Changeset 23393


Ignore:
Timestamp:
10/05/18 10:42:08 (6 years ago)
Author:
Mathieu Morlighem
Message:

merged trunk and trunk-jpl

Location:
issm/trunk-jpl
Files:
1 deleted
13 edited
7 copied

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl

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

    r22031 r23393  
    22set -eu
    33
    4 rm -rf install
     4AUTOCONF_VER="2.69"
     5AUTOMAKE_MIN_VER="1.16"
     6AUTOMAKE_BUILD_VER="${AUTOMAKE_MIN_VER}.1"
     7LIBTOOL_VER="2.4.2"
     8M4_VER="1.4.17"
     9
     10AUTOCONF="autoconf-${AUTOCONF_VER}"
     11AUTOMAKE="automake-${AUTOMAKE_BUILD_VER}"
     12LIBTOOL="libtool-${LIBTOOL_VER}"
     13M4="m4-${M4_VER}"
     14
     15AUTOCONF_TARBALL="${AUTOCONF}.tar.gz"
     16AUTOMAKE_TARBALL="${AUTOMAKE}.tar.gz"
     17LIBTOOL_TARBALL="${LIBTOOL}.tar.gz"
     18M4_TARBALL="${M4}.tar.gz"
     19
     20# Clean up existing assets
     21rm -rf install src
     22
     23# Set up for installation
    524mkdir install
    6 
    725export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH"
    826
    9 #install autoconf
    10 echo " === INSTALLING AUTOCONF =="
    11 rm -rf src
    12 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.69.tar.gz' 'autoconf-2.69.tar.gz'
    13 tar -zxvf autoconf-2.69.tar.gz
    14 mv autoconf-2.69 src
    15 cd src 
    16 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" 
    17 make 
     27# Install m4
     28echo " === INSTALLING M4 =="
     29$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${M4_TARBALL}" $M4_TARBALL
     30tar -zxvf $M4_TARBALL
     31rm -f $M4_TARBALL
     32mv $M4 src
     33cd src
     34./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     35make
    1836make install
    1937cd ..
    2038
    21 #install automake
    22 echo " === INSTALLING AUTOMAKE =="
     39# Install autoconf
     40echo " === INSTALLING AUTOCONF =="
    2341rm -rf src
    24 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.14.tar.gz' 'automake-1.14.tar.gz'
    25 tar -zxvf  automake-1.14.tar.gz
    26 mv automake-1.14 src
    27 cd src
    28 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
    29 make 
     42$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${AUTOCONF_TARBALL}" $AUTOCONF_TARBALL
     43tar -zxvf $AUTOCONF_TARBALL
     44rm -f $AUTOCONF_TARBALL
     45mv $AUTOCONF src
     46cd src
     47./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     48make
    3049make install
    3150cd ..
    3251
    33 #install libtool
    34 echo " === INSTALLING LIBTOOL =="
     52# Install automake
     53echo " === INSTALLING AUTOMAKE =="
    3554rm -rf src
    36 $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.4.2.tar.gz' 'libtool-2.4.2.tar.gz'
    37 tar -zxvf  libtool-2.4.2.tar.gz
    38 rm libtool-2.4.2.tar.gz
    39 mv libtool-2.4.2 src
    40 cd src 
    41 ./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" 
    42 make 
     55$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${AUTOMAKE_TARBALL}" $AUTOMAKE_TARBALL
     56tar -zxvf $AUTOMAKE_TARBALL
     57rm -f $AUTOMAKE_TARBALL
     58mv $AUTOMAKE src
     59cd src
     60./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     61make
    4362make install
    4463cd ..
    4564
    46 # This patch takes care of removing options passed to the linker that casuse
     65# Install libtool
     66echo " === INSTALLING LIBTOOL =="
     67rm -rf src
     68$ISSM_DIR/scripts/DownloadExternalPackage.py "http://issm.jpl.nasa.gov/files/externalpackages/${LIBTOOL_TARBALL}" $LIBTOOL_TARBALL
     69tar -zxvf $LIBTOOL_TARBALL
     70rm -f $LIBTOOL_TARBALL
     71mv $LIBTOOL src
     72cd src
     73./configure --prefix="$ISSM_DIR/externalpackages/autotools/install"
     74make
     75make install
     76cd ..
     77
     78# This patch takes care of removing options passed to the linker that causes
    4779# the build to fail, as well as changing some flags to match up to Microsoft
    4880# compilers.
    … …  
    5486
    5587# This patch is for ar-lib, and removes carriage return characters that cause
    56 # commands to overwrite themselves and be misinterpreted during linking on 
     88# commands to overwrite themselves and be misinterpreted during linking on
    5789# Cygwin Windows.
    58 patch ./install/share/automake-1.14/ar-lib < ./patches/ar-lib.patch
     90patch ./install/share/automake-${AUTOMAKE_MIN_VER}/ar-lib < ./patches/ar-lib.patch

