Changeset 26950


Ignore:
Timestamp:
04/10/22 13:17:30 (3 years ago)
Author:
jdquinn
Message:

CHG: Various changes to external packages and configuration in support of solid earth build on Pleiades; various pending commits

Location:
issm/trunk-jpl
Files:
1 added
1 deleted
12 edited
2 copied
10 moved

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl/etc/environment.sh

    r26885 r26950  
    507507SQLITE_ROOT="${ISSM_EXT_DIR}/sqlite/install"
    508508if [ -d "${SQLITE_ROOT}" ]; then
    509         path_append "${SQLITE_ROOT}/bin"
    510         library_path_append "${SQLITE_ROOT}/lib"
    511         ld_library_path_append "${SQLITE_ROOT}/lib"
     509        path_prepend "${SQLITE_ROOT}/bin"
     510        cpath_prepend "${SQLITE_ROOT}/include"
     511        library_path_prepend "${SQLITE_ROOT}/lib"
     512        ld_library_path_prepend "${SQLITE_ROOT}/lib"
    512513fi
    513514

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

    r26775 r26950  
    22set -eu
    33
    4 #Some cleanup
    5 rm -rf Dakota
    6 rm -rf src
    7 rm -rf build
    8 rm -rf install
    9 mkdir src build install
    104
    11 #Download from ISSM server
    12 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz'
     5## Constants
     6#
     7VER="6.2"
    138
    14 #Untar
    15 tar -zxvf dakota-6.2-public-src.tar.gz
     9PREFIX="${ISSM_DIR}/externalpackages/dakota/install" # Set to location where external package should be installed
    1610
    17 #Move Dakota to src directory
    18 mv dakota-6.2.0.src/* src
    19 rm -rf dakota-6.2.0.src
     11## Environment
     12#
     13export BLAS_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64
     14export CXXFLAGS='-std=c++11'
     15export DAK_BUILD=${ISSM_DIR}/externalpackages/dakota/build # DO NOT CHANGE THIS
     16export DAK_INSTALL=${PREFIX} # DO NOT CHANGE THIS
     17export DAK_SRC=${ISSM_DIR}/externalpackages/dakota/src # DO NOT CHANGE THIS
     18export LAPACK_LIBS="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it; should upate to /nasa/intel/Compiler/2021.4.0/mkl/2021.4.0/lib/intel64
    2019
    21 #Set up Dakota cmake variables and config
    22 export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src
    23 export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build
    24 export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install
     20# Cleanup
     21rm -rf ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
     22mkdir -p ${DAK_BUILD} ${DAK_INSTALL} ${DAK_SRC}
    2523
    26 export CXXFLAGS='-std=c++11' # Setting CXXFLAGS to deal with C++11 incompatibility with MATLAB's Boost (absolutely necessary for this version)
     24# Download source
     25${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
    2726
    28 cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
    29 patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.pfe.patch
    30 patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch
    31 patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.pfe.patch
     27# Unpack source
     28tar -zxvf dakota-${VER}-public-src.tar.gz
    3229
    33 #Apply patches
    34 patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch
    35 patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch
    36 patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch
     30# Move source to 'src' directory
     31mv dakota-${VER}.0.src/* ${DAK_SRC}
     32rm -rf dakota-${VER}.0.src
    3733
    38 #Configure dakota
    39 cd $DAK_BUILD
     34# Copy customized source and configuration files to 'src' directory
     35cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
     36cp configs/${VER}/packages/queso/src/misc/src/1DQuadrature.C ${DAK_SRC}/packages/queso/src/misc/src
     37cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
     38cp configs/${VER}/packages/VPISparseGrid/src/sandia_rules.cpp ${DAK_SRC}/packages/VPISparseGrid/src
     39cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src
     40cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
     41cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
    4042
     43# Copy customized source and configuration files specific to Linux to 'src' directory
     44cp configs/${VER}/linux/cmake/BuildDakotaCustom.pleiades.cmake ${DAK_SRC}/cmake/BuildDakotaCustom.cmake
     45cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
     46
     47# Configure
     48cd ${DAK_BUILD}
    4149cmake \
    42         -DBOOST_ROOT:PATHNAME=$BOOST_ROOT \
    43         -DBoost_LIBRARY_DIRS:FILEPATH=${BOOST_ROOT}/lib \
    44         -DBoost_INCLUDE_DIR:FILEPATH=${BOOST_ROOT}/include \
    45         -DBoost_NO_BOOST_CMAKE=TRUE \
    46         -DBoost_NO_SYSTEM_PATHS=TRUE \
    4750        -DBUILD_SHARED_LIBS=ON \
    4851        -DBUILD_STATIC_LIBS=OFF \
    … …  
    5053        -DCMAKE_C_FLAGS="-Wno-error=implicit-function-declaration" \
    5154        -DCMAKE_CXX_COMPILER=mpicxx \
    52         -DCMAKE_CXX_FLAGS="-lstdc++" \
    5355        -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran \
     56        -DBoost_NO_BOOST_CMAKE=TRUE \
    5457        -DHAVE_ACRO=OFF \
    5558        -DHAVE_JEGA=OFF \
    … …  
    6063        ${DAK_SRC}
    6164
    62 cd ..
    63 
    64 #Compile and install dakota
    65 cd $DAK_BUILD
    66 if [ $# -eq 0 ];
    67 then
     65# Compile and install
     66if [ $# -eq 0 ]; then
    6867        make
    6968        make install
    … …  
    7271        make -j $1 install
    7372fi
    74 cd ..
     73
     74cd ${DAK_INSTALL}
     75
     76# Comment out definition of HAVE_MPI in Teuchos config header file in order to
     77# avoid conflict with our definition
     78sed -i -e "s/#define HAVE_MPI/\/* #define HAVE_MPI *\//g" include/Teuchos_config.h

