Changeset 24649


Ignore:
Timestamp:
03/10/20 10:23:37 (5 years ago)
Author:
jdquinn
Message:

CHG: Initial commit for all macOS binaries; relevant changes to respective Linux scripts/configs; cleanup

Location:
issm/trunk-jpl
Files:
33 added
10 deleted
13 edited
2 copied
2 moved

Legend:

Unmodified
Added
Removed

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

    r24596 r24649  
    22set -eu
    33
    4 #Version numbers
    5 M4_VER="1.4.18"
     4
     5## Constants
     6#
    67AUTOCONF_VER="2.69"
    78AUTOMAKE_VER="1.16.1"
    89LIBTOOL_VER="2.4.2"
     10M4_VER="1.4.18"
    911
    10 # Clean up existing directories
     12## Environment
     13#
     14export PATH="${ISSM_DIR}/externalpackages/autotools/install/bin:$PATH"
     15
     16# Cleanup
    1117rm -rf install src
    12 
    13 # Set up for installation
    1418mkdir install
    15 export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH"
    1619
    1720# Install m4
    1821echo " === INSTALLING M4 =="
    19 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-$M4_VER.tar.gz" "m4-$M4_VER.tar.gz"
    20 tar -zxvf m4-$M4_VER.tar.gz
    21 mv m4-$M4_VER src
     22${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-${M4_VER}.tar.gz" "m4-${M4_VER}.tar.gz"
     23tar -zxvf m4-${M4_VER}.tar.gz
     24mv m4-${M4_VER} src
    2225cd src
    2326
    … …  
    2932echo "#define _IO_IN_BACKUP 0x100" >> lib/stdio-impl.h
    3033
    31 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     34./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    3235make
    3336make install
    3437cd ..
    3538
    36 # Install autoconf
     39# Install Autoconf
    3740echo " === INSTALLING AUTOCONF =="
    3841rm -rf src
    39 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-$AUTOCONF_VER.tar.gz" "autoconf-$AUTOCONF_VER.tar.gz"
    40 tar -zxvf autoconf-$AUTOCONF_VER.tar.gz
    41 mv autoconf-$AUTOCONF_VER src
     42${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-${AUTOCONF_VER}.tar.gz" "autoconf-${AUTOCONF_VER}.tar.gz"
     43tar -zxvf autoconf-${AUTOCONF_VER}.tar.gz
     44mv autoconf-${AUTOCONF_VER} src
    4245cd src
    43 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     46./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    4447make
    4548make install
    4649cd ..
    4750
    48 #install automake
     51# Install Automake
    4952echo " === INSTALLING AUTOMAKE =="
    5053rm -rf src
    51 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-$AUTOMAKE_VER.tar.gz" "automake-$AUTOMAKE_VER.tar.gz"
    52 tar -zxvf  automake-$AUTOMAKE_VER.tar.gz
    53 mv automake-$AUTOMAKE_VER src
     54${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-${AUTOMAKE_VER}.tar.gz" "automake-${AUTOMAKE_VER}.tar.gz"
     55tar -zxvf automake-${AUTOMAKE_VER}.tar.gz
     56mv automake-${AUTOMAKE_VER} src
    5457cd src
    55 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     58./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    5659make
    5760make install
    … …  
    6164echo " === INSTALLING LIBTOOL =="
    6265rm -rf src
    63 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-$LIBTOOL_VER.tar.gz" "libtool-$LIBTOOL_VER.tar.gz"
    64 tar -zxvf  libtool-$LIBTOOL_VER.tar.gz
    65 rm libtool-$LIBTOOL_VER.tar.gz
    66 mv libtool-$LIBTOOL_VER src
     66${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-${LIBTOOL_VER}.tar.gz" "libtool-${LIBTOOL_VER}.tar.gz"
     67tar -zxvf libtool-${LIBTOOL_VER}.tar.gz
     68rm libtool-${LIBTOOL_VER}.tar.gz
     69mv libtool-${LIBTOOL_VER} src
    6770cd src
    68 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     71./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    6972make
    7073make install

