Index: sm/trunk/externalpackages/boost/install-1.55-linux64-static.sh
===================================================================
--- /issm/trunk/externalpackages/boost/install-1.55-linux64-static.sh (revision 23927)
+++ (revision )
@@ -1,39 +1,0 @@
-#!/bin/bash
-#set -eu
-#unhook set -eu because some target do fail and it is not a big deal
-
-#Note of caution: stop after boostrap phase, and run
-#bjam --debug-configuration, to figure out which paths boost is using to include
-#python. make sure everyone of these paths is covered by python. If not, just make
-#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY
-#to get the boost library to include python support without doing that.
-
-#Some cleanup
-rm -rf install boost_1_55_0 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz boost_1_55_0.tar.gz
-
-#Untar
-tar -zxvf boost_1_55_0.tar.gz
-
-#Move boost into install directory
-mv boost_1_55_0/* src
-rm -rf boost_1_55_0
-
-#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
-export CXXFLAGS='-std=c++98'
-
-#Configure and compile
-cd src
-./bootstrap.sh \
- --prefix="$ISSM_DIR/externalpackages/boost/install" \
- --with-python-root="$ISSM_DIR/externalpackages/python/install"
-
-#Compile boost
-./bjam link=static runtime-link=static install
-
-#put bjam into install also
-mkdir ../install/bin
-cp bjam ../install/bin
Index: sm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh
===================================================================
--- /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 23927)
+++ (revision )
@@ -1,47 +1,0 @@
-#!/bin/bash
-set -eu
-
-# NOTE: Stop after boostrap phase, and run
-#
-# bjam --debug-configuration
-#
-# to figure out which paths boost is using to include python. Make sure everyone
-# of these paths is covered by python. If not, just make symlinks in
-# externalpackages/python to what boost is expecting. There is NO WAY to get the
-# boost library to include python support without doing that.
-
-#Some cleanup
-rm -rf install boost_1_55_0 src
-mkdir install src
-
-#Download from ISSM server
-$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz'
-
-#Untar
-tar -zxvf boost_1_55_0.tar.gz
-
-#Move boost into install directory
-mv boost_1_55_0/* src
-rm -rf boost_1_55_0
-
-patch src/boost/atomic/detail/cas128strong.hpp ./configs/1.55/cas128strong.hpp.patch
-patch src/boost/atomic/detail/gcc-atomic.hpp ./configs/1.55/gcc-atomic.hpp.patch
-patch src/tools/build/v2/user-config.jam ./configs/1.55/user-config.jam.patch
-patch src/tools/build/v2/tools/darwin.jam ./configs/1.55/darwin.jam.patch
-patch src/tools/build/v2/tools/darwin.py ./configs/1.55/darwin.py.patch
-
-#Configure and compile
-cd src
-./bootstrap.sh \
- --prefix="$ISSM_DIR/externalpackages/boost/install" \
- --with-python=python
-
-#Compile boost
-# Need gcc with iconv installed in a location that has been added to your path
-# export CC=/usr/local/gfortan/bin/gcc
-# export CXX=/usr/local/gfortran/bin/g++
-./bjam toolset=darwin link=static runtime-link=static install
-
-#put bjam into install also:
-mkdir ../install/bin
-cp bjam ../install/bin
Index: sm/trunk/externalpackages/dakota/install-6.2-linux64-static.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-linux64-static.sh (revision 23927)
+++ (revision )
@@ -1,81 +1,0 @@
-#!/bin/bash
-set -eu
-
-# Constants
-DAK_VER="6.2"
-
-#Some cleanup
-rm -rf Dakota
-rm -rf src
-rm -rf build
-rm -rf install
-mkdir src build install
-
-#Download from ISSM server
-$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
-
-#Untar
-tar -zxvf dakota-${DAK_VER}-public-src.tar.gz
-
-#Move Dakota to src directory
-mv dakota-${DAK_VER}.0.src/* src
-rm -rf dakota-${DAK_VER}.0.src
-
-#Set up Dakota cmake variables and config
-DAK_PATH=$ISSM_DIR/externalpackages/dakota
-
-export DAK_BUILD=$DAK_PATH/build
-export DAK_INSTALL=$DAK_PATH/install
-export DAK_SRC=$DAK_PATH/src
-export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
-export BOOST_ROOT=$ISSM_DIR/externalpackages/boost/install
-
-cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
-patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/${DAK_VER}/BuildDakotaCustom.cmake.patch
-patch $DAK_SRC/cmake/DakotaDev.cmake configs/${DAK_VER}/DakotaDev.cmake.patch
-patch $DAK_SRC/CMakeLists.txt configs/${DAK_VER}/CMakeLists.txt.petsclibs.patch
-
-#Apply patches
-patch src/src/NonDSampling.cpp configs/${DAK_VER}/NonDSampling.cpp.patch
-patch src/src/NonDLocalReliability.cpp configs/${DAK_VER}/NonDLocalReliability.cpp.patch
-patch src/packages/pecos/src/pecos_global_defs.hpp configs/${DAK_VER}/pecos_global_defs.hpp.patch
-
-#Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost
-export CXXFLAGS='-std=c++98'
-
-#Configure dakota
-cd $DAK_BUILD
-
-cmake -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \
- -C$DAK_SRC/cmake/DakotaDev.cmake \
- -DBUILD_STATIC_LIBS=ON \
- -DBUILD_SHARED_LIBS=OFF \
- -DBOOST_ROOT=$BOOST_ROOT \
- -DBoost_LIBRARY_DIRS=$BOOST_ROOT/lib \
- -DBoost_NO_BOOST_CMAKE=TRUE \
- -DBoost_NO_SYSTEM_PATHS=TRUE \
- -DBoost_INSTALL_PREFIX=$DAK_INSTALL \
- -DCMAKE_C_FLAGS="-O2 -g -fPIC" \
- -DCMAKE_CXX_FLAGS="-O2 -g -fPIC" \
- -DCMAKE_Fortran_FLAGS="-O2 -g -fPIC" \
- -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \
- -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \
- -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \
- -DHAVE_ACRO=off \
- -DHAVE_JEGA=off \
- $DAK_SRC
-cd ..
