Index: /issm/trunk-jpl/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch =================================================================== --- /issm/trunk-jpl/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 19581) +++ /issm/trunk-jpl/externalpackages/boost/configs/1.55/adl.hpp.lonestar.patch (revision 19581) @@ -0,0 +1,7 @@ +33,34c33,35 +< || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +< ) +--- +> ) +> // || BOOST_WORKAROUND(BOOST_INTEL_CXX_VERSION, BOOST_TESTED_AT(810)) \ +> // ) Index: /issm/trunk-jpl/externalpackages/boost/install-1.55-lonestar.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.55-lonestar.sh (revision 19581) +++ /issm/trunk-jpl/externalpackages/boost/install-1.55-lonestar.sh (revision 19581) @@ -0,0 +1,38 @@ +#!/bin/bash +set -eu + +#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 +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/boost_1_55_0.tar.gz' 'boost_1_55_0.tar.gz' + +#Untar +tar -zxvf boost_1_55_0.tar.gz + +#Move boost into install directory +mv boost_1_55_0/* src +rm -rf boost_1_55_0 + +patch src/boost/mpl/aux_/config/adl.hpp ./configs/1.55/adl.hpp.lonestar.patch + +#Configure and compile +cd src +./bootstrap.sh \ + --prefix="$ISSM_DIR/externalpackages/boost/install" \ + --with-python=python3.2 \ + --with-python-root="$ISSM_DIR/externalpackages/python/install" + +#Compile boost +./bjam install + +#put bjam into install also: +mkdir ../install/bin +cp bjam ../install/bin Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.lonestar.patch =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.lonestar.patch (revision 19581) +++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/BuildDakotaCustom.cmake.lonestar.patch (revision 19581) @@ -0,0 +1,26 @@ +64,65c64,65 +< #set( DAKOTA_HAVE MPI ON +< # CACHE BOOL "Build with MPI enabled" FORCE) +--- +> set( DAKOTA_HAVE MPI OFF +> CACHE BOOL "Build with MPI disabled" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$ENV{ISSM_DIR}/externalpackages/boost/install" +> CACHE PATH "Use non-standard Boost install" FORCE) +> set( Boost_NO_SYSTEM_PATHS TRUE +> CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +91,93c91,93 +< #set( CMAKE_INSTALL_PREFIX +< # "/path/to/Dakota/installation" +< # CACHE PATH "Path to Dakota installation" ) +--- +> set( CMAKE_INSTALL_PREFIX +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 19581) +++ /issm/trunk-jpl/externalpackages/dakota/configs/5.3.1/CMakeLists.txt.lonestar.patch (revision 19581) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/opt/apps/intel/11.1/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/opt/apps/intel/11.1/mkl/lib/em64t/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-lonestar.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 19581) +++ /issm/trunk-jpl/externalpackages/dakota/install-5.3.1-lonestar.sh (revision 19581) @@ -0,0 +1,51 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-5.3.1-public-src.tar.gz' 'dakota-5.3.1-public-src.tar.gz' + +#Untar +tar -zxvf dakota-5.3.1-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-5.3.1.src/* src +rm -rf dakota-5.3.1.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/5.3.1/BuildDakotaCustom.cmake.lonestar.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/5.3.1/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/5.3.1/CMakeLists.txt.lonestar.patch + +#Apply patches +patch src/src/ParallelLibrary.cpp configs/5.3.1/ParallelLibrary.cpp.patch +patch src/src/ParallelLibrary.hpp configs/5.3.1/ParallelLibrary.hpp.patch +patch src/src/NonDSampling.cpp configs/5.3.1/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/5.3.1/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/5.3.1/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD +cmake -C $DAK_SRC/cmake/BuildDakotaCustom.cmake -C $DAK_SRC/cmake/DakotaDev.cmake $DAK_SRC +cd .. + +#Compile and install dakota +cd $DAK_BUILD +if [ $# -eq 0 ]; +then + make + make install +else + make -j $1 + make -j $1 install +fi +cd .. Index: /issm/trunk-jpl/externalpackages/petsc/install-3.6-lonestar.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.6-lonestar.sh (revision 19580) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.6-lonestar.sh (revision 19581) @@ -37,15 +37,13 @@ cat > script.queue << EOF #!/bin/bash -#$ -V #Inherit the submission environment -#$ -cwd # Start job in submission directory +#$ -V #Inherit the submission environment +#$ -cwd # Start job in submission directory #$ -N petscinstall # Job Name -#$ -j y # Combine stderr and stdout -#$ -o $JOB_NAME.o$JOB_ID # Name of the output file (eg. myMPI.oJobID) -#$ -pe 12way 12 # Requests 12 tasks/node, 12 cores total -#$ -q normal # Queue name normal -#$ -l h_rt=00:01:00 # Run time (hh:mm:ss) - 1.5 hours -set -x # Echo commands, use set echo with csh +#$ -j y # Combine stderr and stdout +#$ -pe 12way 12 # Requests 12 tasks/node, 12 cores total +#$ -q normal # Queue name normal +#$ -l h_rt=00:01:00 # Run time (hh:mm:ss) - 1.5 hours +set -x # Echo commands, use set echo with csh -module load cmake/2.8.7 module load mkl/10.3