Merge branch 'develop' into feature/chgres_cube_fopen_read

Fixes #869.
ufs-community · Nov 14, 2023 · b529162 · b529162
2 parents e6f2e7b + 892b693
commit b529162
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Showing 9 changed files with 104 additions and 105 deletions.
diff --git a/ci/spack.yaml b/ci/spack.yaml
@@ -4,14 +4,14 @@ spack:
     all:
       compiler: [intel, gcc@10:10, apple-clang@14]
   specs:
-  - netcdf-c@4.7.4
-  - netcdf-fortran@4.5.3
+  - netcdf-c@4.9.2
+  - netcdf-fortran@4.6.0
   - [email protected]
   - [email protected]
-  - ip@3.3.3
+  - ip@4.4.0 precision=d
   - [email protected]
   - [email protected]
-  - w3emc@2.9.2
+  - w3emc@2.10.0
   - [email protected]
   - [email protected]
   - [email protected]

diff --git a/cmake/mpiexec.jet b/cmake/mpiexec.jet
@@ -7,7 +7,7 @@
 #
 
 ACCOUNT=nesdis-rdo2
-QOS=debug
+QOS=batch
 PARTITION=xjet
 
 NP=$1

diff --git a/modulefiles/build.hera.gnu.lua b/modulefiles/build.hera.gnu.lua
@@ -2,39 +2,29 @@ help([[
 Load environment to compile UFS_UTILS on Hera using Gnu
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.20.1"
-load(pathJoin("cmake", cmake_ver))
-
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2/modulefiles/stack")
-
-gnu_ver=os.getenv("gnu_ver") or "9.2"
-load(pathJoin("gnu", gnu_ver))
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-noavx512/install/modulefiles/Core")
+-- For openmpi:
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_gcc_ver=os.getenv("stack_gcc_ver") or "9.2"
+load(pathJoin("stack-gcc", gnu_ver))
 
-hpc_gnu_ver=os.getenv("hpc_gnu_ver") or "9.2"
-load(pathJoin("hpc-gnu", hpc_gnu_ver))
+stack_openmpi_ver=os.getenv("stack_openmpi_ver") or "4.1.5"
+load(pathJoin("stack-openmpi", stack_openmpi_ver))
 
-hpc_mpich_ver=os.getenv("hpc_mpich_ver") or "3.3.2"
-load(pathJoin("hpc-mpich", hpc_mpich_ver))
-
-netcdf_ver=os.getenv("netcdf_ver") or "4.9.1"
-load(pathJoin("netcdf", netcdf_ver))
-
-esmf_ver=os.getenv("esmf_ver") or "8.4.1b07"
-load(pathJoin("esmf", esmf_ver))
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
 g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 
-ip_ver=os.getenv("ip_ver") or "4.0.0"
+ip_ver=os.getenv("ip_ver") or "4.3.0"
 load(pathJoin("ip", ip_ver))
 
 nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
@@ -43,7 +33,7 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
 load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
@@ -52,13 +42,22 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-nccmp_ver=os.getenv("nccmp_ver") or "1.9.1.0"
+hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
+load(pathJoin("hdf5", hdf5_ver))
+
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
+
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
 load(pathJoin("nccmp", nccmp_ver))
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.12"
-load(pathJoin("zlib", zlib_ver))
+esmf_ver=os.getenv("esmf_ver") or "8.4.2"
+load(pathJoin("esmf", esmf_ver))
 
-png_ver=os.getenv("png_ver") or "1.6.37"
-load(pathJoin("libpng", png_ver))
+nco_ver=os.getenv("nco_ver") or "5.0.6"
+load(pathJoin("nco", nco_ver))
 
 whatis("Description: UFS_UTILS build environment")
diff --git a/modulefiles/build.hera.intel.lua b/modulefiles/build.hera.intel.lua
@@ -2,30 +2,27 @@ help([[
 Load environment to compile UFS_UTILS on Hera using Intel
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.20.1"
-load(pathJoin("cmake", cmake_ver))
-
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env-noavx512/install/modulefiles/Core")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
+load(pathJoin("stack-intel", stack_intel_ver))
 
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "2022.1.2"
-load(pathJoin("hpc-intel", hpc_intel_ver))
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
-hpc_impi_ver=os.getenv("hpc_impi_ver") or "2022.1.2"
-load(pathJoin("hpc-impi", hpc_impi_ver))
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
 g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 
-ip_ver=os.getenv("ip_ver") or "4.0.0"
+ip_ver=os.getenv("ip_ver") or "4.3.0"
 load(pathJoin("ip", ip_ver))
 
 nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
@@ -34,7 +31,7 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
 load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
@@ -43,22 +40,22 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.12"
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
 load(pathJoin("zlib", zlib_ver))
 
 png_ver=os.getenv("png_ver") or "1.6.37"
 load(pathJoin("libpng", png_ver))
 
-hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
-load(pathJoin("hdf5", hdf5_ver))
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.9.1"
-load(pathJoin("netcdf", netcdf_ver))
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 
 nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
 load(pathJoin("nccmp", nccmp_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.4.1"
+esmf_ver=os.getenv("esmf_ver") or "8.4.2"
 load(pathJoin("esmf", esmf_ver))
 
 nco_ver=os.getenv("nco_ver") or "5.0.6"

diff --git a/modulefiles/build.jet.intel.lua b/modulefiles/build.jet.intel.lua
@@ -1,64 +1,64 @@
 help([[
-Load environment to compile UFS_UTILS on Jet
+Load environment to compile UFS_UTILS on Jet using Intel
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.16.1"
-load(pathJoin("cmake", cmake_ver))
-
 hpss_ver=os.getenv("hpss_ver") or ""
 load(pathJoin("hpss", hpss_ver))
 
-prepend_path("MODULEPATH", "/lfs4/HFIP/hfv3gfs/role.epic/hpc-stack/libs/intel-2022.1.2/modulefiles/stack")
+prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.5.0/envs/unified-env/install/modulefiles/Core")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
+load(pathJoin("stack-intel", stack_intel_ver))
 
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "2022.1.2"
-load(pathJoin("hpc-intel", hpc_intel_ver))
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
-impi_ver=os.getenv("impi_ver") or "2022.1.2"
-load(pathJoin("hpc-impi", impi_ver))
-
-hdf5_ver=os.getenv("hdf5_ver") or "1.10.6"
-load(pathJoin("hdf5", hdf5_ver))
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.7.4"
-load(pathJoin("netcdf", netcdf_ver))
+bacio_ver=os.getenv("bacio_ver") or "2.4.1"
+load(pathJoin("bacio", bacio_ver))
 
-nccmp_ver=os.getenv("nccmp_ver") or "1.8.9.0"
-load(pathJoin("nccmp", nccmp_ver))
+g2_ver=os.getenv("g2_ver") or "3.4.5"
+load(pathJoin("g2", g2_ver))
 
-esmf_ver=os.getenv("esmf_ver") or "8.4.0b08"
-load(pathJoin("esmf", esmf_ver))
+ip_ver=os.getenv("ip_ver") or "4.3.0"
+load(pathJoin("ip", ip_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
-load(pathJoin("w3emc", w3emc_ver))
+nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
+load(pathJoin("nemsio", nemsio_ver))
 
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-ip_ver=os.getenv("ip_ver") or "4.0.0"
-load(pathJoin("ip", ip_ver))
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
+load(pathJoin("w3emc", w3emc_ver))
 
-bacio_ver=os.getenv("bacio_ver") or "2.4.1"
-load(pathJoin("bacio", bacio_ver))
+sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
+load(pathJoin("sfcio", sfcio_ver))
 
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
-load(pathJoin("sfcio", sfcio_ver))
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
+load(pathJoin("zlib", zlib_ver))
 
-nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
-load(pathJoin("nemsio", nemsio_ver))
+png_ver=os.getenv("png_ver") or "1.6.37"
+load(pathJoin("libpng", png_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.5"
-load(pathJoin("g2", g2_ver))
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
+
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 
-prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
-load(pathJoin("prod_util", prod_util_ver))
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
+load(pathJoin("nccmp", nccmp_ver))
+
+esmf_ver=os.getenv("esmf_ver") or "8.4.2"
+load(pathJoin("esmf", esmf_ver))
 
-nco_ver=os.getenv("nco_ver") or "4.9.3"
+nco_ver=os.getenv("nco_ver") or "5.0.6"
 load(pathJoin("nco", nco_ver))
 
 whatis("Description: UFS_UTILS build environment")
diff --git a/modulefiles/build.orion.intel.lua b/modulefiles/build.orion.intel.lua
@@ -1,28 +1,25 @@
 help([[
-Load environment to compile UFS_UTILS on Orion
+Load environment to compile UFS_UTILS on Orion using Intel
 ]])
 
-cmake_ver=os.getenv("cmake_ver") or "3.22.1"
-load(pathJoin("cmake", cmake_ver))
-
-prepend_path("MODULEPATH", "/work/noaa/epic-ps/role-epic-ps/hpc-stack/libs/intel-2022.1.2_ncdf492/modulefiles/stack")
+prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.5.0/envs/unified-env/install/modulefiles/Core")
 
