DHAVE_ADAPTIVE_SAMPLING -DHAVE_ESM -DHAVE_QUESO -DHAVE_QUESO_GPMSA -DHAVE_CONMIN -DHAVE_DDACE -DHAVE_DREAM -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_NOMAD -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
    708709                                                DAKOTALIB="-L${DAKOTA_ROOT}/lib -ldakota_src -ldakota_src_fortran -lnidr -lteuchos -lpecos -lpecos_src -llhs -llhs_mods -llhs_mod -ldfftpack -lsparsegrid -lsurfpack -lsurfpack -lsurfpack_fortran -lqueso -lconmin -lddace -ldream -lfsudace -lhopspack -lncsuopt -lcport -lnomad -loptpp -lpsuade -lamplsolver"
    709710                                                DAKOTALIB+=" -L${BOOST_ROOT}/lib -lboost_filesystem -lboost_program_options -lboost_regex -lboost_serialization -lboost_system"

  • issm/trunk-jpl/src/c/Makefile.am

    r27154 r27202  
    829829
    830830# External packages
    831 LDADD += $(CHACOLIB) $(DAKOTALIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(SEMICLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
     831LDADD += $(SEMICLIB) $(M1QN3LIB) $(CHACOLIB) $(PETSCLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLASLAPACKLIB) $(PARMETISLIB) $(METISLIB) $(NEOPZLIB) $(TAOLIB) $(PLAPACKLIB) $(MPLAPACKLIB) $(SUPERLULIB) $(SPOOLESLIB) $(BLACSLIB) $(HDF5LIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(SCOTCHLIB) $(MKLLIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJLIB) $(ESMFLIB) $(OSLIBS)
    832832
    833833if FORTRAN
    … …  
    840840issm_slc_SOURCES = main/issm_slc.cpp
    841841issm_slc_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS)
     842issm_slc_LDADD = $(DAKOTALIB) $(LDADD)
    842843
    843844if OCEAN
    … …  
    857858issm_dakota_SOURCES = main/issm_dakota.cpp
    858859issm_dakota_CXXFLAGS= $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS)
    859 issm_dakota_LDADD= $(LDADD)
     860issm_dakota_LDADD = $(DAKOTALIB) $(LDADD)
    860861bin_PROGRAMS += issm_post
    861862issm_post_SOURCES = main/issm_post.cpp

  • issm/trunk-jpl/src/m/dev/devpath.py

    r26353 r27202  
    3737        print('Warning: devpath.py: cluster settings should be in {}'.format(jpl_path))
    3838
    39 from runme import runme  #first because plotmodel may fail
     39try: # Avoid circular import
     40    from runme import runme  # First, because plotmodel may fail
     41except:
     42    pass
    4043from plotmodel import plotmodel
    4144

  • issm/trunk-jpl/test/NightlyRun/IdFromString.py

    r24256 r27202  
    22from IdToName import IdToName
    33import os
     4import re
    45
    56# use verbose = False to print output when this is called by command line
    … …  
    2728    ids = []
    2829    idnames = []
    29     for f in os.listdir('.'):
    30         if f.endswith('.py') and f.startswith('test'):
    31             # all tests look like: "testwxyz.py" so 5th to 3rd to last is always the full id
    32             s = int(f[4:-3])
    33             name = IdToName(s)
    34             if (string == ' * ') or (name is not None and string in name):
    35                 ids.append(s)
    36                 idnames.append(name)
     30    flist = [f for f in os.listdir('.') if re.match('test[0-9]+.py', f)] # File name must follow the format "test<integer>.py"
     31    list_ids = [int(re.search(r'\d+',file.split('.')[0]).group()) for file in flist] # Retrieve test IDs
     32    for i in list_ids:
     33        name = IdToName(i)
     34        if (string == ' * ') or (name is not None and string in name):
     35            ids.append(i)
     36            idnames.append(name)
    3737
    3838#Return if no test found

