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updates for community users to adopt the NOAA hpc-stack stucture #157

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May 19, 2021
Merged

updates for community users to adopt the NOAA hpc-stack stucture #157

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4 changes: 2 additions & 2 deletions CMakeLists.txt
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Expand Up @@ -175,8 +175,8 @@ project(GSI)
find_package( LAPACK )
endif()
# build the WRF I/O libraries
if(DEFINED ENV{GSIWRF_LIB})
set(wrflib "$ENV{GSIWRF_LIB}" CACHE INTERNAL "WRFIO library" )
if(DEFINED ENV{GSIWRFIO_LIB})
set(wrflib "$ENV{GSIWRFIO_LIB}" CACHE INTERNAL "WRFIO library" )
elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/libsrc/wrflib)
add_subdirectory(libsrc/wrflib)
else()
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1 change: 1 addition & 0 deletions cmake/Modules/platforms/Generic.cmake
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Expand Up @@ -20,5 +20,6 @@ macro (setGeneric)
set(BUILD_SP "OFF" CACHE INTERNAL "Build the SP library" )
set(BUILD_CRTM "OFF" CACHE INTERNAL "Build the CRTM library" )
set(BUILD_W3EMC "OFF" CACHE INTERNAL "Build the EMC library" )
set(BUILD_W3NCO "OFF" CACHE INTERNAL "Build the EMC library" )
set(BUILD_NCO "OFF" CACHE INTERNAL "Build the NCO library" )
endmacro()
3 changes: 1 addition & 2 deletions cmake/Modules/setHOST.cmake
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Expand Up @@ -33,8 +33,7 @@ macro( setHOST )
string(REGEX MATCH "discover" HOST-Discover ${HOSTNAME} )
string(REGEX MATCH "cheyenne" HOST-Cheyenne ${HOSTNAME} )
message("done figuring out host--${HOSTNAME}")
if ( BUILD_CORELIBS )
MESSAGE(STATUS "BUILD_CORELIBS manually-specified as ON")
if ( COMGSI )
set( host "GENERIC" )
set( HOST-Generic "TRUE" )
setGeneric()
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144 changes: 91 additions & 53 deletions ush/build.comgsi
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Expand Up @@ -5,9 +5,9 @@
# Cheyenne: source /glade/p/ral/jntp/gge/modulefiles/modulefile.cheyenne.GSI_UPP_WRF
#
# build commands:
# cmake -DENKF_MODE=WRF -DBUILD_CORELIBS=ON -DBUILD_GSDCLOUD_ARW=ON path_to_GSI
# cmake -DENKF_MODE=WRF -DBUILD_CORELIBS=ON -DBUILD_GSDCLOUD_ARW=ON -DBUILD_UTIL_COM=ON -DBUILD_ENKF_PREPROCESS_ARW=ON path_to_GSI"
# (for global: cmake -D-DENKF_MODE=GFS -DBUILD_CORELIBS=ON path_to_GSI)
# cmake -DCOMGSI=ON -DENKF_MODE=WRF -DBUILD_GSDCLOUD_ARW=ON path_to_GSI
# cmake -DCOMGSI=ON -DENKF_MODE=WRF -DBUILD_GSDCLOUD_ARW=ON -DBUILD_UTIL_COM=ON -DBUILD_ENKF_PREPROCESS_ARW=ON path_to_GSI"
# (for global: cmake -DCOMGSI=ON -DENKF_MODE=GFS path_to_GSI)
# make -j8
#

Expand All @@ -16,80 +16,118 @@ dir_root=$(pwd)
################# Hera ####################
if [[ "`grep -i "hera" /etc/hosts | head -n1`" != "" ]] ; then
source /etc/profile.d/modules.sh
modulefile="/home/rtrr/PARM_EXEC/modulefiles/modulefile.hera.GSI_UPP_WRF"
NCEPLIBS="/scratch1/BMC/comgsi/precompiled/NCEPLIBS/b_intel18.0.5.274_impi2018.0.4/install"
GSILIBS="/scratch1/BMC/comgsi/precompiled/GSILIBS/b_intel18.0.5.274_impi2018.0.4"
module purge
module load cmake/3.20.1
module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
module load hpc/1.1.0
module load hpc-intel/18.0.5.274
module load hpc-impi/2018.0.4
module load bufr/11.4.0
module load ip/3.3.3
module load nemsio/2.5.2
module load sfcio/1.4.1
module load sigio/2.3.2
module load sp/2.3.3
module load w3nco/2.4.1
module load w3emc/2.7.3
module load bacio/2.4.1
module load crtm/2.3.0
module load netcdf/4.7.0
module use /scratch1/BMC/comgsi/hpc-stacks/modulefiles/gsiwrfio
module load gsiwrfio/1.0.0