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

    r22821 r23393  
    2727#Configure
    2828cd install
    29 cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" -DENABLE_MPI=0 -DENABLE_METIS=0
     29cmake ../src -DCMAKE_INSTALL_PREFIX="$ISSM_DIR/externalpackages/gmsh/install" -DENABLE_METIS=0
    3030
    3131#Compile and install

  • issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64-static.sh

    r22757 r23393  
    99$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz'
    1010
    11 #Untar 
     11#Untar
    1212tar -zxvf  mpich-3.2.tar.gz
    1313
    … …  
    1919cd src
    2020./configure \
    21         --prefix="$ISSM_DIR/externalpackages/mpich/install"
     21        --prefix="$ISSM_DIR/externalpackages/mpich/install" \
     22        --disable-shared \
     23        --enable-strict=all \
     24        --enable-fast \
     25        --with-pic
    2226
    2327#Compile mpich (this new version supports parallel make)
    … …  
    2731        make -j $1
    2832fi
    29 make install
     33
     34make install

  • issm/trunk-jpl/externalpackages/mpich/install-3.2-linux64.sh

    r21693 r23393  
    99$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/mpich-3.2.tar.gz' 'mpich-3.2.tar.gz'
    1010
    11 #Untar 
     11#Untar
    1212tar -zxvf  mpich-3.2.tar.gz
    1313
    … …  
    2828        make -j $1
    2929fi
    30 make install 
     30make install

  • issm/trunk-jpl/externalpackages/petsc/install-3.7-linux64-static.sh

    r22757 r23393  
    1818./config/configure.py \
    1919        --prefix="$ISSM_DIR/externalpackages/petsc/install" \
     20        --with-single-library=1 \
     21        --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
     22        --with-shared-libraries=0 \
     23        --with-debugging=0 \
    2024        --with-mpi-dir="$ISSM_DIR/externalpackages/mpich/install" \
    21         --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \
    22         --with-debugging=0 \
    23         --with-valgrind=0 \
    24         --with-x=0 \
    25         --with-ssl=0 \
    26         --with-shared-libraries=0 \
     25        --download-fblaslapack=1 \
    2726        --download-metis=1 \
    2827        --download-parmetis=1 \
     28        --with-x=0 \
     29        --download-scalapack=1 \
    2930        --download-mumps=1 \
    30         --download-fblaslapack=1 \
    31         --download-scalapack=1 \
     31        --with-ssl=0 \
     32        --with-valgrind=0 \
     33        --with-pic=1 \
    3234        --COPTFLAGS="-fPIC" \
    3335        --CXXOPTFLAGS="-fPIC" \

  • issm/trunk-jpl/jenkins/linux64_ross_static

    r23155 r23393  
    77MATLAB_PATH="/usr/local/MATLAB/R2015a"
    88
    9 #ISSM CONFIGURATION 
     9#ISSM CONFIGURATION
    1010ISSM_CONFIG='--prefix=$ISSM_DIR \
    11         --disable-static \
    1211        --enable-standalone-executables \
     12        --enable-standalone-modules \
    1313        --enable-standalone-libraries \
    14         --enable-standalone-modules \
    1514        --with-matlab-dir=$MATLAB_PATH \
    1615        --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    1716        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
    18         --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpifort" \
    19         --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install  \
    20         --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
    21         --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
     17        --with-mpi-libflags="$ISSM_DIR/externalpackages/mpich/install/lib/libmpifort.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpi.a -lrt -lpthread" \
     18        --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
     19        --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
     20        --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
    2221        --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
    2322        --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    2423        --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    2524        --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
    26         --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \
     25        --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
     26        --with-pic \
    2727        --with-numthreads=4'
    2828
    … …  
    5252#number of cpus used in ISSM installation and compilation (one is usually
    5353#safer as some packages are very sensitive to parallel compilation)
    54 NUMCPUS_INSTALL=4
     54NUMCPUS_INSTALL=10
    5555
    5656#number of cpus used in the nightly runs.
    57 NUMCPUS_RUN=2
     57NUMCPUS_RUN=10
    5858
    5959#Nightly run options. The matlab routine runme.m will be called
    … …  
    6161#by Matlab and runme.m
    6262#ex: "'id',[101 102 103]"
    63 ##                           FS                   
     63##                           FS
    6464#PYTHON_NROPTIONS="--exclude_name 'Dakota'"
    6565#MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]"

