source: issm/oecreview/Archive/24307-24683/ISSM-24310-24311.diff@ 24684

Last change on this file since 24684 was 24684, checked in by Mathieu Morlighem, 5 years ago

CHG: added new review
File size: 34.3 KB

  • ../trunk-jpl/m4/issm_options.m4

     
    395395                                TRIANGLELIB="-Wl,`cygpath -m $TRIANGLE_ROOT/`triangle.lib"
    396396                                ;;
    397397                                *linux*)
    398                                 TRIANGLELIB=$TRIANGLE_ROOT/triangle.a
    399398                                if test "x$HAVE_JAVASCRIPT" = "xyes"; then
    400399                                        dnl go to the bit code, not the library.
    401400                                        TRIANGLELIB=$TRIANGLE_ROOT/triangle.o
    … …  
    482481                AC_DEFINE_UNQUOTED([_DAKOTA_VERSION_],"$DAKOTA_VERSION",[Dakota version number])
    483482
    484483                DAKOTAFLAGS=""
     484                dnl TODO: Should we also be checking if HAVE_BOOST before adding boost libs?
    485485                case "${host_os}" in
    486486                        *cygwin*)
    487487                                if test x$DAKOTA_VERSION = x5.1 || test x$DAKOTA_VERSION = x5.2; then
    … …  
    506506                                        AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI])
    507507                                else if test x$DAKOTA_VERSION = x6.1 || test x$DAKOTA_VERSION = x6.2; then
    508508                                   DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -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 -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
    509                                         DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_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 -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
     509                                        if test "x$enable_standalone_executables" = "xyes"; then
     510                                                DAKOTALIB="-L$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 $BOOST_ROOT/lib/libboost_serialization.a $BOOST_ROOT/lib/libboost_signals.a $BOOST_ROOT/lib/libboost_regex.a $BOOST_ROOT/lib/libboost_filesystem.a $BOOST_ROOT/lib/libboost_system.a"
     511                                        else
     512                                                DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_ROOT/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
     513                                        fi
    510514                                        AC_DEFINE([DISABLE_DAKOTA_CONFIG_H],[1],[disabling DAKOTA_CONFIG_H])
    511515                                        AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI])
    512516                                else
    … …  
    525529                                        AC_DEFINE([DISABLE_DAKOTA_CONFIG_H],[1],[disabling DAKOTA_CONFIG_H])
    526530                                        AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI])
    527531                                else if test x$DAKOTA_VERSION = x6.1 || test x$DAKOTA_VERSION = x6.2; then
    528                                    DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
    529                                         DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_ROOT/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
     532                                        DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL"
     533                                        if test "x$enable_standalone_executables" = "xyes"; then
     534                                                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 $BOOST_ROOT/lib/libboost_serialization.a $BOOST_ROOT/lib/libboost_signals.a $BOOST_ROOT/lib/libboost_regex.a $BOOST_ROOT/lib/libboost_filesystem.a $BOOST_ROOT/lib/libboost_system.a"
     535                                        else
     536                                                DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_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 -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
     537                                        fi
    530538                                        AC_DEFINE([DISABLE_DAKOTA_CONFIG_H],[1],[disabling DAKOTA_CONFIG_H])
    531539                                        AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI])
    532540                                else

  • ../trunk-jpl/externalpackages/adjoinablempi/install-macosx64.sh

     
    99#hg clone -r 268 http://mercurial.mcs.anl.gov//ad/AdjoinableMPI src
    1010
    1111#Download from ISSM server
    12 $ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz'
     12$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://issm.jpl.nasa.gov/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz'
    1313
    1414#Untar ADOL-C
    1515tar -zxf  adjoinablempi.tar.gz