  • issm/trunk-jpl/externalpackages/hdf5/install-1-parallel-with_tests.sh

    r26949 r26950  
    66#
    77VER="1.10.5"
    8 ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed
    910
    1011## Environnment
    … …  
    1617
    1718# Untar source
    18 tar -zxvf hdf5-$VER.tar.gz
     19tar -zxvf hdf5-${VER}.tar.gz
    1920
    2021# Cleanup
    … …  
    2324
    2425# Move source to 'src' directory
    25 mv hdf5-$VER/* src/
    26 rm -rf hdf5-$VER
     26mv hdf5-${VER}/* src/
     27rm -rf hdf5-${VER}
    2728
    2829# Configure
    2930cd src
    3031./configure \
    31         --prefix="${ISSM_DIR}/externalpackages/hdf5/install" \
     32        --prefix="${PREFIX}" \
    3233        --enable-parallel \
    33         --with-zlib=${ZLIB_ROOT} \
     34        --with-zlib="${ZLIB_ROOT}" \
    3435        --enable-hl
    3536
    … …  
    4546        make -j $1 install
    4647fi
    47 
    48 # Return to initial directory
    49 cd ..

  • issm/trunk-jpl/externalpackages/hdf5/install-1-parallel.sh

    r26949 r26950  
    66#
    77VER="1.10.5"
    8 ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed
    910
    1011## Environnment
    … …  
    1617
    1718# Untar source
    18 tar -zxvf hdf5-$VER.tar.gz
     19tar -zxvf hdf5-${VER}.tar.gz
    1920
    2021# Cleanup
    … …  
    2324
    2425# Move source to 'src' directory
    25 mv hdf5-$VER/* src/
    26 rm -rf hdf5-$VER
     26mv hdf5-${VER}/* src/
     27rm -rf hdf5-${VER}
    2728
    2829# Configure
    2930cd src
    3031./configure \
    31         --prefix="${ISSM_DIR}/externalpackages/hdf5/install" \
     32        --prefix="${PREFIX}" \
    3233        --enable-parallel \
    33         --with-zlib=${ZLIB_ROOT} \
     34        --with-zlib="${ZLIB_ROOT}" \
    3435        --enable-hl
    3536
    … …  
    4344        make -j $1 install
    4445fi
    45 
    46 # Return to initial directory
    47 cd ..

  • issm/trunk-jpl/externalpackages/hdf5/install-1-with_tests.sh

    r26949 r26950  
    66#
    77VER="1.10.5"
    8 ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed
    910
    1011# Download source
    … …  
    1213
    1314# Untar source
    14 tar -zxvf hdf5-$VER.tar.gz
     15tar -zxvf hdf5-${VER}.tar.gz
    1516
    1617# Cleanup
    … …  
    1920
    2021# Move source to 'src' directory
    21 mv hdf5-$VER/* src/
    22 rm -rf hdf5-$VER
     22mv hdf5-${VER}/* src/
     23rm -rf hdf5-${VER}
    2324
    2425# Configure
    2526cd src
    2627./configure \
    27         --prefix="${ISSM_DIR}/externalpackages/hdf5/install" \
    28         --with-zlib=${ZLIB_ROOT} \
     28        --prefix="${PREFIX}" \
     29        --with-zlib="${ZLIB_ROOT}" \
    2930        --enable-hl
    3031
    … …  
    4041        make -j $1 install
    4142fi
    42 
    43 # Return to initial directory
    44 cd ..