-
-#Compile and install dakota
-cd $DAK_BUILD
-
-if [ $# -eq 0 ];
-then
- make
- make install
-else
- make -j $1
- make -j $1 install
-fi
-
-cd ..
Index: sm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh (revision 23927)
+++ (revision )
@@ -1,80 +1,0 @@
-#!/bin/bash
-set -eu
-
-# Constants
-DAK_VER="6.2"
-
-# Some cleanup
-rm -rf build
-rm -rf install
-rm -rf tests
-rm -rf src
-mkdir build install src
-
-# Download from ISSM server
-$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"
-
-# Untar
-tar -zxvf dakota-${DAK_VER}-public-src.tar.gz
-
-# Move Dakota to src directory
-mv dakota-${DAK_VER}.0.src/* src
-rm -rf dakota-${DAK_VER}.0.src
-
-# Set up Dakota and CMake variables
-DAK_PATH=$ISSM_DIR/externalpackages/dakota
-
-export DAK_BUILD=$DAK_PATH/build
-export DAK_INSTALL=$DAK_PATH/install
-export DAK_SRC=$DAK_PATH/src
-export MPIHOME=$ISSM_DIR/externalpackages/mpich/install
-
-
-# Apply patches
-cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake
-patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/$DAK_VER/BuildDakotaCustom.cmake.mac.patch
-patch $DAK_SRC/cmake/DakotaDev.cmake configs/$DAK_VER/DakotaDev.cmake.patch
-patch $DAK_SRC/cmake/InstallDarwinDylibs.cmake configs/$DAK_VER/InstallDarwinDylibs.cmake.patch
-patch $DAK_SRC/CMakeLists.txt configs/$DAK_VER/CMakeLists.txt.patch
-patch src/src/NonDSampling.cpp configs/$DAK_VER/NonDSampling.cpp.patch
-patch src/src/NonDLocalReliability.cpp configs/$DAK_VER/NonDLocalReliability.cpp.patch
-patch src/packages/pecos/src/pecos_global_defs.hpp configs/$DAK_VER/pecos_global_defs.hpp.patch
-
-# Configure and build Dakota
-cd $DAK_BUILD
-cmake \
- -C$DAK_SRC/cmake/BuildDakotaCustom.cmake \
- -C$DAK_SRC/cmake/DakotaDev.cmake \
- -DBUILD_STATIC_LIBS=ON \
- -DBUILD_SHARED_LIBS=OFF \
- -DBOOST_ROOT=$BOOST_ROOT \
- -DBoost_LIBRARY_DIRS=$BOOST_ROOT/lib \
- -DBoost_NO_BOOST_CMAKE=TRUE \
- -DBoost_NO_SYSTEM_PATHS=TRUE \
- -DCMAKE_INSTALL_PREFIX=$DAK_INSTALL \
- -DCMAKE_C_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicc \
- -DCMAKE_CXX_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpicxx \
- -DCMAKE_Fortran_COMPILER=$ISSM_DIR/externalpackages/mpich/install/bin/mpif77 \
- -DCMAKE_CXX_FLAGS=-fdelayed-template-parsing \
- -DHAVE_ACRO=off \
- -DHAVE_JEGA=off \
- $DAK_SRC
-
-if [ $# -eq 0 ];
-then
- make
- make install
-else
- make -j $1
- make -j $1 install
-fi
-
-# Set paths and library paths
-export PATH=$DAK_INSTALL/bin:$DAK_INSTALL/test:$PATH
-
-if [ -z ${DYLD_LIBRARY_PATH+x} ]
-then
- export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin
-else
- export DYLD_LIBRARY_PATH=$DAK_INSTALL/lib:$DAK_INSTALL/bin:$DYLD_LIBRARY_PATH
-fi
Index: sm/trunk/jenkins/jenkins.sh
===================================================================
--- /issm/trunk/jenkins/jenkins.sh (revision 23927)
+++ (revision )
@@ -1,529 +1,0 @@
-#!/bin/bash
-#This bash script calls the nightlyrun.m matlab file to run our nightly test decks.