  • ../trunk-jpl/externalpackages/dakota/install-6.2-macosx64-static.sh

     
     1#!/bin/bash
     2set -eu
     3
     4# Constants
     5DAK_VER="6.2"
     6
     7# Some cleanup
     8rm -rf build
     9rm -rf install
     10rm -rf tests
     11rm -rf src
     12mkdir build install src
     13
     14# Download from ISSM server
     15$ISSM_DIR/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${DAK_VER}-public.src.tar.gz" "dakota-${DAK_VER}-public-src.tar.gz"
     16
     17# Untar
     18tar -zxvf dakota-${DAK_VER}-public-src.tar.gz
     19
     20# Move Dakota to src directory
     21mv dakota-${DAK_VER}.0.src/* src
     22rm -rf dakota-${DAK_VER}.0.src
     23
     24# Set up Dakota and CMake variables
     25DAK_PATH=$ISSM_DIR/externalpackages/dakota
     26
     27export DAK_BUILD=$DAK_PATH/build
     28export DAK_INSTALL=$DAK_PATH/install
     29export DAK_SRC=$DAK_PATH/src
     30export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
     31
     32
     33# Apply patches
     34cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
     35patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/$DAK_VER/BuildDakotaCustom.cmake.mac.patch
     36patch $DAK_SRC/cmake/DakotaDev.cmake configs/$DAK_VER/DakotaDev.cmake.patch
     37patch $DAK_SRC/cmake/InstallDarwinDylibs.cmake configs/$DAK_VER/InstallDarwinDylibs.cmake.patch
     38patch $DAK_SRC/CMakeLists.txt configs/$DAK_VER/CMakeLists.txt.patch
     39patch src/src/NonDSampling.cpp configs/$DAK_VER/NonDSampling.cpp.patch
     40patch src/src/NonDLocalReliability.cpp configs/$DAK_VER/NonDLocalReliability.cpp.patch
     41patch src/packages/pecos/src/pecos_global_defs.hpp configs/$DAK_VER/pecos_global_defs.hpp.patch
     42
     43# Configure and build Dakota
     44cd $DAK_BUILD
     45cmake \
     46        -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \
     47        -C$DAK_SRC/cmake/DakotaDev.cmake \
     48        -DBUILD_STATIC_LIBS=ON \
     49        -DBUILD_SHARED_LIBS=OFF \
     50        -DBOOST_ROOT=$BOOST_ROOT \
     51        -DBoost_LIBRARY_DIRS=$BOOST_ROOT/lib \
     52        -DBoost_NO_BOOST_CMAKE=TRUE \
     53        -DBoost_NO_SYSTEM_PATHS=TRUE \
     54        -DCMAKE_INSTALL_PREFIX=$DAK_INSTALL \
     55        -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \
     56        -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \
     57        -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \
     58        -DCMAKE_CXX_FLAGS=-fdelayed-template-parsing \
     59        -DHAVE_ACRO=off \
     60        -DHAVE_JEGA=off \
     61        $DAK_SRC
     62
     63if [ $# -eq 0 ];
     64then
     65        make
     66        make install
     67else
     68        make -j $1
     69        make -j $1 install
     70fi
     71
     72# Set paths and library paths
     73export PATH=$DAK_INSTALL/bin:$DAK_INSTALL/test:$PATH
     74
     75if [ -z ${DYLD_LIBRARY_PATH+x} ]
     76then
     77        export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin
     78else
     79        export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin:$DYLD_LIBRARY_PATH
     80fi

  • ../trunk-jpl/externalpackages/dakota/install-6.2-linux64-static.sh 

    Property changes on: ../trunk-jpl/externalpackages/dakota/install-6.2-macosx64-static.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
     