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

    r24409 r24649  
    22set -eu
    33
    4 #Version numbers
    5 M4_VER="1.4.18"
     4
     5## Constants
     6#
    67AUTOCONF_VER="2.69"
    78AUTOMAKE_VER="1.16.1"
    89LIBTOOL_VER="2.4.2"
     10M4_VER="1.4.18"
    911
    10 # Clean up existing directories
     12## Environment
     13#
     14export PATH="${ISSM_DIR}/externalpackages/autotools/install/bin:$PATH"
     15
     16# Cleanup
    1117rm -rf install src
    12 
    13 # Set up for installation
    1418mkdir install
    15 export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH"
    1619
    1720# Install m4
    1821echo " === INSTALLING M4 =="
    19 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-$M4_VER.tar.gz" "m4-$M4_VER.tar.gz"
    20 tar -zxvf m4-$M4_VER.tar.gz
    21 mv m4-$M4_VER src
     22${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/m4-${M4_VER}.tar.gz" "m4-${M4_VER}.tar.gz"
     23tar -zxvf m4-${M4_VER}.tar.gz
     24mv m4-${M4_VER} src
    2225cd src
    23 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     26
     27./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    2428make
    2529make install
    2630cd ..
    2731
    28 #install autoconf
     32# Install Autoconf
    2933echo " === INSTALLING AUTOCONF =="
    3034rm -rf src
    31 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-$AUTOCONF_VER.tar.gz" "autoconf-$AUTOCONF_VER.tar.gz"
    32 tar -zxvf autoconf-$AUTOCONF_VER.tar.gz
    33 mv autoconf-$AUTOCONF_VER src
     35${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/autoconf-${AUTOCONF_VER}.tar.gz" "autoconf-${AUTOCONF_VER}.tar.gz"
     36tar -zxvf autoconf-${AUTOCONF_VER}.tar.gz
     37mv autoconf-${AUTOCONF_VER} src
    3438cd src
    35 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     39./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    3640make
    3741make install
    3842cd ..
    3943
    40 #install automake
     44# Install Automake
    4145echo " === INSTALLING AUTOMAKE =="
    4246rm -rf src
    43 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-$AUTOMAKE_VER.tar.gz" "automake-$AUTOMAKE_VER.tar.gz"
    44 tar -zxvf  automake-$AUTOMAKE_VER.tar.gz
    45 mv automake-$AUTOMAKE_VER src
     47${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/automake-${AUTOMAKE_VER}.tar.gz" "automake-${AUTOMAKE_VER}.tar.gz"
     48tar -zxvf automake-${AUTOMAKE_VER}.tar.gz
     49mv automake-${AUTOMAKE_VER} src
    4650cd src
    47 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     51./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    4852make
    4953make install
    5054cd ..
    5155
    52 #install libtool
     56# Install libtool
    5357echo " === INSTALLING LIBTOOL =="
    5458rm -rf src
    55 $ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-$LIBTOOL_VER.tar.gz" "libtool-$LIBTOOL_VER.tar.gz"
    56 tar -zxvf  libtool-$LIBTOOL_VER.tar.gz
    57 rm libtool-$LIBTOOL_VER.tar.gz
    58 mv libtool-$LIBTOOL_VER src
     59${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/libtool-${LIBTOOL_VER}.tar.gz" "libtool-${LIBTOOL_VER}.tar.gz"
     60tar -zxvf libtool-${LIBTOOL_VER}.tar.gz
     61rm libtool-${LIBTOOL_VER}.tar.gz
     62mv libtool-${LIBTOOL_VER} src
    5963cd src
    60 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     64./configure --prefix="${ISSM_DIR}/externalpackages/autotools/install"
    6165make
    6266make install

  • issm/trunk-jpl/externalpackages/boost/install-1.55-linux-static.sh

    r24593 r24649  
    1616VER="1_55_0"
    1717
    18 ## Evnrionment
     18## Environment
    1919#
    2020export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
    … …  
    3434rm -rf boost_${VER}
    3535
    36 # Copy customized source and configuration files to 'src' driectory
    37 cp configs/1.55/linux/boost/multi_index/ordered_index.hpp src/boost/multi_index
     36# Copy customized source and configuration files to 'src' directory
     37cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index
    3838
    3939# Configure
    … …  
    4141./bootstrap.sh \
    4242        --prefix="${ISSM_DIR}/externalpackages/boost/install" \
    43         --with-python=python2.7 \
    44         --with-python-root="${ISSM_DIR}/externalpackages/python/install"
     43        --with-python=python2.7
    4544
    4645# Modify project config to enable MPI