  • issm/trunk-jpl/test/NightlyRun/runme.m

    r27117 r27202  
    8888% }}}
    8989%GET ids  {{{
    90 flist=dir;%use dir, as it seems to act OS independent
     90flist=dir; %use dir, as it seems to act OS independent
    9191list_ids=[];
    9292for i=1:numel(flist),
    … …  
    101101                                disp(['WARNING: ignore file ' flist(i).name]);
    102102                        else
    103                                 list_ids(end+1)=id;%Keep test id only (strip 'test' and '.m')
     103                                list_ids(end+1)=id; %Keep test id only (strip 'test' and '.m')
    104104                        end
    105105                end

  • issm/trunk-jpl/test/NightlyRun/runme.py

    r27167 r27202  
    88#
    99import argparse
    10 from glob import glob
    1110import os
    12 from re import search, split
     11import re
    1312from sys import float_info
    1413from traceback import format_exc
    … …  
    116115    # }}}
    117116    #GET ids  {{{
    118     flist = glob('test*.py')  #File name must start with 'test' and must end by '.py' and must be different than 'test.py'
    119     list_ids = [int(search(r'\d+',file.split('.')[0]).group()) for file in flist if not file == 'test.py'] # Keep test id only (skip 'test' and '.py')
    120 
    121     i1, i2 = parallelrange(rank, numprocs, len(list_ids))  #Get tests for this cpu only
     117    flist = [f for f in os.listdir('.') if re.match('test[0-9]+.py', f)] # File name must follow the format "test<integer>.py"
     118    list_ids = [int(re.search(r'\d+',file.split('.')[0]).group()) for file in flist] # Retrieve test IDs
     119    i1, i2 = parallelrange(rank, numprocs, len(list_ids))  # Get tests for this CPU only
    122120    list_ids = list_ids[i1:i2 + 1]
    123121    if np.size(id) > 0 and id is not None:
    … …  
    172170    test_ids = list(test_ids)
    173171    test_ids.sort()
     172    print(test_ids)
    174173    # }}}
    175174
    … …  
    213212                for key in mdl.results.__dict__.keys():
    214213                    if 'Solution' in key:
    215                         solvetype = split('Solution', key)[0]
     214                        solvetype = re.split('Solution', key)[0]
    216215
    217216                #we save the results, scrap them and solve.
    … …  
    224223                    try:
    225224                        #first look for indexing
    226                         if search(r'\d+$', fieldname):
    227                             index = int(search(r'\d+$', fieldname).group()) - 1
    228                             fieldname = fieldname[:search(r'\d+$', fieldname).start()]
     225                        if re.search(r'\d+$', fieldname):
     226                            index = int(re.search(r'\d+$', fieldname).group()) - 1
     227                            fieldname = fieldname[:re.search(r'\d+$', fieldname).start()]
    229228                        elif 'FirstStep' in fieldname:
    230229                            index = 0
    231                             fieldname = fieldname[:search('FirstStep', fieldname).start()]
     230                            fieldname = fieldname[:re.search('FirstStep', fieldname).start()]
    232231                        elif 'SecondStep' in fieldname:
    233232                            index = 1
    234                             fieldname = fieldname[:search('SecondStep', fieldname).start()]
     233                            fieldname = fieldname[:re.search('SecondStep', fieldname).start()]
    235234                        elif 'ThirdStep' in fieldname:
    236235                            index = 2
    237                             fieldname = fieldname[:search('ThirdStep', fieldname).start()]
     236                            fieldname = fieldname[:re.search('ThirdStep', fieldname).start()]
    238237                        else:
    239238                            index = 0
    … …  
    270269                                    #probably severalmatches, we take the last one which should be the good one (Needs to be controled in the list above)
    271270                                    sufix = sufixes[np.squeeze(np.where([suf in fieldname for suf in sufixes]))[-1]]
    272                                 fieldname = fieldname[:search(sufix, fieldname).start()]
     271                                fieldname = fieldname[:re.search(sufix, fieldname).start()]
    273272                            elif fieldname.endswith("P") and index == 1:
    274273                                #we are looking for P2 but 2 as been considered as an index and so shifted by -1
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