     1#!/bin/bash
     2set -eu
     3
     4# Constants
     5DAK_VER="6.2"
     6
     7#Some cleanup
     8rm -rf Dakota
     9rm -rf src
     10rm -rf build
     11rm -rf install
     12mkdir src build install
     13
     14#Download from ISSM server
     15$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/dakota-${DAK_VER}-public.src.tar.gz dakota-${DAK_VER}-public-src.tar.gz
     16
     17#Untar
     18tar -zxvf dakota-${DAK_VER}-public-src.tar.gz
     19
     20#Move Dakota to src directory
     21mv dakota-${DAK_VER}.0.src/* src
     22rm -rf dakota-${DAK_VER}.0.src
     23
     24#Set up Dakota cmake variables and config
     25DAK_PATH=$ISSM_DIR/externalpackages/dakota
     26
     27export DAK_BUILD=$DAK_PATH/build
     28export DAK_INSTALL=$DAK_PATH/install
     29export DAK_SRC=$DAK_PATH/src
     30export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
     31export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install
     32
     33cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
     34patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/${DAK_VER}/BuildDakotaCustom.cmake.patch
     35patch $DAK_SRC/cmake/DakotaDev.cmake configs/${DAK_VER}/DakotaDev.cmake.patch
     36patch $DAK_SRC/CMakeLists.txt configs/${DAK_VER}/CMakeLists.txt.petsclibs.patch
     37
     38#Apply patches
     39patch src/src/NonDSampling.cpp configs/${DAK_VER}/NonDSampling.cpp.patch
     40patch src/src/NonDLocalReliability.cpp configs/${DAK_VER}/NonDLocalReliability.cpp.patch
     41patch src/packages/pecos/src/pecos_global_defs.hpp configs/${DAK_VER}/pecos_global_defs.hpp.patch
     42
     43#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
     44export CXXFLAGS='-std=c++98'
     45
     46#Configure dakota
     47cd $DAK_BUILD
     48
     49cmake -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \
     50                -C$DAK_SRC/cmake/DakotaDev.cmake \
     51                -DBUILD_STATIC_LIBS=ON \
     52                -DBUILD_SHARED_LIBS=OFF \
     53                -DBOOST_ROOT=$BOOST_ROOT \
     54                -DBoost_LIBRARY_DIRS=$BOOST_ROOT/lib \
     55                -DBoost_NO_BOOST_CMAKE=TRUE \
     56                -DBoost_NO_SYSTEM_PATHS=TRUE \
     57                -DBoost_INSTALL_PREFIX=$DAK_INSTALL \
     58                -DCMAKE_C_FLAGS="-O2 -g -fPIC" \
     59                -DCMAKE_CXX_FLAGS="-O2 -g -fPIC" \
     60                -DCMAKE_Fortran_FLAGS="-O2 -g -fPIC" \
     61                -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \
     62                -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \
     63                -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \
     64                -DHAVE_ACRO=off \
     65                -DHAVE_JEGA=off \
     66                $DAK_SRC
     67cd ..
     68
     69#Compile and install dakota
     70cd $DAK_BUILD
     71
     72if [ $# -eq 0 ];
     73then
     74        make
     75        make install
     76else
     77        make -j $1
     78        make -j $1 install
     79fi
     80
     81cd ..

  • ../trunk-jpl/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh 

    Property changes on: ../trunk-jpl/externalpackages/dakota/install-6.2-linux64-static.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
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     1#!/bin/bash
     2set -eu
     3
     4# NOTE: Stop after boostrap phase, and run
     5#
     6#       bjam --debug-configuration
     7#
     8# to figure out which paths boost is using to include python. Make sure everyone
     9# of these paths is covered by python. If not, just make symlinks in
     10# externalpackages/python to what boost is expecting. There is NO WAY to get the
     11# boost library to include python support without doing that.
     12
     13#Some cleanup
     14rm -rf install boost_1_55_0 src
     15mkdir install src
     16
     17#Download from ISSM server
     18$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz'
     19
     20#Untar
     21tar -zxvf  boost_1_55_0.tar.gz
     22
     23#Move boost into install directory
     24mv boost_1_55_0/* src
     25rm -rf boost_1_55_0
     26
     27patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
     28patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
     29patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch
     30patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch
     31patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch
     32
     33#Configure and compile
     34cd src
     35./bootstrap.sh \
     36        --prefix="$ISSM_DIR/externalpackages/boost/install" \
     37        --with-python=python
     38
     39#Compile boost
     40# Need gcc with iconv installed in a location that has been added to your path
     41# export CC=/usr/local/gfortan/bin/gcc
     42# export CXX=/usr/local/gfortran/bin/g++
     43./bjam toolset=darwin link=static runtime-link=static install
     44
     45#put bjam into install also:
     46mkdir ../install/bin
     47cp bjam ../install/bin