  • issm/trunk-jpl/externalpackages/boost/install-1.55-linux.sh

    r24593 r24649  
    3434rm -rf boost_${VER}
    3535
    36 # Copy customized source and configuration files to 'src' driectory
    37 cp configs/1.55/linux/boost/multi_index/ordered_index.hpp src/boost/multi_index
     36# Copy customized source and configuration files to 'src' directory
     37cp configs/1.55/boost/multi_index/ordered_index.hpp src/boost/multi_index
    3838
    3939# Configure
    … …  
    4141./bootstrap.sh \
    4242        --prefix="${ISSM_DIR}/externalpackages/boost/install" \
    43         --with-python=python2.7 \
    44         --with-python-root="${ISSM_DIR}/externalpackages/python/install"
     43        --with-python=python2.7
    4544
    4645# Modify project config to enable MPI

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

    r24639 r24649  
    1010## Environment
    1111#
    12 export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L${ISSM_DIR}/lib -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
     12export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    1313export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
    1414export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version)
    … …  
    1717export DAK_INSTALL=${DAK_ROOT}/install
    1818export DAK_SRC=${DAK_ROOT}/src
    19 export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L${ISSM_DIR}/lib -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
     19export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
    2020
    2121# Cleanup
    … …  
    3333rm -rf dakota-${VER}.0.src
    3434
    35 # Copy customized source and configuration files to 'src' driectory
     35# Copy customized source and configuration files to 'src' directory
     36cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
     37cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
     38cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src
     39cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
     40cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
     41
     42# Copy customized source and configuration files specific to Linux to 'src' directory
    3643cp configs/${VER}/linux/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
    3744cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
    38 cp configs/${VER}/linux/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
    39 cp configs/${VER}/linux/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
    40 cp configs/${VER}/linux/src/DakotaInterface.cpp ${DAK_SRC}/src
    41 cp configs/${VER}/linux/src/NonDLocalReliability.cpp ${DAK_SRC}/src
    42 cp configs/${VER}/linux/src/NonDSampling.cpp ${DAK_SRC}/src
    4345
    4446# Configure

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

    r24639 r24649  
    3333rm -rf dakota-${VER}.0.src
    3434
    35 # Copy customized source and configuration files to 'src' driectory
     35# Copy customized source and configuration files to 'src' directory
     36cp configs/${VER}/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
     37cp configs/${VER}/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
     38cp configs/${VER}/src/DakotaInterface.cpp ${DAK_SRC}/src
     39cp configs/${VER}/src/NonDLocalReliability.cpp ${DAK_SRC}/src
     40cp configs/${VER}/src/NonDSampling.cpp ${DAK_SRC}/src
     41
     42# Copy customized source and configuration files specific to Linux to 'src' directory
    3643cp configs/${VER}/linux/cmake/BuildDakotaCustom.cmake ${DAK_SRC}/cmake
    3744cp configs/${VER}/linux/cmake/DakotaDev.cmake ${DAK_SRC}/cmake
    38 cp configs/${VER}/linux/packages/DDACE/src/Analyzer/MainEffectsExcelOutput.cpp ${DAK_SRC}/packages/DDACE/src/Analyzer
    39 cp configs/${VER}/linux/packages/surfpack/src/surfaces/nkm/NKM_KrigingModel.cpp ${DAK_SRC}/packages/surfpack/src/surfaces/nkm
    40 cp configs/${VER}/linux/src/DakotaInterface.cpp ${DAK_SRC}/src
    41 cp configs/${VER}/linux/src/NonDLocalReliability.cpp ${DAK_SRC}/src
    42 cp configs/${VER}/linux/src/NonDSampling.cpp ${DAK_SRC}/src
    4345
    4446# Configure

  • issm/trunk-jpl/externalpackages/petsc/install-3.7-mac.sh

    r24427 r24649  
    1111
    1212# Unpack source
    13 tar -zxvf  petsc-$VER.tar.gz
     13tar -zxvf petsc-${VER}.tar.gz
    1414
    1515# Cleanup
    … …  
    1818
    1919# Move source to 'src' directory
    20 mv petsc-$VER/* src/
    21 rm -rf petsc-$VER
     20mv petsc-${VER}/* src/
     21rm -rf petsc-${VER}
    2222
    2323# Configure
    … …  
    4545        make -j $1 install
    4646fi
    47 
    48 # Return to initial directory
    49 cd ..

