From bee36e38d41cdcd4d056161a47edbba1ca912472 Mon Sep 17 00:00:00 2001 From: Cormac Garvey Date: Mon, 20 Apr 2020 10:19:45 -0500 Subject: [PATCH 1/4] Update wrf version to 4.1.5 and changed openmpi version --- apps/wrf/install_wrf_openmpi.sh | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/apps/wrf/install_wrf_openmpi.sh b/apps/wrf/install_wrf_openmpi.sh index a30784859..2e42c852d 100755 --- a/apps/wrf/install_wrf_openmpi.sh +++ b/apps/wrf/install_wrf_openmpi.sh @@ -1,12 +1,13 @@ #!/bin/bash APP_NAME=wrf -APP_VERSION=4.1.3 +APP_VERSION=4.1.5 SKU_TYPE=${SKU_TYPE:-hb} SHARED_APP=${SHARED_APP:-/apps} MODULE_DIR=${SHARED_APP}/modulefiles/${SKU_TYPE}/${APP_NAME} MODULE_NAME=${APP_VERSION}-openmpi APP_DIR=$SHARED_APP/${SKU_TYPE}/${APP_NAME}-openmpi +OPENMPI_VER=4.0.3 APPS_WRF_DIR=`pwd` function create_modulefile { @@ -24,7 +25,7 @@ EOF sudo yum install -y jasper-devel sudo yum install -y libpng-devel -spack install netcdf-fortran+mpi ^netcdf~parallel-netcdf ^hdf5+fortran %gcc@9.2.0 ^openmpi@4.0.2 +spack install netcdf-fortran+mpi ^netcdf~parallel-netcdf ^hdf5+fortran %gcc@9.2.0 ^openmpi@${OPENMPI_VER} source ${SPACK_ROOT}/share/spack/setup-env.sh mkdir -p ${APP_DIR} @@ -36,7 +37,7 @@ spack load netcdf-fortran^openmpi spack load netcdf^openmpi spack load hdf5^openmpi spack load perl -module load mpi/openmpi-4.0.2 +module load mpi/openmpi-${OPENMPI_VER} module load gcc-9.2.0 export HDF5=$(spack location -i hdf5^openmpi) From 47c26b0a9e852d2e8c88c04c2d847e897f24367a Mon Sep 17 00:00:00 2001 From: Cormac Garvey Date: Mon, 20 Apr 2020 10:24:28 -0500 Subject: [PATCH 2/4] Updated wrf to 4.1.5 and added openmpi version variable --- apps/wrf/install_wrf_omp_openmpi.sh | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/apps/wrf/install_wrf_omp_openmpi.sh b/apps/wrf/install_wrf_omp_openmpi.sh index 428f97179..356d2ae39 100755 --- a/apps/wrf/install_wrf_omp_openmpi.sh +++ b/apps/wrf/install_wrf_omp_openmpi.sh @@ -1,12 +1,13 @@ #!/bin/bash APP_NAME=wrf -APP_VERSION=4.1.3 +APP_VERSION=4.1.5 SKU_TYPE=${SKU_TYPE:-hb} SHARED_APP=${SHARED_APP:-/apps} MODULE_DIR=${SHARED_APP}/modulefiles/${SKU_TYPE}/${APP_NAME} MODULE_NAME=${APP_VERSION}-omp-openmpi APP_DIR=$SHARED_APP/${SKU_TYPE}/${APP_NAME}-omp-openmpi +OPENMPI_VER=4.0.3 APPS_WRF_DIR=`pwd` function create_modulefile { @@ -24,7 +25,7 @@ EOF sudo yum install -y jasper-devel sudo yum install -y libpng-devel -spack install netcdf-fortran+mpi ^netcdf~parallel-netcdf ^hdf5+fortran %gcc@9.2.0 ^openmpi@4.0.2 +spack install netcdf-fortran+mpi ^netcdf~parallel-netcdf ^hdf5+fortran %gcc@9.2.0 ^openmpi@${OPENMPI_VER} source ${SPACK_ROOT}/share/spack/setup-env.sh mkdir -p ${APP_DIR} @@ -36,7 +37,7 @@ spack load netcdf-fortran^openmpi spack load netcdf^openmpi spack load hdf5^openmpi spack load perl -module load mpi/openmpi-4.0.2 +module load mpi/openmpi-${OPENMPI_VER} module load gcc-9.2.0 export HDF5=$(spack location -i hdf5^openmpi) From 8c6522ddc136f334055f07594d16e3628557fc32 Mon Sep 17 00:00:00 2001 From: Cormac Garvey Date: Mon, 20 Apr 2020 13:06:19 -0500 Subject: [PATCH 3/4] Removed netcdf and added netcdf-c --- apps/wrf/install_wrf_omp_openmpi.sh | 5 ++--- apps/wrf/install_wrf_openmpi.sh | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/apps/wrf/install_wrf_omp_openmpi.sh