  • ../trunk-jpl/externalpackages/boost/install-1.55-linux64-static.sh 

    Property changes on: ../trunk-jpl/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
     
     1#!/bin/bash
     2#set -eu
     3#unhook set -eu because some target do fail and it is not a big deal
     4
     5#Note of caution:  stop after boostrap phase, and run
     6#bjam --debug-configuration, to figure out which paths boost is using to include
     7#python. make sure everyone of these paths is covered by python. If not, just make
     8#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY
     9#to get the boost library to include python support without doing that.
     10
     11#Some cleanup
     12rm -rf install boost_1_55_0 src
     13mkdir install src
     14
     15#Download from ISSM server
     16$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz boost_1_55_0.tar.gz
     17
     18#Untar
     19tar -zxvf boost_1_55_0.tar.gz
     20
     21#Move boost into install directory
     22mv boost_1_55_0/* src
     23rm -rf boost_1_55_0
     24
     25#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
     26export CXXFLAGS='-std=c++98'
     27
     28#Configure and compile
     29cd src
     30./bootstrap.sh \
     31        --prefix="$ISSM_DIR/externalpackages/boost/install" \
     32        --with-python=python
     33
     34#Compile boost
     35./bjam toolset=gcc link=static install
     36
     37#put bjam into install also
     38mkdir ../install/bin
     39cp bjam ../install/bin

  • ../trunk-jpl/packagers/ubuntu/package.sh 

    Property changes on: ../trunk-jpl/externalpackages/boost/install-1.55-linux64-static.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
     
    11#!/bin/bash
    22
    3 echo "modify generic"
     3MATLAB_PATH="/usr/local/MATLAB/R2015a"
     4PACKAGE="ISSM" # Name of directory to copy distributable files to
     5TARBALL_NAME="issm-ubuntu"
     6TARBALL=$TARBALL_NAME.tar.gz
     7
     8# Clean up from previous packaging
     9echo "Cleaning up existing assets"
     10cd $ISSM_DIR
     11rm -rf $PACKAGE
     12mkdir $PACKAGE
     13
     14# Add/modify required binaries
    415cd $ISSM_DIR/bin
     16
     17echo "Modify generic"
    518cat 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"
     19
     20echo "Moving mpiexec to bin"
     21if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then
     22        cp ../externalpackages/mpich/install/bin/mpiexec .
     23        cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy .
     24else
     25        echo "mpich not found"
     26fi
     27
     28echo "Moving gmsh to bin"
    1029if [ -f ../externalpackages/gmsh/install/gmsh ]; then
    1130        cp ../externalpackages/gmsh/install/gmsh .
    1231else
    … …  
    1332        echo "gmsh not found"
    1433fi
    1534
    16 #Check that test101 runs
     35# Check that test101 runs
    1736cd $ISSM_DIR/test/NightlyRun
    1837rm matlab.log
    19 /usr/local/MATLAB/R2015a/bin/matlab -nojvm -nosplash -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
     38$MATLAB_PATH/bin/matlab -nojvm -nosplash -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
    2039
    2140if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then
    2241        echo "test101 FAILED"
    2342        exit 1;
    2443else
    25         echo "test101 passed"
     44        echo "test101 PASSED"
    2645fi
    2746
    28 tarball_name='issm-ubuntu-static_build.tar.gz'
    29 
    30 echo "Cleanup first"
     47echo "Creating tarball: ${TARBALL_NAME}"
    3148cd $ISSM_DIR
    32 rm $tarball_name
     49rm -f $TARBALL
     50cp -rf bin lib test examples scripts $PACKAGE/
     51tar -czf $TARBALL $PACKAGE
     52ls -lah $TARBALL
    3353
    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
    41 
    4254echo "Shipping binaries to website"
    4355
    4456# We're using public key authentication method to upload the tarball The
    … …  
    5567source ~/.ssh/agent.sh
    5668ssh-add ~/.ssh/ubuntu-bins_jenkins-to-ross
    5769
    58 scp $tarball_name ross.ics.uci.edu:/var/www/html/$tarball_name
     70scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL
    5971
    6072if [ $? -ne 0 ]; then
    6173        echo "The upload failed."