  • issm/trunk-jpl/externalpackages/hdf5/install-1.sh

    r26949 r26950  
    66#
    77VER="1.10.5"
    8 ZLIB_ROOT="${ISSM_DIR}/externalpackages/zlib/install"
     8
     9PREFIX="${ISSM_DIR}/externalpackages/hdf5/install" # Set to location where external package should be installed
    910
    1011# Download source
    … …  
    1213
    1314# Untar source
    14 tar -zxvf hdf5-$VER.tar.gz
     15tar -zxvf hdf5-${VER}.tar.gz
    1516
    1617# Cleanup
    … …  
    1920
    2021# Move source to 'src' directory
    21 mv hdf5-$VER/* src/
    22 rm -rf hdf5-$VER
     22mv hdf5-${VER}/* src/
     23rm -rf hdf5-${VER}
    2324
    2425# Configure
    2526cd src
    2627./configure \
    27         --prefix="${ISSM_DIR}/externalpackages/hdf5/install" \
    28         --with-zlib=${ZLIB_ROOT} \
     28        --prefix="${PREFIX}" \
     29        --with-zlib="${ZLIB_ROOT}" \
    2930        --enable-hl
    3031
    … …  
    3839        make -j $1 install
    3940fi
    40 
    41 # Return to initial directory
    42 cd ..

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

    r26239 r26950  
    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

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

    r25800 r26950  
    44
    55## Constants
     6#
    67VER="3.14.0"
    78
     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
    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 ${PETSC_DIR}
    1721
    18 # Move source to 'src' directory
    19 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2024rm -rf petsc-${VER}
    2125
    … …  
    2327#
    2428# 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).
    2531# - Added -fallow-argument-mismatch to FFLAGS in order to clear,
    2632#
    … …  
    2935#
    3036#       for gfortran 10 or later (may need to remove it for earlier versions).
    31 # - Added -Wno-error=implicit-function-declaration to CFLAGS for Clang >= 12.
    32 #       (may need to remove it for earlier versions not using the C99 standard).
    3337#
    34 cd src
     38cd ${PETSC_DIR}
    3539./config/configure.py \
    36         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    37         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     40        --prefix="${PREFIX}" \
     41        --PETSC_DIR="${PETSC_DIR}" \
    3842        --CFLAGS="-Wno-error=implicit-function-declaration" \
    3943        --FFLAGS="-fallow-argument-mismatch" \

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

    r26771 r26950  
    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="3.14.0"
    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 ${PETSC_DIR}
    2321
    24 # Move source to 'src' directory
    25 mv petsc-${VER}/* src/
     22# Move source to $PETSC_DIR
     23mv petsc-${VER}/* ${PETSC_DIR}
    2624rm -rf petsc-${VER}
    2725
    2826# Configure
    29 cd src
     27cd ${PETSC_DIR}
    3028./config/configure.py \
    31         COPTFLAGS="-g -O3" CXXOPTFLAGS="-g -O3" FOPTFLAGS="-g -O3" \
    32         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    33         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     29        --prefix="${PREFIX}" \
     30        --PETSC_DIR="${PETSC_DIR}" \
     31        --CFLAGS="-g -O3" \
     32        --CXXFLAGS="-g -O3" \
     33        --FFLAGS="-g -O3" \
    3434        --with-debugging=0 \
    3535        --with-valgrind=0 \
    … …  
    4141        --with-scalapack-include=/nasa/intel/Compiler/2018.3.222/mkl/include \
    4242        --with-scalapack-lib="/nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_scalapack_lp64.so /nasa/intel/Compiler/2018.3.222/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so" \
    43         --with-shared-libraries=1 \
    4443        --download-metis=1 \
    4544        --download-parmetis=1 \
    46         --download-scalapack=0 \
    47         --download-mumps=1
     45        --download-scalapack=0
    4846
    4947# Compile and install

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

    r26803 r26950  
    77VER="3.15.0"
    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
    10 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.15.0.tar.gz' 'petsc-3.15.0.tar.gz'
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    1114
    1215# Unpack source
    … …  
    2831cd src
    2932./config/configure.py \
    30         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    31         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     33        --prefix="${PREFIX}" \
     34        --PETSC_DIR="${PETSC_DIR}" \
    3235        --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \
    3336        --with-scalapack-include=/nasa/intel/Compiler/2018.3.222/mkl/include \