################# Jet ####################
elif [[ -d /jetmon ]] ; then
source /etc/profile.d/modules.sh
modulefile="/home/rtrr/PARM_EXEC/modulefiles/modulefile.jet.GSI_UPP_WRF"
NCEPLIBS="/lfs4/BMC/wrfruc/gge/precompiled/NCEPLIBS/b_intel18.0.5.274_impi2018.4.274/install"
GSILIBS="/lfs4/BMC/wrfruc/gge/precompiled/GSILIBS/b_intel18.0.5.274_impi2018.4.274"
module purge
module load cmake/3.16.1
module load intel/18.0.5.274
module load impi/2018.4.274

module use /lfs4/HFIP/hfv3gfs/nwprod/hpc-stack/libs/modulefiles/stack
module load hpc/1.1.0
module load hpc-intel/18.0.5.274
module load hpc-impi/2018.4.274

module load netcdf/4.7.0 #don't load netcdf/4.7.4 from hpc-stack, GSI does not compile with it.
module load bufr/11.4.0
module load bacio/2.4.1
module load crtm/2.3.0
module load ip/3.3.3
module load nemsio/2.5.2
module load sp/2.3.3
module load w3emc/2.7.3
module load w3nco/2.4.1
module load sfcio/1.4.1
module load sigio/2.3.2

module use /mnt/lfs4/BMC/wrfruc/gge/hpc-stacks/modulefiles/gsiwrfio
module load gsiwrfio/1.0.0

################# Cheyenne ####################
elif [[ -d /glade ]] ; then
source /etc/profile.d/modules.sh
modulefile="/glade/p/ral/jntp/gge/modulefiles/modulefile.cheyenne.GSI_UPP_WRF"
NCEPLIBS="/glade/p/ral/jntp/gge/precompiled/NCEPLIBS/b_intel18.0.5_impi2018.4.274/install"
GSILIBS="/glade/p/ral/jntp/gge/precompiled/GSILIBS/b_intel18.0.5_impi2018.4.274"
#modulefile="/glade/p/ral/jntp/gge/precompiled/NCEPLIBS/modulefile.cheyenne.GSI_UPP_WRF.gnu"
#NCEPLIBS="/glade/p/ral/jntp/gge/precompiled/NCEPLIBS/b_gnu8.3.0_openmpi3.1.4/install"
#GSILIBS="/glade/p/ral/jntp/gge/precompiled/GSILIBS/b_gnu8.3.0_openmpi3.1.4/"
module purge
module use /glade/p/ral/jntp/gge/hpc-stacks/modulefiles/stack
module load intel/18.0.5 ncarenv ncarcompilers
module load impi/2018.4.274
module load mkl/2018.0.5
module load netcdf/4.7.4
module load hpc/1.1.0
module load hpc-intel/18.0.5
module load hpc-impi/2018.4.274
module load bufr/11.4.0
module load ip/3.3.3
module load nemsio/2.5.2
module load sfcio/1.4.1
module load sigio/2.3.2
module load sp/2.3.3
module load w3nco/2.4.1
module load w3emc/2.7.3
module load bacio/2.4.1
module load crtm/2.3.0
module load gsiwrfio/1.0.0
module load cmake/3.18.2

################# Orion ####################
elif [[ -d /work/noaa ]] ; then ### orion
modulefile="/home/gge/modulefiles/modulefile.orion.GSI_UPP_WRF"
NCEPLIBS="/work/noaa/wrfruc/gge/precompiled/NCEPLIBS/b_intel2018.4_impi2018.4/install"
GSILIBS="/work/noaa/wrfruc/gge/precompiled/GSILIBS/b_intel2018.4_impi2018.4"
module purge
module use /work/noaa/wrfruc/gge/hpc-stacks/modulefiles/stack
module load intel/2018.4
module load impi/2018.4
module load netcdf/4.7.2
module load hpc/1.1.0
module load hpc-intel/2018.4
module load hpc-impi/2018.4
module load bufr/11.4.0
module load ip/3.3.3
module load nemsio/2.5.2
module load sfcio/1.4.1
module load sigio/2.3.2
module load sp/2.3.3
module load w3nco/2.4.1
module load w3emc/2.7.3
module load bacio/2.4.1
module load crtm/2.3.0
module load gsiwrfio/1.0.0
module load cmake #any version as long as it is later than v3.16