  • ../trunk-jpl/packagers/ubuntu-dakota/package.sh

     
     1#!/bin/bash
     2
     3MATLAB_PATH="/usr/local/MATLAB/R2015a"
     4PACKAGE="ISSM" # Name of directory to copy distributable files to
     5TARBALL_NAME="issm-ubuntu-dakota"
     6TARBALL=$TARBALL_NAME.tar.gz
     7
     8# Clean up from previous packaging
     9echo "Cleaning up existing assets"
     10cd $ISSM_DIR
     11rm -rf $PACKAGE
     12mkdir $PACKAGE
     13
     14# Add/modify required binaries
     15cd $ISSM_DIR/bin
     16
     17echo "Modify generic"
     18cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m
     19
     20echo "Moving mpiexec to bin"
     21if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then
     22        cp ../externalpackages/mpich/install/bin/mpiexec .
     23        cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy .
     24else
     25        echo "mpich not found"
     26fi
     27
     28echo "Moving gmsh to bin"
     29if [ -f ../externalpackages/gmsh/install/gmsh ]; then
     30        cp ../externalpackages/gmsh/install/gmsh .
     31else
     32        echo "gmsh not found"
     33fi
     34
     35# Check that test101 runs
     36cd $ISSM_DIR/test/NightlyRun
     37rm matlab.log
     38$MATLAB_PATH/bin/matlab -nojvm -nosplash -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
     39
     40if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then
     41        echo "test101 FAILED"
     42        exit 1;
     43else
     44        echo "test101 PASSED"
     45fi
     46
     47echo "Creating tarball: ${TARBALL_NAME}"
     48cd $ISSM_DIR
     49rm -f $TARBALL
     50cp -rf bin lib test examples scripts $PACKAGE/
     51tar -czf $TARBALL $PACKAGE
     52ls -lah $TARBALL
     53
     54echo "Shipping binaries to website"
     55
     56# We're using public key authentication method to upload the tarball The
     57# following lines check to see if the SSH Agent is running. If not, then it is
     58# started and relevant information is forwarded to a script.
     59pgrep "ssh-agent" > /dev/null
     60if [ $? -ne 0 ]; then
     61        echo "SSH Agent is not running. Starting it..."
     62        ssh-agent > ~/.ssh/agent.sh
     63else
     64        echo "SSH Agent is running..."
     65fi
     66
     67source ~/.ssh/agent.sh
     68ssh-add ~/.ssh/ubuntu-bins_jenkins-to-ross
     69
     70scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL
     71
     72if [ $? -ne 0 ]; then
     73        echo "The upload failed."
     74        echo "Perhaps the SSH Agent was started by some other means."
     75        echo "Try killing the agent and running again."
     76fi

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

    Property changes on: ../trunk-jpl/packagers/ubuntu-dakota/package.sh
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
     
