Index: /issm/trunk-jpl/examples/Pig2/runme.m =================================================================== --- /issm/trunk-jpl/examples/Pig2/runme.m (revision 24310) +++ /issm/trunk-jpl/examples/Pig2/runme.m (revision 24311) @@ -1,5 +1,5 @@ -steps=[1:8]; - -if any(steps==1) %Mesh Generation #1 +steps=1; + +if any(steps==1) %Mesh Generation #1 %Mesh parameters @@ -158,5 +158,5 @@ if any(steps==6) %Transient Run #1 - md = loadmodel('../Pig/Models/PIG_Control_drag'); + md = loadmodel('./Models/PIG_Control_drag'); md.inversion.iscontrol=0; Index: /issm/trunk-jpl/externalpackages/adjoinablempi/install-macosx64.sh =================================================================== --- /issm/trunk-jpl/externalpackages/adjoinablempi/install-macosx64.sh (revision 24310) +++ /issm/trunk-jpl/externalpackages/adjoinablempi/install-macosx64.sh (revision 24311) @@ -10,5 +10,5 @@ #Download from ISSM server -$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'http://issm.jpl.nasa.gov/files/externalpackages/adjoinablempi' 'adjoinablempi.tar.gz' #Untar ADOL-C Index: /issm/trunk-jpl/externalpackages/boost/install-1.55-linux64-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.55-linux64-static.sh (revision 24311) +++ /issm/trunk-jpl/externalpackages/boost/install-1.55-linux64-static.sh (revision 24311) @@ -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=python + +#Compile boost +./bjam toolset=gcc link=static install + +#put bjam into install also +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk-jpl/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 24311) +++ /issm/trunk-jpl/externalpackages/boost/install-1.55-macosx-el_capitan-static.sh (revision 24311) @@ -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-jpl/externalpackages/dakota/install-6.2-linux64-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux64-static.sh (revision 24311) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-linux64-static.sh (revision 24311) @@ -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 $1 install +fi + +cd .. Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-macosx64-static.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-macosx64-static.sh (revision 24311) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-macosx64-static.sh (revision 24311) @@ -0,0 +1,80 @@ +#!/bin/bash +set -eu + +# Constants +DAK_VER="6.2" + +# Some cleanup +rm -rf build +rm -rf install +rm -rf tests +rm -rf src +mkdir build install src + +# Download from ISSM server +$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-jpl/jenkins/linux64_ross_dakota_static =================================================================== --- /issm/trunk-jpl/jenkins/linux64_ross_dakota_static (revision 24311) +++ /issm/trunk-jpl/jenkins/linux64_ross_dakota_static (revision 24311) @@ -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($MATLAB_NROPTIONS). The options must be understandable +#by Matlab and runme.m +#ex: "'id',[101 102 103]" +#PYTHON_NROPTIONS="" +#MATLAB_NROPTIONS="" Index: /issm/trunk-jpl/jenkins/linux64_ross_static =================================================================== --- /issm/trunk-jpl/jenkins/linux64_ross_static (revision 24310) +++ /issm/trunk-jpl/jenkins/linux64_ross_static (revision 24311) @@ -23,7 +23,7 @@ --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ --with-math77-dir=$ISSM_DIR/externalpackages/math77/install \ - --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \ - --with-pic \ - --with-numthreads=4' + --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu -lgfortran" \ + --with-numthreads=4 \ + --with-pic' #PYTHON and MATLAB testing @@ -52,8 +52,8 @@ #number of cpus used in ISSM installation and compilation (one is usually #safer as some packages are very sensitive to parallel compilation) -NUMCPUS_INSTALL=10 +NUMCPUS_INSTALL=4 #number of cpus used in the nightly runs. -NUMCPUS_RUN=10 +NUMCPUS_RUN=4 #Nightly run options. The matlab routine runme.m will be called @@ -62,4 +62,4 @@ #ex: "'id',[101 102 103]" ## FS -#PYTHON_NROPTIONS="--exclude_name 'Dakota'" -#MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]" +#PYTHON_NROPTIONS="" +#MATLAB_NROPTIONS="" Index: /issm/trunk-jpl/m4/issm_options.m4 =================================================================== --- /issm/trunk-jpl/m4/issm_options.m4 (revision 24310) +++ /issm/trunk-jpl/m4/issm_options.m4 (revision 24311) @@ -396,5 +396,4 @@ ;; *linux*) - TRIANGLELIB=$TRIANGLE_ROOT/triangle.a if test "x$HAVE_JAVASCRIPT" = "xyes"; then dnl go to the bit code, not the library. @@ -483,4 +482,5 @@ DAKOTAFLAGS="" + dnl TODO: Should we also be checking if HAVE_BOOST before adding boost libs? case "${host_os}" in *cygwin*) @@ -507,5 +507,9 @@ else if test x$DAKOTA_VERSION = x6.1 || test x$DAKOTA_VERSION = x6.2; then 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" - 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" + if test "x$enable_standalone_executables" = "xyes"; then + DAKOTALIB="-L$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 $BOOST_ROOT/lib/libboost_system.a" + else + DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_ROOT/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" + fi AC_DEFINE([DISABLE_DAKOTA_CONFIG_H],[1],[disabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI]) @@ -526,6 +530,10 @@ AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI]) else if test x$DAKOTA_VERSION = x6.1 || test x$DAKOTA_VERSION = x6.2; then - DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" - DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_ROOT/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" + DAKOTAFLAGS="-DDISABLE_DAKOTA_CONFIG_H -DBOOST_MULTI_INDEX_DISABLE_SERIALIZATION -DDAKOTA_PLUGIN -DBOOST_DISABLE_ASSERTS -DDAKOTA_HAVE_BOOST_FS -DHAVE_UNISTD_H -DHAVE_SYSTEM -DHAVE_WORKING_FORK -DHAVE_WORKING_VFORK -DHAVE_SYS_WAIT_H -DHAVE_USLEEP -DDAKOTA_F90 -DDAKOTA_HAVE_MPI -DHAVE_PECOS -DHAVE_SURFPACK -DDAKOTA_UTILIB -DHAVE_ADAPTIVE_SAMPLING -DHAVE_CONMIN -DDAKOTA_DDACE -DHAVE_FSUDACE -DDAKOTA_HOPS -DHAVE_NCSU -DHAVE_NL2SOL -DHAVE_OPTPP -DDAKOTA_OPTPP -DHAVE_PSUADE -DHAVE_AMPL" + if test "x$enable_standalone_executables" = "xyes"; then + 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 $BOOST_ROOT/lib/libboost_system.a" + else + DAKOTALIB="-L$DAKOTA_ROOT/lib -L$BOOST_ROOT/lib -ldakota_src -ldream -lfsudace -lddace -lnomad -lpecos_src -llhs -llhs_mods -loptpp -lsurfpack -lconmin -ldakota_src_fortran -llhs_mod -lncsuopt -lsurfpack_fortran -lteuchos -lamplsolver -lcport -ldfftpack -lfsudace -lhopspack -lnidr -lpecos -lpsuade -lsparsegrid -lboost_serialization -lboost_signals -lboost_regex -lboost_filesystem -lboost_system" + fi AC_DEFINE([DISABLE_DAKOTA_CONFIG_H],[1],[disabling DAKOTA_CONFIG_H]) AC_DEFINE([DAKOTA_HAVE_MPI],[1],[enabling parallel MPI]) Index: /issm/trunk-jpl/packagers/macosx-dakota/package.sh =================================================================== --- /issm/trunk-jpl/packagers/macosx-dakota/package.sh (revision 24310) +++ /issm/trunk-jpl/packagers/macosx-dakota/package.sh (revision 24311) @@ -1,15 +1,33 @@ #!