Changeset 24311


Ignore:
Timestamp:
11/01/19 09:58:30 (5 years ago)
Author:
Mathieu Morlighem
Message:

merged trunk and trunk-jpl

Location:
issm/trunk-jpl
Files:
8 edited
7 copied

Legend:

Unmodified
Added
Removed

  • issm/trunk-jpl

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

    r23388 r24311  
    1 steps=[1:8];
    2 
    3 if any(steps==1)   %Mesh Generation #1
     1steps=1;
     2
     3if any(steps==1) %Mesh Generation #1
    44
    55        %Mesh parameters
    … …  
    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;

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

    r23435 r24311  
    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

  • issm/trunk-jpl/m4/issm_options.m4

    r24215 r24311  
    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.
    … …  
    483482
    484483                DAKOTAFLAGS=""
     484                dnl TODO: Should we also be checking if HAVE_BOOST before adding boost libs?
    485485                case "${host_os}" in
    486486                        *cygwin*)
    … …  
    507507                                else if test x$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$BOOST_ROOT/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system"
     513                                        fi
    510514                                        AC_DEFINE([DISABLE_DAKOTA_CONFIG_H],[1],[disabling DAKOTA_CONFIG_H])
    511515                                        AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI])
    … …  
    526530                                        AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI])
    527531                                else if test x$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])

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

    r22757 r24311  
    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
    … …  
    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
    28 
    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
     42rm -f $TARBALL
     43cp -rf bin lib test examples scripts $PACKAGE/
     44tar -czf $TARBALL $PACKAGE
     45ls -lah $TARBALL
    3646
    3747echo "Shipping binaries to website"
    … …  
    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

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

    r23393 r24311  
    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
    … …  
    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
    … …  
    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"
    … …  
    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
    … …  
    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

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

    r22821 r24311  
    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 .
    … …  
    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
    … …  
    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
    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
     49rm -f $TARBALL
     50cp -rf bin lib test examples scripts $PACKAGE/
     51tar -czf $TARBALL $PACKAGE
     52ls -lah $TARBALL
    4153
    4254echo "Shipping binaries to website"
    … …  
    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

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

    r23385 r24311  
    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
    … …  
    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
    … …  
    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"
    … …  
    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
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