-#It then processes the results and sends an email to the Ice developpers.
-
-echo "Cleaning up execution directory"
-rm -rf $ISSM_DIR/execution/*
-rm -rf $ISSM_DIR/nightlylog
-mkdir $ISSM_DIR/nightlylog
-
-#Server URI
-SERVER='https://ross.ics.uci.edu:8080'
-#SERVER='http://ross.ics.uci.edu:8080'
-
-#Get configuration
-#Source config file{{{
-if [ $# -ne 1 ];
-then
- #no config file specified: exit
- echo "no config file specified. Exiting..." >&2 # Error message to stderr.
- exit 1
-fi
-if [ ! -f "$1" ]
-then
- echo "File $1 not found!" >&2 # Error message to stderr.
- exit 1
-fi
-
-#Defaults (to avoid -eq: unary operator expected)
-EXAMPLES_TEST=0
-MATLAB_TEST=0
-PYTHON_TEST=0
-JAVASCRIPT_TEST=0
-
-#source configuration script
-source $1;
-#}}}
-#Get Operating system (OS) name{{{
-OS=$(uname -s)
-if [[ $OS == CYGWIN* ]]; then
- OS="win";
-fi
-#}}}
-
-#Install ISSM
-#Determinig Installation type depending on svn changes{{{
-echo "======================================================";
-echo " Determining Installation type "
-echo "======================================================";
-if [ -a $ISSM_DIR/svn_revision_old ]
-then
- SVN_PREVIOUS=$(cat $ISSM_DIR/svn_revision_old)
- SVN_CURRENT=$SVN_REVISION_1
- echo "Previous revision number: $SVN_PREVIOUS"
- echo "Current revision number: $SVN_CURRENT"
-
- #Get changes from jenkins itself (svn requires credentials)
- #svn --non-interactive --no-auth-cache --trust-server-cert diff -r $SVN_PREVIOUS:$SVN_CURRENT --summarize $ISSM_DIR | awk '{print $NF}' > $ISSM_DIR/TEMP
- rm -rf changes
- wget $SERVER/job/$JOB_NAME/$BUILD_NUMBER/changes > /dev/null 2>&1
-
- #Process html page and get the list of files that has changed (tricky...)
- #cat changes | grep '="The file was modified"' | sed -e 's/.*<\/td>| \(.*\)<\/a><\/td> | .*/\1/' > $ISSM_DIR/TEMP
- #cat changes | grep 'document_edit' |sed -e 's/document_edit.png/document_edit.png\
- #/g' | sed -e 's/.*<\/a><\/td> | \(.*\)<\/td><\/tr>.*/\1/' | grep -v 'document_edit.png' > $ISSM_DIR/TEMP
- cat changes | tr " " "\n" | grep trunk | sed -e 's/.*\(.*\)<\/a>.*/\1/' > $ISSM_DIR/TEMP
-
- #Print list of files
- echo " "
- echo "List of updated files"
- cat $ISSM_DIR/TEMP
- echo " "
-
- #Do we need to reinstall externalpackages?
- echo "Determining installation type"
- if [ ! -z "$(cat $ISSM_DIR/TEMP | grep externalpackages)" ] ; then
- echo " -- checking for changed externalpackages... yes";
- ISSM_EXTERNALPACKAGES="yes"
- else
- echo " -- checking for changed externalpackages... no";
- ISSM_EXTERNALPACKAGES="no"
- fi
-
- #Do we need to reconfigure
- if [ ! -z "$(cat $ISSM_DIR/TEMP | grep -e "Makefile.am" -e "m4" )" ] ||
- [ ! -f "$ISSM_DIR/bin/issm.exe" ] ||
- [ "$ISSM_EXTERNALPACKAGES" == "yes" ] ;
- then
- echo " -- checking for reconfiguration... yes";
- ISSM_RECONFIGURE="yes"
- else
- echo " -- checking for reconfiguration... no";
- ISSM_RECONFIGURE="no"
- fi
-
- #Do we need to recompile
- if [ ! -z "$(cat $ISSM_DIR/TEMP | grep -e "\.cpp" -e "\.h" )" ] ||
- [ "$ISSM_RECONFIGURE" == "yes" ] ;
- then
- echo " -- checking for recompilation... yes";
- ISSM_COMPILATION="yes"
- else
- echo " -- checking for recompilation... no";
- ISSM_COMPILATION="no"
- fi
- #ISSM_COMPILATION="yes"
- rm $ISSM_DIR/changes
-
-else
- echo "Previous revision not found, this must be a fresh install"
- echo " -- checking for changed externalpackages... yes";
- echo " -- checking for reconfiguration... yes";
- echo " -- checking for recompilation... yes";
- ISSM_EXTERNALPACKAGES="yes"
- ISSM_RECONFIGURE="yes"
- ISSM_COMPILATION="yes"
-fi
-echo " "
-echo "Recording current svn version: $SVN_REVISION_1"
-echo $SVN_REVISION_1 > $ISSM_DIR/svn_revision_old
-#}}}
-#Install external packages (ISSM_EXTERNALPACKAGES){{{
-
-#number of packages:
-NUMPACKAGES=$(($(echo $EXTERNALPACKAGES | wc -w )/2))
-
-#Jenkins xml files for individual packages
-EXTERNAL_TEST_FILE="$ISSM_DIR/nightlylog/results/external.xml"
-mkdir -p $ISSM_DIR/nightlylog/results
-echo "" > $EXTERNAL_TEST_FILE
-
-# Need a source here for when builds start midway through installation of externalpackages.