    11#!/bin/bash
    22
    3 TARBALL_NAME='issm-mac-static_build'
     3MATLAB_PATH="/Applications/MATLAB_R2015b.app"
     4PACKAGE="ISSM" # Name of directory to copy distributable files to
     5TARBALL_NAME="issm-mac"
    46TARBALL=$TARBALL_NAME.tar.gz
    57
    68# Clean up from previous packaging
    79echo "Cleaning up existing assets"
    810cd $ISSM_DIR
    9 rm -rf trunk
    10 mkdir trunk
     11rm -rf $PACKAGE
     12mkdir $PACKAGE
    1113
    1214# Add/modify required binaries
    1315cd $ISSM_DIR/bin
    … …  
    3032        echo "gmsh not found"
    3133fi
    3234
    33 # Copy gmt to trunk
     35# Copy gmt to package
    3436# NOTE: The following assumes the precompiled version of gmt
    3537echo "Moving gmt to externalpackages"
    3638if [ -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
     39        mkdir $ISSM_DIR/$PACKAGE/externalpackages
     40        mkdir $ISSM_DIR/$PACKAGE/externalpackages/gmt
     41        cp -a $ISSM_DIR/externalpackages/gmt/install $ISSM_DIR/$PACKAGE/externalpackages/gmt/install
    4042else
    4143        echo "gmt not found"
    4244fi
    … …  
    4446# Check that test101 runs
    4547cd $ISSM_DIR/test/NightlyRun
    4648rm matlab.log
    47 /Applications/MATLAB_R2015b.app/bin/matlab -nodisplay -nojvm -nosplash -nodesktop -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
     49$MATLAB_PATH/bin/matlab -nodisplay -nojvm -nosplash -nodesktop -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
    4850
    4951if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then
    5052        echo "test101 FAILED"
    … …  
    5658echo "Creating tarball: ${TARBALL_NAME}"
    5759cd $ISSM_DIR
    5860rm -f $TARBALL
    59 cp -rf bin lib test examples scripts trunk/
     61cp -rf bin lib test examples scripts $PACKAGE/
    6062
    6163# Create link to gmt from bin
    6264# NOTE: It is important that we are in the destination dir when sym linking so that the path is relative
    63 if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then
    64         cd $ISSM_DIR/trunk/bin
    65         ln -s ../externalpackages/gmt/bin/gmt ./gmt
     65if [ -f $ISSM_DIR/$PACKAGE/externalpackages/gmt/install/bin/gmt ]; then
     66        cd $ISSM_DIR/$PACKAGE/bin
     67        ln -s ../externalpackages/gmt/install/bin/gmt ./gmt
    6668fi
    6769
    6870cd $ISSM_DIR
    69 tar -czf $TARBALL trunk
     71tar -czf $TARBALL $PACKAGE
    7072ls -lah $TARBALL
    7173
    7274echo "Shipping binaries to website"

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

     
    11#!/bin/bash
    22
    3 echo "modify generic"
     3MATLAB_PATH="/Applications/MATLAB_R2015b.app"
     4PACKAGE="ISSM" # Name of directory to copy distributable files to
     5TARBALL_NAME="issm-mac-dakota"
     6TARBALL=$TARBALL_NAME.tar.gz
     7
     8# Clean up from previous packaging
     9echo "Cleaning up existing assets"
     10cd $ISSM_DIR
     11rm -rf $PACKAGE
     12mkdir $PACKAGE
     13
     14# Add/modify required binaries
    415cd $ISSM_DIR/bin
     16
     17echo "Modifying generic"
    518cat 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 .
    919
    10 #Check that test101 runs
     20echo "Moving mpiexec to bin"
     21if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then
     22        cp ../externalpackages/mpich/install/bin/mpiexec .
     23        cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy .
     24else
     25        echo "mpich not found"
     26fi
     27
     28# Check that test101 runs
    1129cd $ISSM_DIR/test/NightlyRun
    1230rm matlab.log
    13 /Applications/MATLAB_R2015b.app/bin/matlab -nodisplay -nojvm -nosplash -nodesktop -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
     31$MATLAB_PATH/bin/matlab -nodisplay -nojvm -nosplash -nodesktop -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101); exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log
    1432
    1533if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then
    1634        echo "test101 FAILED"
    1735        exit 1;
    1836else
    19         echo "test101 passed"
     37        echo "test101 PASSED"
    2038fi
    2139
    22 #Package using the Package Maker from OSX, driven by command line.
    23 tarball_name='issm-mac-dakota-static_build.tar.gz'
    24 
    25 echo "Cleanup first"
     40echo "Creating tarball: ${TARBALL_NAME}"
    2641cd $ISSM_DIR
    27 rm $tarball_name
     42rm -f $TARBALL
     43cp -rf bin lib test examples scripts $PACKAGE/
     44tar -czf $TARBALL $PACKAGE
     45ls -lah $TARBALL
    2846
    29 echo "Creating tarball: ${tarball_name}"
    30 cd $ISSM_DIR
    31 rm -rf trunk
    32 mkdir trunk
    33 cp -rf bin lib test examples trunk/
    34 tar -czf $tarball_name trunk
    35 ls -lah $tarball_name
    36 
    3747echo "Shipping binaries to website"
    3848
    3949# We're using public key authentication method to upload the tarball. The
    … …  
    5060source ~/.ssh/agent.sh
    5161ssh-add ~/.ssh/macosx-bins_richese-to-ross
    5262
    53 scp $tarball_name ross.ics.uci.edu:/var/www/html/$tarball_name
     63scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL
    5464
    5565if [ $? -ne 0 ]; then
    5666        echo "The upload failed."

