Index: /issm/trunk-jpl/externalpackages/boost/install-1.55-stallo.sh =================================================================== --- /issm/trunk-jpl/externalpackages/boost/install-1.55-stallo.sh (revision 23789) +++ /issm/trunk-jpl/externalpackages/boost/install-1.55-stallo.sh (revision 23790) @@ -25,5 +25,5 @@ #Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost -export PATH="/usr/bin":$PATH +#export PATH="/usr/bin":$PATH export CXXFLAGS='-std=c++98' export CC=mpicc Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.stallo.patch =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.stallo.patch (revision 23789) +++ /issm/trunk-jpl/externalpackages/dakota/configs/6.2/BuildDakotaCustom.cmake.stallo.patch (revision 23790) @@ -13,11 +13,11 @@ > CACHE BOOL "Always build with MPI enabled" FORCE) > set( MPI_INCLUDE_PATH -> "/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/include64/" +> "/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/include64/" > CACHE FILEPATH "Use installed MPI headers" FORCE) > set( MPI_LIBRARY -> "/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/lib64/libmpich.so" +> "/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/lib64/libmpi.so" > CACHE FILEPATH "Use installed MPI library" FORCE) > set( MPI_EXTRA_LIBRARY -> "/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/lib64/libmpich.so" +> "/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/lib64/libmpi.so" > CACHE FILEPATH "Use MPI extra libraries" FORCE) 73,77c84,88 Index: /issm/trunk-jpl/externalpackages/dakota/configs/6.2/CMakeLists.txt.stallo.patch =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/configs/6.2/CMakeLists.txt.stallo.patch (revision 23789) +++ /issm/trunk-jpl/externalpackages/dakota/configs/6.2/CMakeLists.txt.stallo.patch (revision 23790) @@ -6,4 +6,4 @@ > 237a240,241 -> set(BLAS_LIBS "-Wl,--no-as-needed -L/global/hds/software/cpu/eb3/imkl/2017.1.132-iimpi-2017a/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/lib64/libc.so.6 -L/lib64/ -lpthread -lm -ldl") -> set(LAPACK_LIBS "-Wl,--no-as-needed -L/global/hds/software/cpu/eb3/imkl/2017.1.132-iimpi-2017a/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/lib64/libc.so.6 -L/lib64/ -lpthread -lm -ldl") +> set(BLAS_LIBS "-Wl,--no-as-needed -L/global/hds/software/cpu/eb3/imkl/11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/lib64/libc.so.6 -L/lib64/ -lpthread -lm -ldl") +> set(LAPACK_LIBS "-Wl,--no-as-needed -L/global/hds/software/cpu/eb3/imkl/11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -L/lib64/libc.so.6 -L/lib64/ -lpthread -lm -ldl") Index: /issm/trunk-jpl/externalpackages/dakota/install-6.2-stallo.sh =================================================================== --- /issm/trunk-jpl/externalpackages/dakota/install-6.2-stallo.sh (revision 23789) +++ /issm/trunk-jpl/externalpackages/dakota/install-6.2-stallo.sh (revision 23790) @@ -20,8 +20,8 @@ #Set up Dakota cmake variables and config -export PATH="/usr/bin":$PATH +#export PATH="/usr/bin":$PATH export DAK_SRC=$ISSM_DIR/externalpackages/dakota/src export DAK_BUILD=$ISSM_DIR/externalpackages/dakota/build -export MPIHOME=/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/ +export MPIHOME=/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/ cp $DAK_SRC/cmake/BuildDakotaTemplate.cmake $DAK_SRC/cmake/BuildDakotaCustom.cmake @@ -41,6 +41,6 @@ cd $DAK_BUILD -cmake -D CMAKE_C_COMPILER=/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/intel64/bin/mpicc \ - -D CMAKE_CXX_COMPILER=/global/hds/software/cpu/eb3/impi/2017.1.132-iccifort-2017.1.132-GCC-6.3.0-2.27/intel64/bin/mpicxx \ +cmake -D CMAKE_C_COMPILER=/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/bin64/mpicc \ + -D CMAKE_CXX_COMPILER=/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/bin64/mpicxx \ -D CMAKE_Fortran_COMPILER=gfortran \ -DHAVE_ACRO=off \ Index: /issm/trunk-jpl/externalpackages/petsc/install-3.6-stallo.sh =================================================================== --- /issm/trunk-jpl/externalpackages/petsc/install-3.6-stallo.sh (revision 23790) +++ /issm/trunk-jpl/externalpackages/petsc/install-3.6-stallo.sh (revision 23790) @@ -0,0 +1,59 @@ +#!/bin/bash +set -eu + +#Some cleanup +rm -rf install petsc-3.6.3 src +mkdir install src + +#Download from ISSM server +$ISSM_DIR/scripts/DownloadExternalPackage.sh 'https://issm.ess.uci.edu/files/externalpackages/petsc-lite-3.6.3.tar.gz' 'petsc-3.6.3.tar.gz' + +#Untar and move petsc to install directory +tar -zxvf petsc-3.6.3.tar.gz +mv petsc-3.6.3/* src/ +rm -rf petsc-3.6.3 + +#configure +cd src +./config/configure.py \ + --prefix="$ISSM_DIR/externalpackages/petsc/install" \ + --PETSC_DIR="$ISSM_DIR/externalpackages/petsc/src" \ + --with-blas-lapack-dir="/global/hds/software/cpu/eb3/imkl/11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25/mkl/" \ + --with-mpi-lib="/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/lib64/libmpi.so" \ + --with-mpi-include="/global/hds/software/cpu/eb3/impi/5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25/include64/" \ + --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 -t 00:01:00 # Run time (hh:mm:ss) - 1.5 hours +#SBATCH --qos=devel +#SBATCH -o petscinstall.outlog +#SBATCH -e petscinstall.errlog + +module purge +module load CMake/3.3.2-GNU-4.9.3-2.25 +module load Automake/1.15-GNU-4.9.3-2.25 +module load libtool/2.4.6-GNU-4.9.3-2.25 +module load intel/2015b + +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"