/bin/bash -echo "modify generic" +MATLAB_PATH="/Applications/MATLAB_R2015b.app" +PACKAGE="ISSM" # Name of directory to copy distributable files to +TARBALL_NAME="issm-mac-dakota" +TARBALL=$TARBALL_NAME.tar.gz + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd $ISSM_DIR +rm -rf $PACKAGE +mkdir $PACKAGE + +# Add/modify required binaries cd $ISSM_DIR/bin + +echo "Modifying generic" cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m -echo "move mpiexec to bin" -cp ../externalpackages/mpich/install/bin/mpiexec . -cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . -#Check that test101 runs +echo "Moving mpiexec to bin" +if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then + cp ../externalpackages/mpich/install/bin/mpiexec . + cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "mpich not found" +fi + +# Check that test101 runs cd $ISSM_DIR/test/NightlyRun rm matlab.log -/Applications/MATLAB_R2015b.app/bin/matlab -nodisplay -nojvm -nosplash -nodesktop -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log +$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 if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then @@ -17,21 +35,13 @@ exit 1; else - echo "test101 passed" + echo "test101 PASSED" fi -#Package using the Package Maker from OSX, driven by command line. -tarball_name='issm-mac-dakota-static_build.tar.gz' - -echo "Cleanup first" +echo "Creating tarball: ${TARBALL_NAME}" cd $ISSM_DIR -rm $tarball_name - -echo "Creating tarball: ${tarball_name}" -cd $ISSM_DIR -rm -rf trunk -mkdir trunk -cp -rf bin lib test examples trunk/ -tar -czf $tarball_name trunk -ls -lah $tarball_name +rm -f $TARBALL +cp -rf bin lib test examples scripts $PACKAGE/ +tar -czf $TARBALL $PACKAGE +ls -lah $TARBALL echo "Shipping binaries to website" @@ -51,5 +61,5 @@ ssh-add ~/.ssh/macosx-bins_richese-to-ross -scp $tarball_name ross.ics.uci.edu:/var/www/html/$tarball_name +scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL if [ $? -ne 0 ]; then Index: /issm/trunk-jpl/packagers/macosx/package.sh =================================================================== --- /issm/trunk-jpl/packagers/macosx/package.sh (revision 24310) +++ /issm/trunk-jpl/packagers/macosx/package.sh (revision 24311) @@ -1,5 +1,7 @@ #!/bin/bash -TARBALL_NAME='issm-mac-static_build' +MATLAB_PATH="/Applications/MATLAB_R2015b.app" +PACKAGE="ISSM" # Name of directory to copy distributable files to +TARBALL_NAME="issm-mac" TARBALL=$TARBALL_NAME.tar.gz @@ -7,6 +9,6 @@ echo "Cleaning up existing assets" cd $ISSM_DIR -rm -rf trunk -mkdir trunk +rm -rf $PACKAGE +mkdir $PACKAGE # Add/modify required binaries @@ -31,11 +33,11 @@ fi -# Copy gmt to trunk +# Copy gmt to package # NOTE: The following assumes the precompiled version of gmt echo "Moving gmt to externalpackages" if [ -f $ISSM_DIR/externalpackages/gmt/install/bin/gmt ]; then - mkdir $ISSM_DIR/trunk/externalpackages - mkdir $ISSM_DIR/trunk/externalpackages/gmt - cp -a $ISSM_DIR/externalpackages/gmt/install/. $ISSM_DIR/trunk/externalpackages/gmt + mkdir $ISSM_DIR/$PACKAGE/externalpackages + mkdir $ISSM_DIR/$PACKAGE/externalpackages/gmt + cp -a $ISSM_DIR/externalpackages/gmt/install $ISSM_DIR/$PACKAGE/externalpackages/gmt/install else echo "gmt not found" @@ -45,5 +47,5 @@ cd $ISSM_DIR/test/NightlyRun rm matlab.log -/Applications/MATLAB_R2015b.app/bin/matlab -nodisplay -nojvm -nosplash -nodesktop -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log +$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 if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then @@ -57,15 +59,15 @@ cd $ISSM_DIR rm -f $TARBALL -cp -rf bin lib test examples scripts trunk/ +cp -rf bin lib test examples scripts $PACKAGE/ # Create link to gmt from bin # NOTE: It is important that we are in the destination dir when sym linking so that the