  • ../trunk-jpl/packagers/win10/package64.sh

     
    11#!/bin/bash
    22
     3MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a"
     4PACKAGE="ISSM" # Name of directory to copy distributable files to
    35TARBALL_NAME='ISSM-Win10-64'
    46TARBALL=$TARBALL_NAME.tar.gz
    5 MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a"
    67
    78# Source Windows environment
    89source $ISSM_DIR/externalpackages/windows/windows_environment.sh
    … …  
    1011# Clean up from previous packaging
    1112echo "Cleaning up existing assets"
    1213cd $ISSM_DIR
    13 rm -rf trunk
    14 mkdir trunk
     14rm -rf $PACKAGE
     15mkdir $PACKAGE
    1516
    1617# Add/modify required binaries
    1718cd $ISSM_DIR/bin
    … …  
    2526
    2627echo "Copying gmsh to bin"
    2728if [ -f ../externalpackages/gmsh/install/gmsh.exe ]; then
    28         cp ../externalpackages/gmsh/install/gmsh.exe .
     29        cp ../externalpackages/gmsh/install/gmsh.exe ./gmsh.exe
    2930else
    3031        echo "gmsh not found"
    3132fi
    3233
    33 # Copy gmt to trunk
     34# Copy gmt to package
    3435# NOTE: The following assumes the precompiled version of gmt
    3536echo "Moving gmt to externalpackages"
    3637if [ -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
     38        mkdir $ISSM_DIR/$PACKAGE/externalpackages
     39        mkdir $ISSM_DIR/$PACKAGE/externalpackages/gmt
     40        cp -a $ISSM_DIR/externalpackages/gmt/install $ISSM_DIR/$PACKAGE/externalpackages/gmt/install
    4041else
    4142        echo "gmt not found"
    4243fi
    … …  
    6667echo "Creating tarball: ${TARBALL_NAME}"
    6768cd $ISSM_DIR
    6869rm -f $TARBALL
    69 cp -rf bin lib test examples scripts trunk/
     70cp -rf bin lib test examples scripts $PACKAGE/
    7071
    7172# Create link to gmt from bin
    7273# NOTE: It is important that we are in the destination dir when sym linking so that the path is relative
    73 if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then
    74         cd $ISSM_DIR/trunk/bin
    75         ln -s ../externalpackages/gmt/bin/gmt.exe ./gmt
     74if [ -f $ISSM_DIR/$PACKAGE/externalpackages/gmt/bin/gmt ]; then
     75        cd $ISSM_DIR/$PACKAGE/bin
     76        ln -s ../externalpackages/gmt/bin/gmt.exe ./gmt.exe
    7677fi
    7778
    7879cd $ISSM_DIR
    79 tar -czf $TARBALL trunk
     80tar -czf $TARBALL $PACKAGE
    8081ls -lah $TARBALL
    8182
    8283# Ship binaries to website