  • issm/trunk-jpl/jenkins/jenkins.sh

    r24647 r24649  
    547547
    548548        # Check that MATLAB did not exit in error
    549         matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab_log.log | wc -l`
     549        matlabExitedInError=`grep -E "Error|Activation cannot proceed|license" matlab_log.log | wc -l`
    550550
    551551        if [ $matlabExitedInError -ne 0 ]

  • issm/trunk-jpl/jenkins/pine-island-mac-dakota

    r24642 r24649  
    1 #-------------------------------#
    2 # 1: ISSM general configuration #
    3 #-------------------------------#
     1#--------------------#
     2# ISSM Configuration #
     3#--------------------#
    44
    55# MATLAB path
    … …  
    88# ISSM CONFIGURATION
    99ISSM_CONFIG='\
    10         --prefix=$ISSM_DIR \
    11         --with-matlab-dir=$MATLAB_PATH \
     10        --prefix=${ISSM_DIR} \
     11        --disable-static \
     12        --enable-development \
     13        --enable-debugging \
     14        --with-numthreads=4 \
     15        --with-matlab-dir=${MATLAB_PATH} \
    1216        --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \
    1317        --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \
    14         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
    15         --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \
    16         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    17         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    18         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
    19         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    20         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    21         --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
    22         --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    23         --with-semic-dir=$ISSM_DIR/externalpackages/semic/install \
    24         --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
    25         --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
    26         --with-cxxoptflags="-std=c++11" \
    27         --with-numthreads=4 \
    28         --enable-debugging \
    29         --enable-development'
     18        --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \
     19        --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
     20        --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
     21        --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     22        --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
     23        --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     24        --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
     25        --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
     26        --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
     27        --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
     28        --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
     29        --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
     30        --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
     31        --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
     32'
    3033
    3134# Test suites
    … …  
    4346        autotools       install.sh
    4447        cmake           install.sh
    45         mpich           install-3.3.sh
    46         petsc           install-3.7-mac.sh
     48        petsc           install-3.12-mac.sh
     49        boost           install-1.55-mac.sh
     50        dakota          install-6.2-mac.sh
    4751        triangle        install-mac.sh
    4852        chaco           install.sh
    4953        m1qn3           install.sh
    5054        semic           install.sh
    51         boost           install-1.55-macosx-el_capitan.sh
    52         dakota          install-6.2-macosx64.sh
    5355        shell2junit     install.sh
    5456"

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

    r24642 r24649  
    1 #-------------------------------#
    2 # 1: ISSM general configuration #
    3 #-------------------------------#
     1#--------------------#
     2# ISSM Configuration #
     3#--------------------#
    44
    55# MATLAB path
    … …  
    88# ISSM CONFIGURATION
    99ISSM_CONFIG='\
    10         --prefix=$ISSM_DIR \
     10        --prefix=${ISSM_DIR} \
    1111        --disable-static \
    12         --with-matlab-dir=$MATLAB_PATH \
    13         --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include \
    14         --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
    15         --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    16         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    17         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    18         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
    19         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    20         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    21         --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
    22         --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    23         --with-semic-dir=$ISSM_DIR/externalpackages/semic/install \
    24         --with-numthreads=4 \
    2512        --enable-development \
    2613        --enable-debugging \
     14        --with-numthreads=4 \
     15        --with-matlab-dir=${MATLAB_PATH} \
     16        --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \
     17        --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
     18        --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
     19        --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     20        --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
     21        --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     22        --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
     23        --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
     24        --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
     25        --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
     26        --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
     27        --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
    2728'
    2829
    … …  
    3334EXAMPLES_TEST=0
    3435
    35 #-----------------------------------#
    36 # 3: External packages installation #
    37 #-----------------------------------#
     36#-------------------#
     37# External Packages #
     38#-------------------#
    3839
    3940# List of external pakages to be installed and their installation scripts
    … …  
    4142        autotools       install.sh
    4243        cmake           install.sh
    43         petsc           install-3.11-mac.sh
     44        petsc           install-3.12-mac.sh
    4445        triangle        install-mac.sh
    4546        chaco           install.sh
    … …  
    4950"
    5051
    51 #-----------------#
    52 # 4: test options #
    53 #-----------------#
     52#---------#
     53# Testing #
     54#---------#
    5455
    5556# Number of CPUs used in ISSM compilation