path is relative -if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then - cd $ISSM_DIR/trunk/bin - ln -s ../externalpackages/gmt/bin/gmt ./gmt +if [ -f $ISSM_DIR/$PACKAGE/externalpackages/gmt/install/bin/gmt ]; then + cd $ISSM_DIR/$PACKAGE/bin + ln -s ../externalpackages/gmt/install/bin/gmt ./gmt fi cd $ISSM_DIR -tar -czf $TARBALL trunk +tar -czf $TARBALL $PACKAGE ls -lah $TARBALL Index: /issm/trunk-jpl/packagers/ubuntu-dakota/package.sh =================================================================== --- /issm/trunk-jpl/packagers/ubuntu-dakota/package.sh (revision 24311) +++ /issm/trunk-jpl/packagers/ubuntu-dakota/package.sh (revision 24311) @@ -0,0 +1,76 @@ +#!/bin/bash + +MATLAB_PATH="/usr/local/MATLAB/R2015a" +PACKAGE="ISSM" # Name of directory to copy distributable files to +TARBALL_NAME="issm-ubuntu-dakota" +TARBALL=$TARBALL_NAME.tar.gz + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd $ISSM_DIR +rm -rf $PACKAGE +mkdir $PACKAGE + +# Add/modify required binaries +cd $ISSM_DIR/bin + +echo "Modify generic" +cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m + +echo "Moving mpiexec to bin" +if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then + cp ../externalpackages/mpich/install/bin/mpiexec . + cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "mpich not found" +fi + +echo "Moving gmsh to bin" +if [ -f ../externalpackages/gmsh/install/gmsh ]; then + cp ../externalpackages/gmsh/install/gmsh . +else + echo "gmsh not found" +fi + +# Check that test101 runs +cd $ISSM_DIR/test/NightlyRun +rm matlab.log +$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 + +if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then + echo "test101 FAILED" + exit 1; +else + echo "test101 PASSED" +fi + +echo "Creating tarball: ${TARBALL_NAME}" +cd $ISSM_DIR +rm -f $TARBALL +cp -rf bin lib test examples scripts $PACKAGE/ +tar -czf $TARBALL $PACKAGE +ls -lah $TARBALL + +echo "Shipping binaries to website" + +# We're using public key authentication method to upload the tarball The +# following lines check to see if the SSH Agent is running. If not, then it is +# started and relevant information is forwarded to a script. +pgrep "ssh-agent" > /dev/null +if [ $? -ne 0 ]; then + echo "SSH Agent is not running. Starting it..." + ssh-agent > ~/.ssh/agent.sh +else + echo "SSH Agent is running..." +fi + +source ~/.ssh/agent.sh +ssh-add ~/.ssh/ubuntu-bins_jenkins-to-ross + +scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL + +if [ $? -ne 0 ]; then + echo "The upload failed." + echo "Perhaps the SSH Agent was started by some other means." + echo "Try killing the agent and running again." +fi Index: /issm/trunk-jpl/packagers/ubuntu/package.sh =================================================================== --- /issm/trunk-jpl/packagers/ubuntu/package.sh (revision 24310) +++ /issm/trunk-jpl/packagers/ubuntu/package.sh (revision 24311) @@ -1,11 +1,30 @@ #!/bin/bash -echo "modify generic" +MATLAB_PATH="/usr/local/MATLAB/R2015a" +PACKAGE="ISSM" # Name of directory to copy distributable files to +TARBALL_NAME="issm-ubuntu" +TARBALL=$TARBALL_NAME.tar.gz + +# Clean up from previous packaging +echo "Cleaning up existing assets" +cd $ISSM_DIR +rm -rf $PACKAGE +mkdir $PACKAGE + +# Add/modify required binaries cd $ISSM_DIR/bin + +echo "Modify generic" cat generic_static.m | sed -e "s/generic_static/generic/g" > generic.m -echo "move mpiexec to bin" -cp ../externalpackages/mpich/install/bin/mpiexec . -cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . -echo "move gmsh to bin" + +echo "Moving mpiexec to bin" +if [ -f ../externalpackages/mpich/install/bin/mpiexec ]; then + cp ../externalpackages/mpich/install/bin/mpiexec . + cp ../externalpackages/mpich/install/bin/hydra_pmi_proxy . +else + echo "mpich not found" +fi + +echo "Moving gmsh to bin" if [ -f ../externalpackages/gmsh/install/gmsh ]; then cp ../externalpackages/gmsh/install/gmsh . @@ -14,8 +33,8 @@ fi -#Check that test101 runs +# Check that test101 runs cd $ISSM_DIR/test/NightlyRun rm matlab.log -/usr/local/MATLAB/R2015a/bin/matlab -nojvm -nosplash -r "try, addpath $ISSM_DIR/bin $ISSM_DIR/lib; runme('id',101);exit; catch me,fprintf('%s',getReport(me)); exit; end" -logfile matlab.log +$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 if [[ $(cat matlab.log | grep -c SUCCESS) -lt 10 ]]; then @@ -23,20 +42,13 @@ exit 1; else - echo "test101 passed" + echo "test101 PASSED" fi -tarball_name='issm-ubuntu-static_build.tar.gz' - -echo "Cleanup first" +echo "Creating tarball: ${TARBALL_NAME}" cd $ISSM_DIR -rm $tarball_name - -echo "Creating tarball: ${tarball_name}" -cd $ISSM_DIR -rm -rf trunk -mkdir trunk -cp -rf bin lib test examples scripts trunk/ -tar -czf $tarball_name trunk -ls -lah $tarball_name +rm -f $TARBALL +cp -rf bin lib test examples scripts $PACKAGE/ +tar -czf $TARBALL $PACKAGE +ls -lah $TARBALL echo "Shipping binaries to website" @@ -56,5 +68,5 @@ ssh-add ~/.ssh/ubuntu-bins_jenkins-to-ross -scp $tarball_name ross.ics.uci.edu:/var/www/html/$tarball_name +scp $TARBALL ross.ics.uci.edu:/var/www/html/$TARBALL if [ $? -ne 0 ]; then Index: /issm/trunk-jpl/packagers/win10/package64.sh =================================================================== --- /issm/trunk-jpl/packagers/win10/package64.sh (revision 24310) +++ /issm/trunk-jpl/packagers/win10/package64.sh (revision 24311) @@ -1,7 +1,8 @@ #!/bin/bash +MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a" +PACKAGE="ISSM" # Name of directory to copy distributable files to TARBALL_NAME='ISSM-Win10-64' TARBALL=$TARBALL_NAME.tar.gz -MATLAB_PATH="/cygdrive/c/Programs/MATLAB/R2015a" # Source Windows environment @@ -11,6 +12,6 @@ echo "Cleaning up existing assets" cd $ISSM_DIR -rm -rf trunk -mkdir trunk +rm -rf $PACKAGE +mkdir $PACKAGE # Add/modify required binaries @@ -26,16 +27,16 @@ echo "Copying gmsh to bin" if [ -f ../externalpackages/gmsh/install/gmsh.exe ]; then - cp ../externalpackages/gmsh/install/gmsh.exe . + cp ../externalpackages/gmsh/install/gmsh.exe ./gmsh.exe else echo "gmsh not found" fi -# Copy gmt to trunk +# Copy gmt to package # NOTE: The following assumes the precompiled version of gmt echo "Moving gmt to externalpackages" if [ -f $ISSM_DIR/externalpackages/gmt/install/bin/gmt ]; then - mkdir $ISSM_DIR/trunk/externalpackages - mkdir $ISSM_DIR/trunk/externalpackages/gmt - cp -a $ISSM_DIR/externalpackages/gmt/install/. $ISSM_DIR/trunk/externalpackages/gmt + mkdir $ISSM_DIR/$PACKAGE/externalpackages + mkdir $ISSM_DIR/$PACKAGE/externalpackages/gmt + cp -a $ISSM_DIR/externalpackages/gmt/install $ISSM_DIR/$PACKAGE/externalpackages/gmt/install else echo "gmt not found" @@ -67,15 +68,15 @@ cd $ISSM_DIR rm -f $TARBALL -cp -rf bin lib test examples scripts trunk/ +cp -rf bin lib test examples scripts $PACKAGE/ # Create link to gmt from bin # NOTE: It is important that we are in the destination dir when sym linking so that the path is relative -if [ -f $ISSM_DIR/trunk/externalpackages/gmt/bin/gmt ]; then - cd $ISSM_DIR/trunk/bin - ln -s ../externalpackages/gmt/bin/gmt.exe ./gmt +if [ -f $ISSM_DIR/$PACKAGE/externalpackages/gmt/bin/gmt ]; then + cd $ISSM_DIR/$PACKAGE/bin + ln -s ../externalpackages/gmt/bin/gmt.exe ./gmt.exe fi cd $ISSM_DIR -tar -czf $TARBALL trunk +tar -czf $TARBALL $PACKAGE ls -lah $TARBALL