  • ../trunk-jpl/jenkins/linux64_ross_static

     
    2222        --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
    2323        --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
    2424        --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
    25         --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
    26         --with-pic \
    27         --with-numthreads=4'
     25        --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu -lgfortran" \
     26        --with-numthreads=4 \
     27        --with-pic'
    2828
    2929#PYTHON and MATLAB testing
    3030MATLAB_TEST=0
    … …  
    5151
    5252#number of cpus used in ISSM installation and compilation (one is usually
    5353#safer as some packages are very sensitive to parallel compilation)
    54 NUMCPUS_INSTALL=10
     54NUMCPUS_INSTALL=4
    5555
    5656#number of cpus used in the nightly runs.
    57 NUMCPUS_RUN=10
     57NUMCPUS_RUN=4
    5858
    5959#Nightly run options. The matlab routine runme.m will be called
    6060#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
    … …  
    6161#by Matlab and runme.m
    6262#ex: "'id',[101 102 103]"
    6363##                           FS
    64 #PYTHON_NROPTIONS="--exclude_name 'Dakota'"
    65 #MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]"
     64#PYTHON_NROPTIONS=""
     65#MATLAB_NROPTIONS=""

  • ../trunk-jpl/jenkins/linux64_ross_dakota_static

     
     1
     2#-------------------------------#
     3# 1: ISSM general configuration #
     4#-------------------------------#
     5
     6#MATLAB path
     7MATLAB_PATH="/usr/local/MATLAB/R2015a"
     8
     9#ISSM CONFIGURATION
     10ISSM_CONFIG='--prefix=$ISSM_DIR\
     11        --enable-standalone-executables \
     12        --enable-standalone-modules \
     13        --enable-standalone-libraries \
     14        --with-matlab-dir=$MATLAB_PATH \
     15        --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
     16        --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
     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 \
     21        --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
     22        --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
     23        --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
     24        --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
     25        --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
     26        --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
     27        --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu -lgfortran" \
     28        --with-numthreads=4 \
     29        --with-pic'
     30
     31#PYTHON and MATLAB testing
     32MATLAB_TEST=0
     33PYTHON_TEST=0
     34
     35#-----------------------------------#
     36# 3: External packages installation #
     37#-----------------------------------#
     38
     39#List of external pakages to be installed and their installation scripts
     40EXTERNALPACKAGES="autotools     install.sh
     41                                                cmake        install.sh
     42                                                chaco         install.sh
     43                                                mpich         install-3.2-linux64-static.sh
     44                                                m1qn3         install.sh
     45                                                petsc         install-3.7-linux64-static.sh
     46                                                triangle      install-linux64.sh
     47                                                boost         install-1.55-linux64-static.sh
     48                                                dakota        install-6.2-linux64-static.sh
     49                                                shell2junit   install.sh"
     50
     51#-----------------#
     52# 4: test options #
     53#-----------------#
     54
     55#number of cpus used in ISSM installation and compilation (one is usually
     56#safer as some packages are very sensitive to parallel compilation)
     57NUMCPUS_INSTALL=4
     58
     59#number of cpus used in the nightly runs.
     60NUMCPUS_RUN=4
     61
     62#Nightly run options. The matlab routine runme.m will be called
     63#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
     64#by Matlab and runme.m
     65#ex: "'id',[101 102 103]"
     66#PYTHON_NROPTIONS=""
     67#MATLAB_NROPTIONS=""

  • ../trunk-jpl/examples/Pig2/runme.m 

    Property changes on: ../trunk-jpl/jenkins/linux64_ross_dakota_static
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
     
    1 steps=[1:8];
     1steps=1;
    22
    3 if any(steps==1)   %Mesh Generation #1
     3if any(steps==1) %Mesh Generation #1
    44
    55        %Mesh parameters
    66        domain =['./DomainOutline.exp'];
    … …  
    157157
    158158if any(steps==6) %Transient Run #1
    159159
    160         md = loadmodel('../Pig/Models/PIG_Control_drag');       
     160        md = loadmodel('./Models/PIG_Control_drag');   
    161161
    162162        md.inversion.iscontrol=0;
    163163        md.transient.ismasstransport=1;

  • ../trunk-jpl

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