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

    r24642 r24649  
    1 #-------------------------------#
    2 # 1: ISSM general configuration #
    3 #-------------------------------#
     1#--------------------#
     2# ISSM Configuration #
     3#--------------------#
    44
    55# MATLAB path
    66MATLAB_PATH="/Applications/MATLAB_R2015b.app"
    77
     8# NOTE:
     9# - We can disable dependency tracking in the Autotools because the binaries
     10#       should always be a one-time build.
     11# - libgfortran is copied to $ISSM_DIR/lib by packaging script.
     12#
    813# ISSM CONFIGURATION
    914ISSM_CONFIG='\
    10         --prefix=$ISSM_DIR \
     15        --prefix=${ISSM_DIR} \
    1116        --disable-static \
    1217        --enable-standalone-executables \
     18        --enable-standalone-modules \
    1319        --enable-standalone-libraries \
    14         --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a /usr/local/gfortran/lib/libquadmath.a /usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0/libgcc.a" \
    15         --with-matlab-dir=$MATLAB_PATH \
    16         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
    17         --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lpmpi -lmpifort -lmpicxx" \
    18         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    19         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    20         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
    21         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    22         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    23         --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
    24         --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    25         --with-semic-dir=$ISSM_DIR/externalpackages/semic/install \
    26         --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
     20        --disable-dependency-tracking \
     21        --with-matlab-dir=${MATLAB_PATH} \
     22        --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \
     23        --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
     24        --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
     25        --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     26        --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
     27        --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     28        --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
     29        --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
     30        --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
     31        --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
     32        --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
     33        --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
    2734'
    2835
    … …  
    3340EXAMPLES_TEST=0
    3441
    35 #-----------------------------------#
    36 # 3: External packages installation #
    37 #-----------------------------------#
     42#-------------------#
     43# External Packages #
     44#-------------------#
    3845
    39 # List of external pakages to be installed and their installation scripts
    40 #
    41 # NOTE:
    42 # - For SLR capabilities, we need gmsh, math77, and gmt
    43 # - GMT depends on GDAL and NetCDF
    44 #
    4546EXTERNALPACKAGES="
    4647        autotools       install.sh
    4748        cmake           install.sh
    48         mpich           install-3.2-mac-static.sh
    49         petsc           install-3.7-mac-static.sh
     49        petsc           install-3.12-mac-static.sh
    5050        triangle        install-mac-static.sh
    5151        chaco           install.sh
    5252        m1qn3           install.sh
    5353        semic           install.sh
    54         math77          install.sh
    55         gmt                     install-mac-precompiled.sh
    56         gmsh            install-mac-precompiled.sh
    5754        shell2junit     install.sh
    5855"
    5956
    60 #-----------------#
    61 # 4: test options #
    62 #-----------------#
     57#---------#
     58# Testing #
     59#---------#
    6360
    6461# Number of CPUs used in ISSM compilation
    … …  
    6764#               compilation
    6865#
    69 NUMCPUS_INSTALL=4
     66NUMCPUS_INSTALL=1
    7067
    7168# Number of CPUs used in the nightly runs
    72 NUMCPUS_RUN=2
     69NUMCPUS_RUN=1
    7370
    7471# Nightly run options