-source $ISSM_DIR/etc/environment.sh
-
-if [ "$OS" == "win" ]; then
- echo " == WINDOWS ENVIRONMENT DETECTED =="
- source $ISSM_DIR/externalpackages/windows/windows_environment.sh
-fi
-
-EXTERNALPACKAGES_FAILED=0;
-
-for ((i=1;i<=$NUMPACKAGES;i++))
-do
- NUM1=$((2*$i-1))
- NUM2=$((2*$i))
- PACKAGENAME=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM1-$NUM1)
- PACKAGEINST=$(echo $EXTERNALPACKAGES | cut -d " " -f $NUM2-$NUM2)
-
- cd $ISSM_DIR/externalpackages/$PACKAGENAME
-
- #install if requested or if previous install has not been successful
- if [ "$ISSM_EXTERNALPACKAGES" == "yes" ] || [ ! -d ./install -a ! -d ./install-javascript ] || ([ -d ./install ] && [ ! "$(ls -A ./install)" ]) || ([ -d ./install-javascript ] && [ ! "$(ls -A ./install-javascript)" ]); then
- echo "======================================================";
- echo " Installing $PACKAGENAME ";
- echo "======================================================";
-
- ./$PACKAGEINST &> compil.log
- if [ $? -ne 0 ] && [ "$PACKAGENAME" != "boost" ]; then
- cat compil.log
- echo "======================================================";
- echo " ERROR: installation of $PACKAGENAME failed ";
- echo "======================================================";
- echo "" >> $EXTERNAL_TEST_FILE
- echo 'External packages did not install right. Check it.' >> $EXTERNAL_TEST_FILE
- cat compil.log >> $EXTERNAL_TEST_FILE
- echo '' >> $EXTERNAL_TEST_FILE
- echo '' >> $EXTERNAL_TEST_FILE
- EXTERNALPACKAGES_FAILED=1;
- else
- echo "" >> $EXTERNAL_TEST_FILE
- fi
- source $ISSM_DIR/etc/environment.sh
-
- #If external package is rebuilt, we also need to recompile
- ISSM_RECONFIGURE="yes"
- ISSM_COMPILATION="yes"
- else
- echo "======================================================";
- echo " Skipping $PACKAGENAME ";
- echo "======================================================";
- echo "" >> $EXTERNAL_TEST_FILE
- fi
-done
-echo '' >> $EXTERNAL_TEST_FILE
-
-if [ $EXTERNALPACKAGES_FAILED -eq 1 ]; then
- echo "===================================================================================================";
- echo " ERROR: One or more of the externalpackages has failed. Skipping everything remaining steps. ";
- echo "===================================================================================================";
- exit 1;
-fi
-
-# Source here to include any newly installed externalpackages on the path.
-source $ISSM_DIR/etc/environment.sh
-
-if [ "$OS" == "win" ]; then
- echo " == WINDOWS ENVIRONMENT DETECTED =="
- source $ISSM_DIR/externalpackages/windows/windows_environment.sh
-fi
-
-#Set CXX/CC flags for JS runs after exnteralpackages to avoid conflicts during their compilation
-CXX_PREVIOUS=$CXX
-CC_PREVIOUS=$CC
-if [ $JAVASCRIPT_TEST -eq 1 ]; then
- export CXX=em++
- export CC=emcc
- source $ISSM_DIR/externalpackages/emscripten/install/emsdk_env.sh
-fi
-
-#}}}
-#ISSM compilation yes/no (ISSM_COMPILATION) {{{
-if [ "$ISSM_COMPILATION" == "yes" ]
-then
- cd $ISSM_DIR
- if [ "$ISSM_RECONFIGURE" == "yes" ]
- then
- echo "======================================================";
- echo " Cleaning up and reconfiguring "
- echo "======================================================";
- make uninstall
- make distclean
- ./scripts/automakererun.sh
- if [ $? -ne 0 ]; then
- echo "autoreconf failed!"
- exit 1
- fi
- eval "./configure $ISSM_CONFIG"
- if [ $? -ne 0 ]; then
- echo "ISSM configuration failed (see options below)"
- echo $ISSM_CONFIG
- echo "ISSM configuration failed!"
- exit 1
- fi
- fi
-
- #4: compile and install ISSM
- echo "======================================================";
- echo " Compiling ISSM "
- echo "======================================================";
- if [ $NUMCPUS_INSTALL -gt 1 ]; then
- echo "Making with " $NUMCPUS_INSTALL " cpus"
- make -j $NUMCPUS_INSTALL
- else
- make
- fi
- if [ $? -ne 0 ] && [ $NUMCPUS_INSTALL -gt 1 ]; then
- echo " "
- echo "Compilation failed, trying to compile with only one thread"
- echo " "
- make
- fi
- if [ $? -ne 0 ]; then
- echo "ISSM_COMPILATION failed!"