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

    r26949 r26950  
    55## Constants
    66#
    7 VER="3.15.0"
     7VER="3.16.4"
     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
    811
    912# Download source
    10 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.15.0.tar.gz' 'petsc-3.15.0.tar.gz'
     13$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/petsc-lite-${VER}.tar.gz" "petsc-${VER}.tar.gz"
    1114
    1215# Unpack source
    13 tar -zxvf petsc-3.15.0.tar.gz
     16tar -zxvf petsc-${VER}.tar.gz
    1417
    1518# Cleanup
    … …  
    1821
    1922# Move source to $PETSC_DIR
    20 mv petsc-3.15.0/* src/
    21 rm -rf petsc-3.15.0
     23mv petsc-${VER}/* src/
     24rm -rf petsc-${VER}
    2225
    2326
    … …  
    2831cd src
    2932./config/configure.py \
    30         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
    31         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
     33        --prefix="${PREFIX}" \
     34        --PETSC_DIR="${PETSC_DIR}" \
    3235        --with-blas-lapack-dir="/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl" \
    3336        --with-scalapack-include=/nasa/intel/Compiler/2018.3.222/mkl/include \

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

    r25968 r26950  
    33
    44
     5# Constants
     6#
    57VER="3300100"
    68
     9PREFIX="${ISSM_DIR}/externalpackages/sqlite/install" # Set to location where external package should be installed
     10
    711# Cleanup
    8 rm -rf install src
    9 mkdir install src
     12rm -rf ${PREFIX} src
     13mkdir -p ${PREFIX} src
    1014
    1115# Download source
    … …  
    1317
    1418# Unpack source
    15 tar -zxvf sqlite-autoconf-$VER.tar.gz
     19tar -zxvf sqlite-autoconf-${VER}.tar.gz
    1620
    1721# Move source into 'src' directory
    18 mv sqlite-autoconf-$VER/* src
    19 rm -rf sqlite-autoconf-$VER
     22mv sqlite-autoconf-${VER}/* src
     23rm -rf sqlite-autoconf-${VER}
    2024
    2125# Configure
    2226cd src
    2327./configure \
    24         --prefix="${ISSM_DIR}/externalpackages/sqlite/install"
     28        --prefix="${PREFIX}"
    2529
    2630# Compile and install

  • issm/trunk-jpl/jenkins/pleiades-dakota

    r26752 r26950  
    99        --with-wrappers=no \
    1010        --with-vendor="intel-pleiades-mpi" \
     11        --with-cxxoptflags="-O3 " \
    1112        --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
    1213        --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
    13         --with-boost-dir=/nasa/pkgsrc/sles12/2018Q3 \
     14        --with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \
    1415        --with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \
    15         --with-gsl-dir=/nasa/pkgsrc/sles12/2018Q3 \
     16        --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
    1617        --with-mpi-include=" " \
    1718        --with-mpi-libflags=" -lmpi" \
    18         --with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -limf -lsvml -lirc" \
     19        --with-mkl-libflags="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
    1920        --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
    2021        --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \
    2122        --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
    22         --with-scalapack-dir=/nasa/pkgsrc/sles12/2018Q3 \
     23        --with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
    2324        --with-graphics-lib="/usr/lib64/libX11.so" \
    24         --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
     25        --with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \
    2526'
    2627
    … …  
    2930#-------------------#
    3031
     32# NOTE: Python 3 is installed only as a build system for GSL
    3133EXTERNALPACKAGES="
    32         petsc   install-3.13-pleiades.sh
     34        python  install-3-linux.sh
     35        petsc   install-3.14-pleiades.sh
     36        gsl             install-pleiades.sh
     37        boost   install-1.55-pleiades.sh
    3338        dakota  install-6.2-pleiades.sh
    3439        m1qn3   install.sh
    … …  
    5358
    5459# Number of CPUs used in the nightly runs
    55 NUMCPUS_RUN=2
     60NUMCPUS_RUN=1
    5661
    5762# Nightly run options