-hpc_ver=os.getenv("hpc_ver") or "1.2.0"
-load(pathJoin("hpc", hpc_ver))
+stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
+load(pathJoin("stack-intel", stack_intel_ver))
 
-hpc_intel_ver=os.getenv("hpc_intel_ver") or "2022.1.2"
-load(pathJoin("hpc-intel", hpc_intel_ver))
+stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
+load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
 
-hpc_impi_ver=os.getenv("hpc_impi_ver") or "2022.1.2"
-load(pathJoin("hpc-impi", hpc_impi_ver))
+cmake_ver=os.getenv("cmake_ver") or "3.23.1"
+load(pathJoin("cmake", cmake_ver))
 
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
 g2_ver=os.getenv("g2_ver") or "3.4.5"
 load(pathJoin("g2", g2_ver))
 
-ip_ver=os.getenv("ip_ver") or "4.0.0"
+ip_ver=os.getenv("ip_ver") or "4.3.0"
 load(pathJoin("ip", ip_ver))
 
 nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
@@ -31,7 +28,7 @@ load(pathJoin("nemsio", nemsio_ver))
 sp_ver=os.getenv("sp_ver") or "2.3.3"
 load(pathJoin("sp", sp_ver))
 
-w3emc_ver=os.getenv("w3emc_ver") or "2.9.2"
+w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
 load(pathJoin("w3emc", w3emc_ver))
 
 sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
@@ -40,16 +37,19 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-zlib_ver=os.getenv("zlib_ver") or "1.2.11"
+zlib_ver=os.getenv("zlib_ver") or "1.2.13"
 load(pathJoin("zlib", zlib_ver))
 
-hdf5_ver=os.getenv("hdf5_ver") or "1.14.0"
-load(pathJoin("hdf5", hdf5_ver))
+png_ver=os.getenv("png_ver") or "1.6.37"
+load(pathJoin("libpng", png_ver))
+
+netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
+load(pathJoin("netcdf-c", netcdf_c_ver))
 
-netcdf_ver=os.getenv("netcdf_ver") or "4.9.2"
-load(pathJoin("netcdf", netcdf_ver))
+netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+load(pathJoin("netcdf-fortran", netcdf_fortran_ver))
 
-nccmp_ver=os.getenv("nccmp_ver") or "1.8.9.0"
+nccmp_ver=os.getenv("nccmp_ver") or "1.9.0.1"
 load(pathJoin("nccmp", nccmp_ver))
 
 esmf_ver=os.getenv("esmf_ver") or "8.4.2"

diff --git a/reg_tests/chgres_cube/driver.orion.sh b/reg_tests/chgres_cube/driver.orion.sh
@@ -102,7 +102,7 @@ TEST3=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 --mem=75G -t 0:15:00 -A
 
 LOG_FILE4=${LOG_FILE}04
 export OMP_NUM_THREADS=6  # needs to match cpus-per-task
-TEST4=$(sbatch --parsable --ntasks-per-node=3 --cpus-per-task=6 --nodes=2 --mem=50G -t 0:15:00 -A $PROJECT_CODE -q $QUEUE -J c96.gfs.sigio \
+TEST4=$(sbatch --parsable --ntasks-per-node=3 --cpus-per-task=6 --nodes=2 --mem=75G -t 0:20:00 -A $PROJECT_CODE -q $QUEUE -J c96.gfs.sigio \
       --open-mode=append -o $LOG_FILE4 -e $LOG_FILE4 ./c96.gfs.sigio.sh)
 
 #-----------------------------------------------------------------------------

diff --git a/reg_tests/cpld_gridgen/rt.sh b/reg_tests/cpld_gridgen/rt.sh
@@ -108,7 +108,7 @@ TESTS_FILE="$PATHRT/rt.conf"
 export TEST_NAME=
 
 # for C3072 on hera, use WLCLK=60 and MEM="--exclusive"
-WLCLK_dflt=15
+WLCLK_dflt=20
 export WLCLK=$WLCLK_dflt
 MEM_dflt="--mem=12g"
 export MEM=$MEM_dflt

diff --git a/util/gdas_init/driver.jet.sh b/util/gdas_init/driver.jet.sh
@@ -20,6 +20,9 @@ PROJECT_CODE=hfv3gfs
 QUEUE=batch
 PARTITION=xjet
 
+# Needed for NDATE utility
+module load prod_util/1.2.2
+
 source config
 
 if [ $EXTRACT_DATA == yes ]; then