  • issm/trunk-jpl/jenkins/macosx_pine-island_static

    r23275 r23393  
    1414        --with-matlab-dir=$MATLAB_PATH \
    1515        --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
    16         --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
     16        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
    1717        --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpl -lpmpich" \
    1818        --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
    … …  
    2323        --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    2424        --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
    25         --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" \
    26         --with-numthreads=4'
     25        --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"'
    2726
    2827#PYTHON and MATLAB testing
    … …  
    3534
    3635#List of external pakages to be installed and their installation scripts
    37 EXTERNALPACKAGES="autotools    install.sh
    38                                                 cmake        install.sh
    39                                                 mpich        install-3.0-macosx64-static.sh
    40                                                 m1qn3        install.sh
    41                                                 petsc        install-3.6-macosx64-static.sh
    42                                                 triangle     install-macosx64.sh
    43                                                 math77        install.sh
    44                                                 gmsh          install-static.sh
    45                                                 shell2junit  install.sh"
     36EXTERNALPACKAGES="autotools             install.sh
     37                                        cmake           install.sh
     38                                        mpich           install-3.0-macosx64-static.sh
     39                                        m1qn3           install.sh
     40                                        petsc           install-3.6-macosx64-static.sh
     41                                        triangle        install-macosx64.sh
     42                                        math77          install.sh
     43                                        gmt                     install-mac-precompiled.sh
     44                                        gmsh            install-mac-precompiled.sh
     45                                        shell2junit     install.sh"
    4646
    4747#for SLR we need gmsh to mesh, math77, and gmt (which itself needs gdal and netcdf...)
    … …  
    6262#ex: "'id',[101 102 103]"
    6363##                           bamg mesh   FS
    64 #PYTHON_NROPTIONS="--exclude_name 'Dakota'"
    65 #MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,435,IdFromString('Dakota')]"
     64#PYTHON_NROPTIONS=""
     65#MATLAB_NROPTIONS=""

  • issm/trunk-jpl/jenkins/windows

    r22073 r23393  
    77MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a/"
    88
    9 #ISSM CONFIGURATION 
     9#ISSM CONFIGURATION
    1010ISSM_CONFIG='--prefix=$ISSM_DIR \
    1111        --with-vendor=MSVC-Win64  \
    … …  
    4141                                                petsc       install-3.6-win10.sh
    4242                                                metis       install-4.0-win10.sh
    43                                                 triangle    install-win10.sh       
     43                                                triangle    install-win10.sh
    4444                                                shell2junit install.sh"
    4545
    … …  
    5050#number of cpus used in ISSM installation and compilation (one is usually
    5151#safer as some packages are very sensitive to parallel compilation)
    52 NUMCPUS_INSTALL=6
     52NUMCPUS_INSTALL=8
    5353
    5454#number of cpus used in the nightly runs.
    55 NUMCPUS_RUN=2
     55NUMCPUS_RUN=8
    5656
    5757#Nightly run options. The matlab routine runme.m will be called