- exit 1
- fi
- make install
-elif [ "$ISSM_COMPILATION" == "no" ]
-then
- echo "Skipping ISSM compilation"
-else
- echo "ISSM_COMPILATION supported values are: yes and no. Exiting..." >&2 # Error message to stderr.
- exit 1
-fi
-#}}}
-
-#Restore CXX/CC to their previous values
-export CXX=$CXX_PREVIOUS
-export CC=$CC_PREVIOUS
-
-#matlab tests
-# {{{
-if [ $MATLAB_TEST -eq 1 ]; then
-#Launch all tests on different cpus
-for (( i=1;i<=$NUMCPUS_RUN;i++ ))
-do
- #Launch matlab and the nightly run script
- cat > $ISSM_DIR/nightlylog/matlab_run$i.m << EOF
- warning off %necessary to avoid a log of several Go for parallel runs
- try,
- $(if [ "$MATLAB_NROPTIONS" = "" ]
- then
- echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
- else
- echo "runme($MATLAB_NROPTIONS,'output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
- fi
- )
- catch me,
- %An error occured, get report and exit
- message=getReport(me)
- directory=strsplit(pwd,'/');
- fid=fopen([issmdir '/nightlylog/matlaberror.log'], 'at');
- fprintf(fid,'\nMatlab error occured in: %s\n\n',directory{end});
- fprintf(fid,'%s',message);
- fclose(fid);
- end
- disp('MATLABEXITEDCORRECTLY');
- exit
-EOF
- cd $ISSM_DIR/test/NightlyRun
- if [ "$OS" = "win" ]; then
- $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR_WIN/src/m/dev; devpath; addpath $ISSM_DIR_WIN/nightlylog/; matlab_run$i" -logfile $ISSM_DIR_WIN/nightlylog/matlab_log$i.log &
- else
- $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; matlab_run$i" -logfile $ISSM_DIR/nightlylog/matlab_log$i.log &
- fi
-done
-
-#wait until matlab closes
-if [ "$OS" = "win" ]; then
- sleep 5;
- echo "Waiting for matlab on windows"
- pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}')
- echo '-----------------------------'
- echo "pid: $pid"
- echo '-----------------------------'
- while [ -n "$pid" ]
- do
- pid=$(ps aux -W | grep MATLAB | awk '{printf("%s\n","MATLAB");}')
- sleep 1;
- done
- echo "DONE!"
-else
- wait
-fi
-
-#concatenate reports
-cd $ISSM_DIR/nightlylog/
-#echo 'CHECKING NIGHTLYLOG DIRECTORY'
-#echo '-----------------------------'
-#ls -la
-#echo '-----------------------------'
-
-if [ -f matlab_log.log ]; then
- rm matlab_log.log
-fi
-
-for job in `jobs -p`
-do
-echo "Waiting on: $job"
- wait $job
-done
-
-for (( i=1;i<=$NUMCPUS_RUN;i++ ))
-do
- cat matlab_log$i.log >> matlab_log.log
-done
-
-#filter out windows characters:
-cat matlab_log.log | tr -cd '\11\12\40-\176' > matlab_log.log2 && mv matlab_log.log2 matlab_log.log
-fi
-# }}}
-
-#python tests
-# {{{
-if [ $PYTHON_TEST -eq 1 ]; then
-#Launch all tests on different cpus
-export PYTHONSTARTUP=$ISSM_DIR/src/m/dev/devpath.py
-export PYTHONUNBUFFERED=1 #we don't want python to buffer otherwise issm.exe output is not captured
-for (( i=1;i<=$NUMCPUS_RUN;i++ ))
-do
- cd $ISSM_DIR/test/NightlyRun
- echo "--------------Running Python test for Rank $i---------------------"
- ./runme.py --output=nightly --rank=$i --numprocs=$NUMCPUS_RUN $PYTHON_NROPTIONS &> $ISSM_DIR/nightlylog/python_log$i.log &
- echo "--------------Running Python test for Rank $i---------------------"
-done
-
-# concatenate reports
-cd $ISSM_DIR/nightlylog/
-if [ -f python_log.log ]; then
- rm python_log.log
-fi
-
-for job in `jobs -p`
-do
-echo "Waiting on: $job"
- wait $job
-done
-
-for (( i=1;i<=$NUMCPUS_RUN;i++ ))
-do
- echo "This is the concatenation phase for rank: python_log$i.log"
- cat python_log$i.log >> python_log.log
-done
-fi
-# }}}
-
-# Examples Test
-# {{{
-# This test will allow us to check on the status of the examples.
-if [ $EXAMPLES_TEST -eq 1 ];
-then
- FILE='runme.m'
- cd $ISSM_DIR/examples
-
- for dir in ./* ;
- do
- if [ -d "${dir}" ];
- then
- # Some of the examples are incomplete (on purpose). As such, we will have to populate the
- # missing steps in order to make sure that everything is working.