b/apps/wrf/install_wrf_omp_openmpi.sh index 356d2ae39..6f8551550 100755 --- a/apps/wrf/install_wrf_omp_openmpi.sh +++ b/apps/wrf/install_wrf_omp_openmpi.sh @@ -25,7 +25,7 @@ EOF sudo yum install -y jasper-devel sudo yum install -y libpng-devel -spack install netcdf-fortran+mpi ^netcdf~parallel-netcdf ^hdf5+fortran %gcc@9.2.0 ^openmpi@${OPENMPI_VER} +spack install netcdf-fortran+mpi ^hdf5+fortran %gcc@9.2.0 ^openmpi@${OPENMPI_VER} source ${SPACK_ROOT}/share/spack/setup-env.sh mkdir -p ${APP_DIR} @@ -34,7 +34,6 @@ wget https://github.com/wrf-model/WRF/archive/v${APP_VERSION}.tar.gz tar xvf v${APP_VERSION}.tar.gz spack load netcdf-fortran^openmpi -spack load netcdf^openmpi spack load hdf5^openmpi spack load perl module load mpi/openmpi-${OPENMPI_VER} @@ -43,7 +42,7 @@ module load gcc-9.2.0 export HDF5=$(spack location -i hdf5^openmpi) export NETCDF=$(spack location -i netcdf-fortran^openmpi) -NETCDF_C=$(spack location -i netcdf^openmpi) +NETCDF_C=$(spack location -i netcdf-c^openmpi) ln -sf $NETCDF_C/include/* $NETCDF/include/ ln -sf $NETCDF_C/lib/* $NETCDF/lib/ ln -sf $NETCDF_C/lib/pkgconfig/* $NETCDF/lib/pkgconfig diff --git a/apps/wrf/install_wrf_openmpi.sh b/apps/wrf/install_wrf_openmpi.sh index 2e42c852d..a1bea1c27 100755 --- a/apps/wrf/install_wrf_openmpi.sh +++ b/apps/wrf/install_wrf_openmpi.sh @@ -25,7 +25,7 @@ EOF sudo yum install -y jasper-devel sudo yum install -y libpng-devel -spack install netcdf-fortran+mpi ^netcdf~parallel-netcdf ^hdf5+fortran %gcc@9.2.0 ^openmpi@${OPENMPI_VER} +spack install netcdf-fortran+mpi ^hdf5+fortran %gcc@9.2.0 ^openmpi@${OPENMPI_VER} source ${SPACK_ROOT}/share/spack/setup-env.sh mkdir -p ${APP_DIR} @@ -34,7 +34,6 @@ wget https://github.com/wrf-model/WRF/archive/v${APP_VERSION}.tar.gz tar xvf v${APP_VERSION}.tar.gz spack load netcdf-fortran^openmpi -spack load netcdf^openmpi spack load hdf5^openmpi spack load perl module load mpi/openmpi-${OPENMPI_VER} @@ -43,7 +42,7 @@ module load gcc-9.2.0 export HDF5=$(spack location -i hdf5^openmpi) export NETCDF=$(spack location -i netcdf-fortran^openmpi) -NETCDF_C=$(spack location -i netcdf^openmpi) +NETCDF_C=$(spack location -i netcdf-c^openmpi) ln -sf $NETCDF_C/include/* $NETCDF/include/ ln -sf $NETCDF_C/lib/* $NETCDF/lib/ ln -sf $NETCDF_C/lib/pkgconfig/* $NETCDF/lib/pkgconfig From 5666c8c688a5f12a93f28dd58ab1c73307d75ff5 Mon Sep 17 00:00:00 2001 From: Cormac Garvey Date: Mon, 20 Apr 2020 13:26:56 -0500 Subject: [PATCH 4/4] Updated openmpi pbs script. --- apps/wrf/run_wrf_openmpi.pbs | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/apps/wrf/run_wrf_openmpi.pbs b/apps/wrf/run_wrf_openmpi.pbs index 85c6fc364..c2a1e88ba 100755 --- a/apps/wrf/run_wrf_openmpi.pbs +++ b/apps/wrf/run_wrf_openmpi.pbs @@ -1,14 +1,15 @@ #!/bin/bash -export MODULEPATH=/apps/modulefiles/${SKU_TYPE}:$MODULEPATH +SHARED_APP=${SHARED_APP:-/apps} + +export MODULEPATH=${SHARED_APP}/modulefiles/${SKU_TYPE}:$MODULEPATH spack load netcdf-fortran^openmpi -spack load netcdf^openmpi spack load hdf5^openmpi spack load perl -module load mpi/openmpi-4.0.2 +module load mpi/openmpi-4.0.3 module load gcc-9.2.0 -module load wrf/4.1.3-openmpi +module load wrf/4.1.5-openmpi which mpicc which wrf.exe