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

    r24642 r24649  
    1 #-------------------------------#
    2 # 1: ISSM general configuration #
    3 #-------------------------------#
     1#--------------------#
     2# ISSM Configuration #
     3#--------------------#
    44
    55# MATLAB path
    66MATLAB_PATH="/Applications/MATLAB_R2015b.app"
    77
     8# NOTE:
     9# - We can disable dependency tracking in the Autotools because the binaries
     10#       should always be a one-time build.
     11# - libgfortran is copied to $ISSM_DIR/lib by packaging script.
     12#
    813# ISSM CONFIGURATION
    914ISSM_CONFIG='\
    10         --prefix=$ISSM_DIR \
     15        --prefix=${ISSM_DIR} \
    1116        --disable-static \
    12         --with-matlab-dir=$MATLAB_PATH \
    13         --with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include \
     17        --enable-standalone-executables \
     18        --enable-standalone-modules \
     19        --enable-standalone-libraries \
     20        --disable-dependency-tracking \
     21        --with-matlab-dir=${MATLAB_PATH} \
     22        --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \
     23        --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \
     24        --with-fortran-lib="-L/usr/local/gfortran/lib -lgfortran" \
     25        --with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
    1426        --with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
    15         --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    16         --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    17         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    18         --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
    19         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    20         --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    21         --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
    22         --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    23         --with-semic-dir=$ISSM_DIR/externalpackages/semic/install \
    24         --with-numthreads=4 \
    25         --enable-development \
    26         --enable-debugging \
     27        --with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     28        --with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
     29        --with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
     30        --with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
     31        --with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
     32        --with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
     33        --with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
     34        --with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
     35        --with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
     36        --with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
     37        --with-semic-dir=${ISSM_DIR}/externalpackages/semic/install \
    2738'
    2839
    2940# Test suites
    30 MATLAB_TEST=1
     41MATLAB_TEST=0
    3142PYTHON_TEST=0
    3243JAVASCRIPT_TEST=0
    3344EXAMPLES_TEST=0
    3445
    35 #-----------------------------------#
    36 # 3: External packages installation #
    37 #-----------------------------------#
     46#-------------------#
     47# External Packages #
     48#-------------------#
    3849
    39 # List of external pakages to be installed and their installation scripts
    4050EXTERNALPACKAGES="
    4151        autotools       install.sh
    4252        cmake           install.sh
    43         petsc           install-3.11-mac.sh
    44         triangle        install-mac.sh
     53        petsc           install-3.12-mac-static.sh
     54        boost           install-1.55-mac-static.sh
     55        dakota          install-6.2-mac-static.sh
     56        triangle        install-mac-static.sh
    4557        chaco           install.sh
    4658        m1qn3           install.sh
    … …  
    4961"
    5062
    51 #-----------------#
    52 # 4: test options #
    53 #-----------------#
     63#---------#
     64# Testing #
     65#---------#
    5466
    5567# Number of CPUs used in ISSM compilation
    … …  
    5870#               compilation
    5971#
    60 NUMCPUS_INSTALL=4
     72NUMCPUS_INSTALL=1
    6173
    6274# Number of CPUs used in the nightly runs
    63 NUMCPUS_RUN=2
     75NUMCPUS_RUN=1
    6476
    6577# Nightly run options
    6678#
    67 # See documentation in test/NightlyRun/runme.* for more information
     79# See documentation in test/NightlyRun/runme.* for more information.
    6880#
    69 # NOTE:
    70 #       - test701.m is skipped because it uses full Stokes equations
    71 #
    72 MATLAB_NROPTIONS="'exclude',[701,702,703,435,IdFromString('Dakota')]"
    73 PYTHON_NROPTIONS="--exclude_name 'Dakota'"
     81PYTHON_NROPTIONS=""
     82MATLAB_NROPTIONS=""

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

    r24648 r24649  
    55MATLAB_PATH="/usr/local/MATLAB/R2019b"
    66
    7 # NOTE: We can disable dependency tracking in the Autotools because the
    8 #               binaries should always be a one-time build.
     7# NOTE:
     8# - We can disable dependency tracking in the Autotools because the binaries
     9#       should always be a one-time build.
     10# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is
     11#       copied by packaging script.
    912#
    1013ISSM_CONFIG='\

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

    r24648 r24649  
    55MATLAB_PATH="/usr/local/MATLAB/R2019b"
    66
    7 # NOTE: We can disable dependency tracking in the Autotools because the
    8 #               binaries should always be a one-time build.
     7# NOTE:
     8# - We can disable dependency tracking in the Autotools because the binaries
     9#       should always be a one-time build.
     10# - libgfortran will not be available in $ISSM_DIR/lib at compile time: it is
     11#       copied by packaging script.
    912#
    1013ISSM_CONFIG='\