- echo "Testing directory example: $(basename $dir)"
-
- # Greenland is missing step 8
- if [ -z "$SED" ];
- then
- SED='sed'
- fi
-
- cd ${dir}
-
- if [ "${dir}" == "./Greenland" ];
- then
- STEP_EIGHT="\n disp(' Step 8: Plotting exercise');\n md = loadmodel('.\/Models\/Greenland.HistoricTransient');\n figure\n surfmb=[]; for i=2:201; surfmb=[surfmb ...\n md.results.TransientSolution(i).SmbMassBalance]; end\n subplot(3,1,1); plot([1:200],mean(surfmb));\n title('Mean Surface mass balance');\n vel=[]; for i=2:201; vel=[vel md.results.TransientSolution(i).Vel]; end\n subplot(3,1,2); plot([1:200],mean(vel));\n title('Mean Velocity');\n volume=[]; for i=2:201; volume=[volume md.results.TransientSolution(i).IceVolume]; end\n subplot(3,1,3); plot([1:200],volume);\n title('Ice Volume'); xlabel('years');"
-
- $SED -i.bak 's/steps=\[1\];/steps=\[1:8\];\n\ntry\n/' $FILE
- $SED -i.bak "s/if any(steps==8)/&${STEP_EIGHT}/" $FILE
- elif [ "${dir}" == "./IceBridge" ];
- then
- $SED -i.bak 's/steps=\[1\];/steps=\[1:5\];\n\ntry\n/' $FILE
- elif [ "${dir}" == "./IceflowModels" ];
- then
- # Almost nothing to this example
- $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
- elif [ "${dir}" == "./ISMIP" ];
- then
- # Eight steps... none of which are implmented in the script...
- $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
- elif [ "${dir}" == "./Inversion" ];
- then
- $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
- elif [ "${dir}" == "./Jakobshavn" ];
- then
- $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
- elif [ "${dir}" == "./Jakobshavn" ];
- then
- $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
- elif [ "${dir}" == "./Pig" ];
- then
- # Step 6 is needed
- STEP_SIX="\n disp('Needs work!')"
- $SED -i.bak 's/steps=\[1\];/steps=\[1:7\];\n!mv DomainOutline.bkp DomainOutline.exp;\n\ntry\n/' $FILE
- $SED -i.bak "s/if any(steps==6)/&${STEP_SIX}/" $FILE
- elif [ "${dir}" == "./PigSensitivity" ];
- then
- # Step 4 is needed
- STEP_FOUR="\n disp('Needs work!')"
- $SED -i.bak 's/steps=\[1\];/steps=\[1:4\];\n\ntry\n/' $FILE
- $SED -i.bak "s/if any(steps==6)/&${STEP_FOUR}/" $FILE
- elif [ "${dir}" == "./SquareIceShelf" ];
- then
- # Almost nothing to this example
- $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
- elif [ "${dir}" == "./UncertaintyQuantification" ];
- then
- $SED -i.bak 's/steps=\[1\];/steps=\[1:7\];\n\ntry\n/' $FILE
- elif [ "${dir}" == "./Data" ];
- then
- echo "Data directory is used by examples. No modifications required."
- else
- echo "Not implemented yet!"
- $SED -i.bak '1 s/^.*$/try\n\n&/' $FILE
- fi
-
- if [ "${dir}" == "./Data" ];
- then
- ./Download.sh
- else
- LOG_FILE="matlab_log_$(basename $dir)_examples.log"
- echo "disp('SUCCESS');" >> $FILE
- echo 'catch me' >> $FILE
- echo 'message=getReport(me);' >> $FILE
- echo "fprintf('%s',message);" >> $FILE
- echo "disp('FAILURE');" >> $FILE
- echo 'end' >> $FILE
-
- $MATLAB_PATH/bin/matlab -nodisplay -nosplash -r "addpath $ISSM_DIR/src/m/dev; devpath; addpath $ISSM_DIR/nightlylog/; runme" -logfile $ISSM_DIR/nightlylog/$LOG_FILE
- echo "starting: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
- cat $ISSM_DIR/nightlylog/$LOG_FILE >> $ISSM_DIR/nightlylog/matlab_log_examples.log
- echo "finished: $(basename $dir)" >> $ISSM_DIR/nightlylog/matlab_log_examples.log
- fi
- cd ..
