Index: /issm/trunk/externalpackages/boost/install-1.55-linux64-static.sh
===================================================================
--- /issm/trunk/externalpackages/boost/install-1.55-linux64-static.sh (revision 23929)
+++ /issm/trunk/externalpackages/boost/install-1.55-linux64-static.sh (revision 23929)
@@ -0,0 +1,39 @@
+#!/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="$ISSM_DIR/externalpackages/python/install"
+
+#Compile boost
+./bjam link=static runtime-link=static install
+
+#put bjam into install also
+mkdir ../install/bin
+cp bjam ../install/bin
Index: /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh
===================================================================
--- /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 23929)
+++ /issm/trunk/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 23929)
@@ -0,0 +1,47 @@
+#!/bin/bash
+set -eu
+
+# NOTE: Stop after boostrap phase, and run
+#
+# bjam --debug-configuration
+#
+# to figure out which paths boost is using to include python. Make sure everyone
+# of these paths is covered by python. If not, just make symlinks in
+# externalpackages/python to what boost is expecting. There is NO WAY to get the
+# boost library to include python support without doing that.
+
+#Some cleanup
+rm -rf install boost_1_55_0 src
+mkdir install src
+
+#Download from ISSM server
+$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="$ISSM_DIR/externalpackages/boost/install" \
+ --with-python=python
+
+#Compile boost
+# Need gcc with iconv installed in a location that has been added to your path
+# export CC=/usr/local/gfortan/bin/gcc
+# export CXX=/usr/local/gfortran/bin/g++
+./bjam toolset=darwin link=static runtime-link=static install
+
+#put bjam into install also:
+mkdir ../install/bin
+cp bjam ../install/bin
Index: /issm/trunk/externalpackages/dakota/install-6.2-linux64-static.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-linux64-static.sh (revision 23929)
+++ /issm/trunk/externalpackages/dakota/install-6.2-linux64-static.sh (revision 23929)
@@ -0,0 +1,81 @@
+#!/bin/bash
+set -eu
+
+# Constants
+DAK_VER="6.2"
+
+#Some cleanup
+rm -rf Dakota
+rm -rf src
+rm -rf build
+rm -rf install
+mkdir src build install
+
+#Download from ISSM server
+$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 $1 install
+fi
+
+cd ..
Index: /issm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh
===================================================================
--- /issm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh (revision 23929)
+++ /issm/trunk/externalpackages/dakota/install-6.2-macosx64-static.sh (revision 23929)
@@ -0,0 +1,80 @@
+#!/bin/bash
+set -eu
+
+# Constants
+DAK_VER="6.2"
+
+# Some cleanup
+rm -rf build
+rm -rf install
+rm -rf tests
+rm -rf src
+mkdir build install src
+
+# Download from ISSM server
+$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: /issm/trunk/jenkins/jenkins.sh
===================================================================
--- /issm/trunk/jenkins/jenkins.sh (revision 23929)
+++ /issm/trunk/jenkins/jenkins.sh (revision 23929)
@@ -0,0 +1,529 @@
+#!/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: $i/{flag=0} flag{print}" matlab_log_examples.log
+ done
+fi
+#}}}
Index: /issm/trunk/jenkins/linux64_ross_dakota_static
===================================================================
--- /issm/trunk/jenkins/linux64_ross_dakota_static (revision 23929)
+++ /issm/trunk/jenkins/linux64_ross_dakota_static (revision 23929)
@@ -0,0 +1,67 @@
+
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
+
+#MATLAB path
+MATLAB_PATH="/usr/local/MATLAB/R2015a"
+
+#ISSM CONFIGURATION
+ISSM_CONFIG='--prefix=$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($MATLAB_NROPTIONS). The options must be understandable
+#by Matlab and runme.m
+#ex: "'id',[101 102 103]"
+#PYTHON_NROPTIONS=""
+#MATLAB_NROPTIONS=""
Index: /issm/trunk/jenkins/linux64_ross_static
===================================================================
--- /issm/trunk/jenkins/linux64_ross_static (revision 23929)
+++ /issm/trunk/jenkins/linux64_ross_static (revision 23929)
@@ -0,0 +1,65 @@
+
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
+
+#MATLAB path
+MATLAB_PATH="/usr/local/MATLAB/R2015a"
+
+#ISSM CONFIGURATION
+ISSM_CONFIG='--prefix=$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($MATLAB_NROPTIONS). The options must be understandable
+#by Matlab and runme.m
+#ex: "'id',[101 102 103]"
+## FS
+#PYTHON_NROPTIONS=""
+#MATLAB_NROPTIONS=""
Index: /issm/trunk/jenkins/macosx_pine-island_dakota
===================================================================
--- /issm/trunk/jenkins/macosx_pine-island_dakota (revision 23929)
+++ /issm/trunk/jenkins/macosx_pine-island_dakota (revision 23929)
@@ -0,0 +1,65 @@
+
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
+
+#MATLAB path
+MATLAB_PATH="/Applications/MATLAB_R2015b.app"
+
+#ISSM CONFIGURATION
+ISSM_CONFIG='--prefix=$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($MATLAB_NROPTIONS). The options must be understandable
+#by Matlab and runme.m
+#ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420
+PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 234 235 418 420 --include_name 'Dakota'"
+MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,234,235,418,420]"
Index: /issm/trunk/jenkins/macosx_pine-island_dakota_static
===================================================================
--- /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 23929)
+++ /issm/trunk/jenkins/macosx_pine-island_dakota_static (revision 23929)
@@ -0,0 +1,65 @@
+#-------------------------------#
+# 1: ISSM general configuration #
+#-------------------------------#
+
+#MATLAB path
+MATLAB_PATH="/Applications/MATLAB_R2015b.app"
+
+#ISSM CONFIGURATION
+ISSM_CONFIG='--prefix=$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: /issm/trunk/jenkins/macosx_pine-island_static
===================================================================
--- /issm/trunk/jenkins/macosx_pine-island_static (revision 23929)
+++ /issm/trunk/jenkins/macosx_pine-island_static (revision 23929)
@@ -0,0 +1,65 @@
+
+#-------------------------------#
+# 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=""
|