  • issm/trunk-jpl/m4/issm_options.m4

    r24632 r24649  
    190190                [VENDOR=""]                                                                                                                     dnl action if not given
    191191        )
     192        dnl defaults for host OS related variables
     193        IS_MAC=no
     194        IS_WINDOWS=no
    192195        AC_MSG_CHECKING([for vendor compilers])
    193196        if test -n "${VENDOR}"; then
    … …  
    282285        AC_SUBST([OSLIBS])
    283286        AC_MSG_RESULT([done])
     287
     288        AC_MSG_CHECKING([if this is a Mac build])
     289        dnl TODO: The following test is a POSIX-compliant way of testing for a
     290        dnl               substring, but is not very readable. Perhaps there is a more
     291        dnl               readable method of achieving the same?
     292        if test "${host_os#*\"darwin\"}" == "$host_os"; then
     293                IS_MAC=yes
     294        fi
     295        AM_CONDITIONAL([MAC], [test "${IS_MAC}" == "yes"])
     296        AC_MSG_RESULT([${IS_MAC}])
     297
     298        AC_MSG_CHECKING([if this is a Windows build])
     299        AM_CONDITIONAL([WINDOWS], [test "x${IS_WINDOWS}" == "xyes"])
     300        AC_MSG_RESULT([${IS_WINDOWS}])
    284301        dnl }}}
    285302        dnl MATLAB{{{
    … …  
    368385                AC_SUBST([MEXLINK])
    369386        fi
    370         dnl }}}
    371         dnl Windows {{{
    372         AC_MSG_CHECKING([Checking if this is a Windows build... ])
    373         AM_CONDITIONAL([WINDOWS], [test "x${IS_WINDOWS}" == "xyes"])
    374         AC_MSG_RESULT([done])
    375387        dnl }}}
    376388        dnl JavaScript{{{

  • issm/trunk-jpl/packagers/linux/package-issm-linux-binaries-with_dakota.sh

    r24632 r24649  
    66LIBGFORTRAN="/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0" # Important that this is the library itself
    77LIBGFORTRAN_DIST="${ISSM_DIR}/lib/libgfortran.so.5" # Important the file name matches the SONAME entry in the binaries and other shared libraries which link to it
    8 MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,244,250,417,444,445]"
    9 MATLAB_PATH="/usr/local/MATLAB/R2019b" # Exclude any tests with transient solutions that require a restart
     8MATLAB_NROPTIONS="'id',[IdFromString('Dakota')],'exclude',[234,244,250,417,444,445]" # Exclude any tests with transient solutions that require a restart
     9MATLAB_PATH="/usr/local/MATLAB/R2019b"
    1010PACKAGE="ISSM" # Name of directory to copy distributable files to
    1111
    … …  
    4747# Add/modify required libraries
    4848echo "Moving libgfortran to lib/"
    49 cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST}
     49cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
    5050
    5151# Run tests
    … …  
    6363# Check that MATLAB did not exit in error
    6464matlabExitCode=`echo $?`
    65 matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
     65matlabExitedInError=`grep -E "Error|Activation cannot proceed|license" matlab.log | wc -l`
    6666
    6767if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
    … …  
    9999# Check that Python did not exit in error
    100100pythonExitCode=`echo $?`
    101 pythonExitedInError=`grep -E "runme.py: error" python.log | wc -l`
     101pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python.log | wc -l`
    102102
    103103if [[ ${pythonExitCode} -ne 0 || ${pythonExitedInError} -ne 0 ]]; then

  • issm/trunk-jpl/packagers/linux/package-issm-linux-binaries.sh

    r24632 r24649  
    3737
    3838echo "Moving libgfortran to lib/"
    39 cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST}
     39cp ${LIBGFORTRAN} ${LIBGFORTRAN_DIST} 2> /dev/null
    4040
    4141# Run tests
    … …  
    5353# Check that MATLAB did not exit in error
    5454matlabExitCode=`echo $?`
    55 matlabExitedInError=`grep -E "Activation cannot proceed|license|Error" matlab.log | wc -l`
     55matlabExitedInError=`grep -E "Error|Activation cannot proceed|license" matlab.log | wc -l`
    5656
    5757if [[ ${matlabExitCode} -ne 0 || ${matlabExitedInError} -ne 0 ]]; then
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