  • issm/trunk-jpl/jenkins/pleiades-solid_earth

    r26946 r26950  
    99        --with-wrappers=no \
    1010        --with-vendor="intel-pleiades-mpi" \
     11        --with-cxxoptflags="-O3 " \
    1112        --with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
    1213        --with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
    13         --with-boost-dir=/nasa/pkgsrc/sles12/2018Q3 \
     14        --with-boost-dir="${ISSM_DIR}/externalpackages/boost/install" \
    1415        --with-dakota-dir="${ISSM_DIR}/externalpackages/dakota/install" \
    15         --with-gsl-dir=/nasa/pkgsrc/sles12/2018Q3 \
     16        --with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
    1617        --with-mpi-include=" " \
    1718        --with-mpi-libflags=" -lmpi" \
    18         --with-mkl-libflags="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -limf -lsvml -lirc" \
     19        --with-mkl-libflags="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm" \
    1920        --with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
    2021        --with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \
    2122        --with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
    22         --with-scalapack-dir=/nasa/pkgsrc/sles12/2018Q3 \
     23        --with-scalapack-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so" \
    2324        --with-graphics-lib="/usr/lib64/libX11.so" \
    24         --with-fortran-lib="-L/nasa/intel/Compiler/2016.2.181/compilers_and_libraries_2016.2.181/linux/compiler/lib/intel64/ -lifcore -lifport" \
     25        --with-fortran-lib="-L/nasa/intel/Compiler/2018.3.222/compilers_and_libraries_2018.3.222/linux/compiler/lib/intel64_lin/ -lifcore -lifport -lgfortran" \
    2526'
    2627
    … …  
    2930#-------------------#
    3031
     32# NOTE:
     33# - Python 3 is installed only as a build system for GSL
     34# - shell2junit is included to run test suites via jenkins.sh
     35#
    3136EXTERNALPACKAGES="
    32         petsc   install-3.13-pleiades.sh
    33         dakota  install-6.2-pleiades.sh
    34         m1qn3   install.sh
     37        python          install-3-linux.sh
     38        petsc           install-3.14-pleiades.sh
     39        zlib            install-1.sh
     40        hdf5            install-1-parallel.sh
     41        gsl                     install-pleiades.sh
     42        boost           install-1.55-pleiades.sh
     43        dakota          install-6.2-pleiades.sh
     44        curl            install-7-linux.sh
     45        netcdf          install-4.7-parallel.sh
     46        sqlite          install.sh
     47        proj            install-6.sh
     48        gdal            install-3-python.sh
     49        gshhg           install.sh
     50        gmt                     install-6-linux.sh
     51        gmsh            install-4.sh
     52        triangle        install-linux.sh
     53        chaco           install.sh
     54        m1qn3           install.sh
     55        semic           install.sh
    3556"
    3657
    … …  
    5374
    5475# Number of CPUs used in the nightly runs
    55 NUMCPUS_RUN=2
     76NUMCPUS_RUN=1
    5677
    5778# Nightly run options

  • issm/trunk-jpl/m4/issm_options.m4

    r26934 r26950  
    292292                        export CFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"
    293293                elif test "${VENDOR}" == "intel-discover"; then
    294                    export CC=mpicc
    295                    export CXX=mpicxx
     294                        export CC=mpicc
     295                        export CXX=mpicxx
    296296                        export CXXFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK -std=c++11"
    297297                        export CFLAGS="-O3 -D_INTEL_LINUX_ -DMPICH_IGNORE_CXX_SEEK"

  • issm/trunk-jpl/packagers/mac/sign-issm-mac-binaries-matlab.sh

    r26762 r26950  
    6767# NOTE: May be able to remove this after updating macOS.
    6868#
    69 alias svn='/usr/local/bin/svn'
     69#alias svn='/usr/local/bin/svn'
    7070
    7171## Override certain other aliases

  • issm/trunk-jpl/packagers/mac/sign-issm-mac-binaries-python.sh

    r26762 r26950  
    6767# NOTE: May be able to remove this after updating macOS.
    6868#
    69 alias svn='/usr/local/bin/svn'
     69#alias svn='/usr/local/bin/svn'
    7070
    7171## Override certain other aliases

  • issm/trunk-jpl/scripts/DownloadExternalPackage.sh

    r25932 r26950  
    4141
    4242## Download file
     43#
     44if [ ! -z `which curl` ]; then
     45        curl --silent $URL -o $OUT_FILE
    4346
    44 if [ ! -z `which curl` ]
    45 then
    46         curl --silent $URL -o $OUT_FILE
    47 elif [ ! -z `which wget` ]
    48 then
     47        # Try wget if curl exists but fails
     48        if [ $? -ne 0 ]; then
     49                if [ ! -z `which wget` ]; then
     50                        wget --quiet -O $OUT_FILE $URL
     51
     52                        if [ $? -ne 0 ]; then
     53                                echo "Error: both curl and wget failed. To debug, download package manually using curl without '--silent' option and/or wget without '--quiet' option."
     54                                exit 0
     55                        fi
     56                else
     57                        echo $MSG_ERR_NO_GET_CMD
     58                        exit 0
     59                fi
     60        fi
     61elif [ ! -z `which wget` ]; then
    4962        wget --quiet -O $OUT_FILE $URL
    5063else
    5164        echo $MSG_ERR_NO_GET_CMD
    52         exit 0
    5365fi
    54 
    55 exit 0
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