################# Generic ####################
else
echo -e "\nunknown machine"
echo "Please modify build.comgsi at this location"
echo "to load required modules and setup NCEPLIBS and GSILIBS"
echo "to load required modules"
##follow the above examples and delete the following "exit 9" to go forward
exit 9
source /etc/profile.d/modules.sh
modulefile="/my/modulefile.me.GSI_UPP_WRF"
NCEPLIBS="/my/NCEPLIBS/b_intel18.0.5_impi2018.4.274/install"
GSILIBS="/my/GSILIBS/b_intel18.0.5_impi2018.4.274/"
#load modules from the NOAA hpc-stack
fi

if [ ! -f $modulefile ]; then
echo "modulefiles $modulefile does not exist"
exit 10
fi
source $modulefile

## if NETCDF4 is set to 0 or 1, unset it
if [[ "$NETCDF4" == "1" ]] || [[ "$NETCDF4" == "0" ]]; then
unset NETCDF4
fi

export BACIO_LIB4=${NCEPLIBS}/lib/libbacio_4.a
#export BUFR_LIBd=${NCEPLIBS}/lib/libbufr_d.a
export BUFR_LIBd=${GSILIBS}/lib/libbufr_v.a
export GSIWRF_LIB=${GSILIBS}/lib/libWRFLIB.a
export CRTM_LIB=${NCEPLIBS}/lib/libcrtm.a
export CRTM_INC=${NCEPLIBS}/include
export NEMSIO_LIB=${NCEPLIBS}/lib/libnemsio.a
export NEMSIO_INC=${NCEPLIBS}/include
export SFCIO_LIB4=${NCEPLIBS}/lib/libsfcio_4.a
export SFCIO_INC4=${NCEPLIBS}/include_4
export SIGIO_LIB4=${NCEPLIBS}/lib/libsigio_4.a
export SIGIO_INC4=${NCEPLIBS}/include_4
export SP_LIBd=${NCEPLIBS}/lib/libsp_d.a
export SP_LIB4=${NCEPLIBS}/lib/libsp_4.a
export W3EMC_LIBd=${NCEPLIBS}/lib/libw3emc_d.a
export W3EMC_LIB4=${NCEPLIBS}/lib/libw3emc_4.a
export W3EMC_INCd=${NCEPLIBS}/include_d
export W3EMC_INC4=${NCEPLIBS}/include_4
export W3NCO_LIBd=${NCEPLIBS}/lib/libw3nco_d.a
export W3NCO_LIB4=${NCEPLIBS}/lib/libw3nco_4.a
export IP_LIBd=${NCEPLIBS}/lib/libip_d.a
export IP_LIB4=${NCEPLIBS}/lib/libip_4.a

set -x
rm -rf $dir_root/build
mkdir -p $dir_root/build
Expand All @@ -107,12 +145,12 @@ git log -1 | head -n1 >> output.log
echo -e "\ngit status:" >> output.log
git status >> output.log
echo -e "\nCompiling commands:" >> output.log
echo " cmake -DENKF_MODE=WRF -DBUILD_CORELIBS=ON -DBUILD_GSDCLOUD_ARW=ON -DBUILD_ENKF_PREPROCESS_ARW=ON -DBUILD_UTIL_COM=ON -Wno-dev .." >> output.log
echo " cmake -DCOMGSI=ON -DENKF_MODE=WRF -DBUILD_GSDCLOUD_ARW=ON -DBUILD_ENKF_PREPROCESS_ARW=ON -DBUILD_UTIL_COM=ON .." >> output.log
echo " make -j8" >> output.log
cat output.log


cmake -DENKF_MODE=WRF -DBUILD_CORELIBS=ON -DBUILD_GSDCLOUD_ARW=ON -DBUILD_ENKF_PREPROCESS_ARW=ON -DBUILD_UTIL_COM=ON -Wno-dev .. 2>&1 | tee output.cmake
cmake -DCOMGSI=ON -DENKF_MODE=WRF -DBUILD_GSDCLOUD_ARW=ON -DBUILD_ENKF_PREPROCESS_ARW=ON -DBUILD_UTIL_COM=ON .. 2>&1 | tee output.cmake
make -j 8 2>&1 | tee output.compile

