Index: /issm/trunk-jpl/externalpackages/autotools/install-discover.sh =================================================================== --- /issm/trunk-jpl/externalpackages/autotools/install-discover.sh (revision 20319) +++ /issm/trunk-jpl/externalpackages/autotools/install-discover.sh (revision 20319) @@ -0,0 +1,57 @@ +#!/bin/bash +set -eu + +rm -rf install +mkdir install + +export PATH="$ISSM_DIR/externalpackages/autotools/install/bin:$PATH" + +#install m4 +echo " === INSTALLING M4 ==" +rm -rf src +wget http://ftp.gnu.org/gnu/m4/m4-latest.tar.gz +tar zxvf m4* +rm m4-latest.tar.gz +mv m4-* src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd ../ + +#install autoconf +echo " === INSTALLING AUTOCONF ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/autoconf-2.69.tar.gz' 'autoconf-2.69.tar.gz' +tar -zxvf autoconf-2.69.tar.gz +mv autoconf-2.69 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install automake +echo " === INSTALLING AUTOMAKE ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/automake-1.14.tar.gz' 'automake-1.14.tar.gz' +tar -zxvf automake-1.14.tar.gz +mv automake-1.14 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. + +#install libtool +echo " === INSTALLING LIBTOOL ==" +rm -rf src +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/libtool-2.4.2.tar.gz' 'libtool-2.4.2.tar.gz' +tar -zxvf libtool-2.4.2.tar.gz +rm libtool-2.4.2.tar.gz +mv libtool-2.4.2 src +cd src +./configure --prefix="$ISSM_DIR/externalpackages/autotools/install" +make +make install +cd .. Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 20319) +++ /issm/trunk-jpl/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.discover.patch (revision 20319) @@ -0,0 +1,35 @@ +54,55c54,55 +< #set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} " +< # CACHE STRING "CXX Flags for my platform" ) +--- +> set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMPICH_IGNORE_CXX_SEEK" +> CACHE STRING "CXX Flags for my platform" ) +67a68,75 +> set( DAKOTA_HAVE_MPI ON +> CACHE BOOL "Always build with MPI enabled" FORCE) +> set( MPI_INCLUDE_PATH +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/include" +> CACHE FILEPATH "Use installed MPI headers" FORCE) +> set( MPI_LIBRARY +> "$ENV{ISSM_DIR}/externalpackages/mpich/install/lib/libmpich.so" +> CACHE FILEPATH "Use installed MPI library" FORCE) +73,77c73,77 +< #set(BOOST_ROOT +< # "path/to/custom/Boost/install/directory" +< # CACHE PATH "Use non-standard Boost install" FORCE) +< #set( Boost_NO_SYSTEM_PATHS TRUE +< # CACHE BOOL "Supress search paths other than BOOST_ROOT" FORCE) +--- +> set(BOOST_ROOT +> "$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 +> "$ENV{ISSM_DIR}/externalpackages/dakota/install" +> CACHE PATH "Path to Dakota installation" ) Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 20319) +++ /issm/trunk-jpl/externalpackages/dakota/configs/6.2/CMakeLists.txt.discover.patch (revision 20319) @@ -0,0 +1,6 @@ +156c153,155 +< # TODO: Can't this be integrated into the following logic? +--- +> # TODO: Can't this be integrated into the following logic? +> set(BLAS_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") +> set(LAPACK_LIBS "-L/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/usr/lib64/ -lpthread -lm") Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-intel15-discover.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-intel15-discover.sh (revision 20319) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-intel15-discover.sh (revision 20319) @@ -0,0 +1,56 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf Dakota +rm -rf src +rm -rf build +rm -rf install +mkdir src build install + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/dakota-6.2-public.src.tar.gz' 'dakota-6.2-public-src.tar.gz' + +#Untar +tar -zxvf dakota-6.2-public-src.tar.gz + +#Move Dakota to src directory +mv dakota-6.2.0.src/* src +rm -rf dakota-6.2.0.src + +#Set up Dakota cmake variables and config +export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src +export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build +export MPIHOME=$ISSM_DIR/externalpackages/mpich/install +cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake +patch $DAK_SRC/cmake/BuildDakotaCustom.cmake configs/6.2/BuildDakotaCustom.cmake.discover.patch +patch $DAK_SRC/cmake/DakotaDev.cmake configs/6.2/DakotaDev.cmake.patch +patch $DAK_SRC/CMakeLists.txt configs/6.2/CMakeLists.txt.discover.patch + +#Apply patches +patch src/src/NonDSampling.cpp configs/6.2/NonDSampling.cpp.patch +patch src/src/NonDLocalReliability.cpp configs/6.2/NonDLocalReliability.cpp.patch +patch src/packages/pecos/src/pecos_global_defs.hpp configs/6.2/pecos_global_defs.hpp.patch + +#Configure dakota +cd $DAK_BUILD + +cmake -D CMAKE_C_COMPILER=mpicc \ + -D CMAKE_CXX_COMPILER=mpicxx \ + -D CMAKE_Fortran_COMPILER=/usr/bin/gfortran \ + -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 $1 install +fi +cd .. Index: /issm/trunk-jpl/externalpackages/petsc/install-3.6-discover.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.6-discover.sh (revision 20319) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.6-discover.sh (revision 20319) @@ -0,0 +1,62 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.6.0 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/petsc-lite-3.6.0.tar.gz' 'petsc-3.6.0.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.6.0.tar.gz +mv petsc-3.6.0/* src/ +rm -rf petsc-3.6.0 + +#--with-cc=icc --with-cxx=icpc --with-fc=ifort --with-f77=ifort \ + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-blas-lapack-dir="/usr/local/intel/Composer/composer_xe_2015.0.090/mkl/" \ + --with-mpi-lib="/usr/local/intel/mpi/4.0.3.008/lib64/libmpi.so" \ + --with-mpi-include="/usr/local/intel/mpi/4.0.3.008/intel64/include/" \ + --known-mpi-shared-libraries=1 \ + --with-debugging=0 \ + --with-valgrind=0 \ + --with-x=0 \ + --with-ssl=0 \ + --with-batch=1 \ + --with-shared-libraries=1 \ + --download-metis=1 \ + --download-parmetis=1 \ + --download-mumps=1 \ + --download-scalapack=1 + +#prepare script to reconfigure petsc +cat > script.queue << EOF +#!/bin/bash +#SBATCH -J petscinstall # Job Name +#SBATCH -N 1 +#SBATCH -n 1 +#SBATCH -A s1010 +#SBATCH -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours +#SBATCH --qos=debug +#SBATCH -o petscinstall.outlog +#SBATCH -e petscinstall.errlog + +. /usr/share/modules/init/bash +module load comp/intel-15.0.0.090 +module load mpi/impi-4.0.3.008 + +export PATH="$PATH:." +export MPI_GROUP_MAX=64 +mpirun -np 1 ./conftest-arch-linux2-c-opt +EOF + +#print instructions +echo "== Now: cd src/ " +echo "== sbatch script.queue " +echo "== Then run reconfigure script generated by PETSc and follow instructions"