  • issm/trunk-jpl/packagers/macosx/package.sh

    r22821 r23393  
    11#!/bin/bash
    22
    3 echo "modify generic"
     3TARBALL_NAME='issm-mac-static_build'
     4TARBALL=$TARBALL_NAME.tar.gz
     5
     6# Clean up from previous packaging
     7echo "Cleaning up existing assets"
     8cd $ISSM_DIR
     9rm -rf trunk
     10mkdir trunk
     11
     12# Add/modify required binaries
    413cd $ISSM_DIR/bin
     14
     15echo "Modifying generic"
    516cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
    6 echo "move mpiexec to bin"
    7 cp ../externalpackages/mpich/install/bin/mpiexec .
    8 cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy .
    9 echo "move gmsh to bin"
     17
     18echo "Moving mpiexec to bin"
     19if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then
     20        cp ../externalpackages/mpich/install/bin/mpiexec .
     21        cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy .
     22else
     23        echo "mpich not found"
     24fi
     25
     26echo "Moving gmsh to bin"
    1027if [ -f ../externalpackages/gmsh/install/gmsh ]; then
    1128        cp ../externalpackages/gmsh/install/gmsh .
    … …  
    1431fi
    1532
    16 #Check that test101 runs
     33# Copy gmt to trunk
     34# NOTE: The following assumes the precompiled version of gmt
     35echo "Moving gmt to externalpackages"
     36if [ -f $ISSM_DIR/externalpackages/gmt/install/bin/gmt ]; then
     37        mkdir $ISSM_DIR/trunk/externalpackages
     38        mkdir $ISSM_DIR/trunk/externalpackages/gmt
     39        cp -a $ISSM_DIR/externalpackages/gmt/install/. $ISSM_DIR/trunk/externalpackages/gmt
     40else
     41        echo "gmt not found"
     42fi
     43
     44# Check that test101 runs
    1745cd $ISSM_DIR/test/NightlyRun
    1846rm matlab.log
    … …  
    2654fi
    2755
    28 tarball_name='issm-mac-static_build.tar.gz'
     56echo "Creating tarball: ${TARBALL_NAME}"
     57cd $ISSM_DIR
     58rm -f $TARBALL
     59cp -rf bin lib test examples scripts trunk/
    2960
    30 echo "Cleanup first"
     61# Create link to gmt from bin
     62# NOTE: It is important that we are in the destination dir when sym linking so that the path is relative
     63if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then
     64        cd $ISSM_DIR/trunk/bin
     65        ln -s ../externalpackages/gmt/bin/gmt ./gmt
     66fi
     67
    3168cd $ISSM_DIR
    32 rm $tarball_name
    33 
    34 echo "Creating tarball: ${tarball_name}"
    35 cd $ISSM_DIR
    36 rm -rf trunk
    37 mkdir trunk
    38 cp -rf bin lib test examples scripts trunk/
    39 tar -czf $tarball_name trunk
    40 ls -lah $tarball_name
     69tar -czf $TARBALL trunk
     70ls -lah $TARBALL
    4171
    4272echo "Shipping binaries to website"
    … …  
    5686ssh-add ~/.ssh/macosx-bins_richese-to-ross
    5787
    58 scp $tarball_name ross.ics.uci.edu:/var/www/html/$tarball_name
     88scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL
    5989
    6090if [ $? -ne 0 ]; then

  • issm/trunk-jpl/src

  • issm/trunk-jpl/src/c/modules/InterpFromGridToMeshx/InterpFromGridToMeshx.cpp

    r23046 r23393  
    8080        /*launch the thread manager with InterpFromGridToMeshxt as a core: */
    8181        LaunchThread(InterpFromGridToMeshxt,(void*)&gate,_NUMTHREADS_);
    82         _printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%  \n");
     82        //_printf_("\r      interpolation progress: "<<fixed<<setw(6)<<setprecision(2)<<100.<<"%  \n");
    8383
    8484        /*Assign output pointers:*/
    … …  
    133133
    134134                if(debug && my_thread==0)
    135                  _printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%   ");
     135                 //_printf_("\r      interpolation progress: "<<setw(6)<<setprecision(2)<<double(i-i0)/double(i1-i0)*100<<"%   ");
    136136                x_grid=*(x_mesh+i);
    137137                y_grid=*(y_mesh+i);

  • issm/trunk-jpl/src/wrappers/matlab/io/ApiPrintf.cpp

    r22730 r23393  
    1515
    1616        /*use mexPrintf in matlab: */
    17         //mexPrintf(string); /*Messes up percentages (like "interpolation progress: 100.00%")*/
    18         printf("%s",string);
     17        mexPrintf(string); /*Messes up percentages (like "interpolation progress: 100.00%")*/
     18        //printf("%s",string);
    1919        return;
    2020}
Note: See TracChangeset for help on using the changeset viewer.