###aftermath
Expand Down
11 changes: 0 additions & 11 deletions util/bufr_tools/CMakeLists.txt
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Expand Up @@ -6,56 +6,45 @@ cmake_minimum_required(VERSION 2.6)
set_source_files_properties( ${LOCAL_SRC} PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )

add_executable(bufr_append_sample.x bufr_append_sample.f90 )
add_dependencies( bufr_append_sample.x ${BUFR_LIBRARY} )
set_target_properties( bufr_append_sample.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( bufr_append_sample.x ${BUFR_LIBRARY} )

add_executable(bufr_decode_sample.x bufr_decode_sample.f90 )
add_dependencies( bufr_decode_sample.x ${BUFR_LIBRARY} )
set_target_properties( bufr_decode_sample.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( bufr_decode_sample.x ${BUFR_LIBRARY} )

add_executable(bufr_encode_sample.x bufr_encode_sample.f90 )
add_dependencies( bufr_encode_sample.x ${BUFR_LIBRARY} )
set_target_properties( bufr_encode_sample.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( bufr_encode_sample.x ${BUFR_LIBRARY} )

add_executable(bufr_decode_radiance.x bufr_decode_radiance.f90 )
add_dependencies( bufr_decode_radiance.x ${BUFR_LIBRARY} )
set_target_properties( bufr_decode_radiance.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( bufr_decode_radiance.x ${BUFR_LIBRARY} )

add_executable(prepbufr_decode_all.x prepbufr_decode_all.f90 )
add_dependencies( prepbufr_decode_all.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_decode_all.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_decode_all.x ${BUFR_LIBRARY} )

add_executable(prepbufr_encode_surface.x prepbufr_encode_surface.f90 )
add_dependencies( prepbufr_encode_surface.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_encode_surface.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_encode_surface.x ${BUFR_LIBRARY} )

add_executable(prepbufr_encode_upperair.x prepbufr_encode_upperair.f90 )
add_dependencies( prepbufr_encode_upperair.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_encode_upperair.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_encode_upperair.x ${BUFR_LIBRARY} )

add_executable(prepbufr_inventory.x prepbufr_inventory.f90 )
add_dependencies( prepbufr_inventory.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_inventory.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_inventory.x ${BUFR_LIBRARY} )

add_executable(prepbufr_append_retrieve.x prepbufr_append_retrieve.f90 )
add_dependencies( prepbufr_append_retrieve.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_append_retrieve.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_append_retrieve.x ${BUFR_LIBRARY} )

add_executable(prepbufr_append_surface.x prepbufr_append_surface.f90 )
add_dependencies( prepbufr_append_surface.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_append_surface.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_append_surface.x ${BUFR_LIBRARY} )

add_executable(prepbufr_append_upperair.x prepbufr_append_upperair.f90 )
add_dependencies( prepbufr_append_upperair.x ${BUFR_LIBRARY} )
set_target_properties( prepbufr_append_upperair.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( prepbufr_append_upperair.x ${BUFR_LIBRARY} )
1 change: 0 additions & 1 deletion util/ndate/CMakeLists.txt
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Expand Up @@ -4,6 +4,5 @@ cmake_minimum_required(VERSION 2.6)
set_source_files_properties( ${NDATE_SRC} PROPERTIES COMPILE_FLAGS ${NDATE_Fortran_FLAGS} )

add_executable( ndate.x ${NDATE_SRC} )
add_dependencies( ndate.x ${W3NCO_4_LIBRARY} )
target_link_libraries( ndate.x ${W3NCO_4_LIBRARY} )

2 changes: 1 addition & 1 deletion util/radar_process/reflectivity/CMakeLists.txt
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Expand Up @@ -4,6 +4,6 @@ cmake_minimum_required(VERSION 2.6)
include_directories( ${NETCDF_INCLUDE_DIRS} ${MPI_Fortran_INCLUDE_PATH} )

add_executable(process_NSSL_mosaic.x ${LOCAL_SRC} )
add_dependencies(process_NSSL_mosaic.x ${GSILIB} ${GSISHAREDLIB} ${BUFR_LIBRARY} )
add_dependencies(process_NSSL_mosaic.x ${GSILIB} ${GSISHAREDLIB} )
set_target_properties( process_NSSL_mosaic.x PROPERTIES COMPILE_FLAGS ${UTIL_COM_Fortran_FLAGS} )
target_link_libraries( process_NSSL_mosaic.x ${GSISHAREDLIB} ${BUFR_LIBRARY} ${NETCDF_Fortran_LIBRARIES} ${NETCDF_C_LIBRARIES} ${MPI_Fortran_LIBRARIES} )