- fi
- done
-fi
-# }}}
-
-#process logs to be junit compatible
-#{{{
-cd $ISSM_DIR/nightlylog/
-source $ISSM_DIR/externalpackages/shell2junit/install/sh2ju.sh
-juLogClean
-
-if [ $MATLAB_TEST -eq 1 ]; then
- #number tests:
- numtests=`cat matlab_log.log | grep "\-\-\-\-\-\-\-\-starting" | wc -l`
- testlist=`cat matlab_log.log | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g' | sed 's/-//g'`
-
- #look through numtests:
- for i in `echo $testlist`
- do
- juLog -test=MATLAB-$i -name=Error -error=ERROR awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" matlab_log.log
- juLog -test=MATLAB-$i -name=Failure -error=FAILURE awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" matlab_log.log
- done
-fi
-if [ $PYTHON_TEST -eq 1 ]; then
- #number tests:
- numtests=`cat python_log.log | grep "\-\-\-\-\-\-\-\-starting" | wc -l`
- testlist=`cat python_log.log | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g' | sed 's/-//g'`
-
- #look through numtests:
- for i in `echo $testlist`
- do
- juLog -test=PYTHON-$i -name=Error -error=ERROR awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" python_log.log
- juLog -test=PYTHON-$i -name=Failure -error=FAILURE awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" python_log.log
- done
-fi
-if [ $EXAMPLES_TEST -eq 1 ];
-then
- # Inexplicably, there are backspace chars in the error output that are causing issues
- $SED -i.bak 's///g' matlab_log_examples.log
-
- numtests=`cat matlab_log_examples.log | grep "starting: " | wc -l`
- testlist=`cat matlab_log_examples.log | grep "starting: " | sed 's/starting: //'`
-
- echo "Processing: $numtests"
- for i in `echo $testlist`
- do
- juLog -test=Example-$i -name=Error -error=FAILURE awk "/starting: $i/{flag=1;next}/finished: $i/{flag=0} flag{print}" matlab_log_examples.log
- done
-fi
-#}}}
Index: sm/trunk/jenkins/linux64_ross_dakota_static
===================================================================
--- /issm/trunk/jenkins/linux64_ross_dakota_static (revision 23927)
+++ (revision )
@@ -1,67 +1,0 @@
-
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#MATLAB path
-MATLAB_PATH="/usr/local/MATLAB/R2015a"
-
-#ISSM CONFIGURATION
-ISSM_CONFIG='--prefix=$ISSM_DIR\
- --enable-standalone-executables \
- --enable-standalone-modules \
- --enable-standalone-libraries \
- --with-matlab-dir=$MATLAB_PATH \
- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
- --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
- --with-mpi-libflags="$ISSM_DIR/externalpackages/mpich/install/lib/libmpifort.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpi.a -lrt -lpthread" \
- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
- --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
- --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
- --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
- --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu -lgfortran" \
- --with-numthreads=4 \
- --with-pic'
-
-#PYTHON and MATLAB testing
-MATLAB_TEST=0
-PYTHON_TEST=0
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh
- cmake install.sh
- chaco install.sh
- mpich install-3.2-linux64-static.sh
- m1qn3 install.sh
- petsc install-3.7-linux64-static.sh
- triangle install-linux64.sh
- boost install-1.55-linux64-static.sh
- dakota install-6.2-linux64-static.sh
- shell2junit install.sh"
-
-#-----------------#
-# 4: test options #
-#-----------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=4
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=4
-
-#Nightly run options. The matlab routine runme.m will be called
-#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
-#by Matlab and runme.m
-#ex: "'id',[101 102 103]"
-#PYTHON_NROPTIONS=""
-#MATLAB_NROPTIONS=""
Index: sm/trunk/jenkins/linux64_ross_static
===================================================================
--- /issm/trunk/jenkins/linux64_ross_static (revision 23927)
+++ (revision )
@@ -1,65 +1,0 @@
-
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#MATLAB path
-MATLAB_PATH="/usr/local/MATLAB/R2015a"
-
-#ISSM CONFIGURATION
-ISSM_CONFIG='--prefix=$ISSM_DIR \
- --enable-standalone-executables \
- --enable-standalone-modules \
- --enable-standalone-libraries \
- --with-matlab-dir=$MATLAB_PATH \
- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
- --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
- --with-mpi-libflags="$ISSM_DIR/externalpackages/mpich/install/lib/libmpifort.a $ISSM_DIR/externalpackages/mpich/install/lib/libmpi.a -lrt -lpthread" \
- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
- --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
- --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu -lgfortran" \
- --with-numthreads=4 \
- --with-pic'
-
-#PYTHON and MATLAB testing
-MATLAB_TEST=0
-PYTHON_TEST=0
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh
- cmake install.sh
- mpich install-3.2-linux64-static.sh
- m1qn3 install.sh
- petsc install-3.7-linux64-static.sh
- triangle install-linux64.sh
- math77 install.sh
- gmsh install-static.sh
- shell2junit install.sh"
-
-#-----------------#
-# 4: test options #
-#-----------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=4
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=4
-
-#Nightly run options. The matlab routine runme.m will be called
-#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
-#by Matlab and runme.m
-#ex: "'id',[101 102 103]"
-## FS
-#PYTHON_NROPTIONS=""
-#MATLAB_NROPTIONS=""
Index: sm/trunk/jenkins/macosx_pine-island_dakota
===================================================================
--- /issm/trunk/jenkins/macosx_pine-island_dakota (revision 23927)
+++ (revision )
@@ -1,65 +1,0 @@
-
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#MATLAB path
-MATLAB_PATH="/Applications/MATLAB_R2015b.app"
-
-#ISSM CONFIGURATION
-ISSM_CONFIG='--prefix=$ISSM_DIR \
- --with-matlab-dir=$MATLAB_PATH \
- --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \
- --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \
- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
- --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
- --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \
- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \
- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
- --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
- --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
- --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
- --with-numthreads=4 \
- --enable-debugging \
- --enable-development'
-
-#PYTHON and MATLAB testing
-MATLAB_TEST=1
-PYTHON_TEST=1
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh
- cmake install.sh
- mpich install-3.2-macosx64.sh
- chaco install-macosx64.sh
- m1qn3 install.sh
- petsc install-3.7-macosx64.sh
- triangle install-macosx64.sh
- boost install-1.55-macosx-el_capitan.sh
- dakota install-6.2-macosx64.sh
- shell2junit install.sh"
-
-#-----------------#
-# 4: test options #
-#-----------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=4
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=4
-
-#Nightly run options. The matlab routine runme.m will be called
-#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
-#by Matlab and runme.m
-#ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420
-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 234 235 418 420 --include_name 'Dakota'"
-MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,234,235,418,420]"
Index: sm/trunk/jenkins/macosx_pine-island_dakota_static
===================================================================
--- /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 23927)
+++ (revision )
@@ -1,65 +1,0 @@
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#MATLAB path
-MATLAB_PATH="/Applications/MATLAB_R2015b.app"
-
-#ISSM CONFIGURATION
-ISSM_CONFIG='--prefix=$ISSM_DIR \
- --disable-static \
- --enable-standalone-executables \
- --enable-standalone-libraries \
- --with-matlab-dir=$MATLAB_PATH \
- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
- --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
- --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lpmpi -lmpifort -lmpicxx" \
- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
- --with-boost-dir=$ISSM_DIR/externalpackages/boost/install \
- --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \
- --with-chaco-dir=$ISSM_DIR/externalpackages/chaco/install \
- --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a /usr/local/gfortran/lib/libquadmath.a /usr/local/gfortran/lib/gcc/x86_64-apple-darwin14/5.2.0/libgcc.a" \
- --with-numthreads=4'
-
-#PYTHON and MATLAB testing
-MATLAB_TEST=0
-PYTHON_TEST=0
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh
- cmake install.sh
- chaco install-macosx64.sh
- mpich install-3.2-macosx64-static.sh
- m1qn3 install.sh
- petsc install-3.7-macosx64-static.sh
- triangle install-macosx64.sh
- boost install-1.55-macosx-el_capitan-static.sh
- dakota install-6.2-macosx64-static.sh
- shell2junit install.sh"
-
-#-----------------#
-# 4: test options #
-#-----------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=4
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=4
-
-#Nightly run options. The matlab routine runme.m will be called
-#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
-#by Matlab and runme.m
-#ex: "'id',[101 102 103]"
-#PYTHON_NROPTIONS=""
-#MATLAB_NROPTIONS=""
Index: sm/trunk/jenkins/macosx_pine-island_static
===================================================================
--- /issm/trunk/jenkins/macosx_pine-island_static (revision 23927)
+++ (revision )
@@ -1,65 +1,0 @@
-
-#-------------------------------#
-# 1: ISSM general configuration #
-#-------------------------------#
-
-#MATLAB path
-MATLAB_PATH="/Applications/MATLAB_R2015b.app"
-
-#ISSM CONFIGURATION
-ISSM_CONFIG='--prefix=$ISSM_DIR \
- --disable-static \
- --enable-standalone-executables \
- --enable-standalone-libraries \
- --with-matlab-dir=$MATLAB_PATH \
- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
- --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \
- --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lpmpi -lmpifort -lmpicxx" \
- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
- --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \
- --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
- --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"'
-
-#PYTHON and MATLAB testing
-MATLAB_TEST=0
-PYTHON_TEST=0
-
-#-----------------------------------#
-# 3: External packages installation #
-#-----------------------------------#
-
-#List of external pakages to be installed and their installation scripts
-EXTERNALPACKAGES="autotools install.sh
- cmake install.sh
- mpich install-3.2-macosx64-static.sh
- m1qn3 install.sh
- petsc install-3.7-macosx64-static.sh
- triangle install-macosx64.sh
- math77 install.sh
- gmt install-mac-precompiled.sh
- gmsh install-mac-precompiled.sh
- shell2junit install.sh"
-
-#for SLR we need gmsh to mesh, math77, and gmt (which itself needs gdal and netcdf...)
-#-----------------#
-# 4: test options #
-#-----------------#
-
-#number of cpus used in ISSM installation and compilation (one is usually
-#safer as some packages are very sensitive to parallel compilation)
-NUMCPUS_INSTALL=4
-
-#number of cpus used in the nightly runs.
-NUMCPUS_RUN=4
-
-#Nightly run options. The matlab routine runme.m will be called
-#as follows: runme($MATLAB_NROPTIONS). The options must be understandable
-#by Matlab and runme.m
-#ex: "'id',[101 102 103]"
-## bamg mesh FS
-#PYTHON_NROPTIONS=""
-#MATLAB_NROPTIONS=""
|