Upgrade the GSI to Spack-Stack version 1.6.0 (#684)

ci/spack.yaml

@@ -7,19 +7,19 @@ spack:
         - gcc@10:10
   specs:
   - netcdf-c@4.9.2
-  - netcdf-fortran@4.6.0
+  - netcdf-fortran@4.6.1
   - bufr@11.7.0
   - bacio@2.4.1
-  - w3emc@2.9.2
-  - sp@2.3.3
-  - ip@3.3.3
+  - w3emc@2.10.0
+  - sp@2.5.0
+  - ip@4.3.0
   - sigio@2.3.2
   - sfcio@1.4.1
   - nemsio@2.5.4
   - wrf-io@1.2.0
   - ncio@1.1.2
-  - crtm@2.4.0
-  - gsi-ncdiag@1.1.1
+  - crtm@2.4.0.1
+  - gsi-ncdiag@1.1.2
   view: true
   concretizer:
     unify: true

modulefiles/gsi_common.lua

@@ -3,19 +3,19 @@ Load common modules to build GSI on all machines
 ]])
 
 local netcdf_c_ver=os.getenv("netcdf_c_ver") or "4.9.2"
-local netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.0"
+local netcdf_fortran_ver=os.getenv("netcdf_fortran_ver") or "4.6.1"
 
 local bufr_ver=os.getenv("bufr_ver") or "11.7.0"
 local bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 local w3emc_ver=os.getenv("w3emc_ver") or "2.10.0"
-local sp_ver=os.getenv("sp_ver") or "2.3.3"
+local sp_ver=os.getenv("sp_ver") or "2.5.0"
 local ip_ver=os.getenv("ip_ver") or "4.3.0"
 local sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 local sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 local nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
 local wrf_io_ver=os.getenv("wrf_io_ver") or "1.2.0"
 local ncio_ver=os.getenv("ncio_ver") or "1.1.2"
-local crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+local crtm_ver=os.getenv("crtm_ver") or "2.4.0.1"
 local ncdiag_ver=os.getenv("ncdiag_ver") or "1.1.2"
 
 load(pathJoin("netcdf-c", netcdf_c_ver))

modulefiles/gsi_hera.gnu.lua

@@ -1,16 +1,16 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/gsi-addon/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/Core")
 --Needed for openmpi build
 prepend_path("MODULEPATH", "/scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles")
 
-local python_ver=os.getenv("python_ver") or "3.10.8"
+local python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_gnu_ver=os.getenv("stack_gnu_ver") or "9.2.0"
 local stack_openmpi_ver=os.getenv("stack_openmpi_ver") or "4.1.5"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
-local openblas_ver=os.getenv("openblas_ver") or "0.3.19"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
+local openblas_ver=os.getenv("openblas_ver") or "0.3.24"
 
 load(pathJoin("stack-gcc", stack_gnu_ver))
 load(pathJoin("stack-openmpi", stack_openmpi_ver))

modulefiles/gsi_hera.intel.lua

@@ -1,13 +1,13 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/gsi-addon/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/Core")
 
-local python_ver=os.getenv("python_ver") or "3.10.8"
+local python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
 
 load(pathJoin("stack-intel", stack_intel_ver))
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))

modulefiles/gsi_hercules.intel.lua

@@ -1,13 +1,13 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.1/envs/gsi-addon/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core")
 
-local stack_python_ver=os.getenv("stack_python_ver") or "3.10.8"
+local stack_python_ver=os.getenv("stack_python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.9.0"
 local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.9.0"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
 
 load(pathJoin("stack-intel", stack_intel_ver))
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))

modulefiles/gsi_jet.intel.lua

@@ -1,13 +1,13 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.5.1/envs/gsi-addon/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/Core")
 
-local python_ver=os.getenv("python_ver") or "3.10.8"
+local python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
 
 load(pathJoin("stack-intel", stack_intel_ver))
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))

modulefiles/gsi_orion.intel.lua

@@ -1,13 +1,13 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.5.1/envs/gsi-addon/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core")
 
-local stack_python_ver=os.getenv("python_ver") or "3.10.8"
+local stack_python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2022.0.2"
 local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.1"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
 
 load(pathJoin("stack-intel", stack_intel_ver))
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))

modulefiles/gsi_s4.intel.lua

@@ -1,13 +1,13 @@
 help([[
 ]])
 
-prepend_path("MODULEPATH", "/data/prod/jedi/spack-stack/spack-stack-1.5.1/envs/gsi-addon/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/data/prod/jedi/spack-stack/spack-stack-1.6.0/envs/gsi-addon-env/install/modulefiles/Core")
 
-local python_ver=os.getenv("python_ver") or "3.10.8"
+local python_ver=os.getenv("python_ver") or "3.11.6"
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 local stack_impi_ver=os.getenv("stack_impi_ver") or "2021.5.0"
 local cmake_ver=os.getenv("cmake_ver") or "3.23.1"
-local prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
+local prod_util_ver=os.getenv("prod_util_ver") or "2.1.1"
 
 load(pathJoin("stack-intel", stack_intel_ver))
 load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))

modulefiles/gsi_wcoss2.intel.lua

@@ -20,7 +20,7 @@ local sfcio_ver=os.getenv("sfcio_ver") or "1.4.1"
 local nemsio_ver=os.getenv("nemsio_ver") or "2.5.4"
 local wrf_io_ver=os.getenv("wrf_io_ver") or "1.2.0"
 local ncio_ver=os.getenv("ncio_ver") or "1.1.2"
-local crtm_ver=os.getenv("crtm_ver") or "2.4.0"
+local crtm_ver=os.getenv("crtm_ver") or "2.4.0.1"
 local ncdiag_ver=os.getenv("ncdiag_ver") or "1.1.1"
 
 load(pathJoin("PrgEnv-intel", PrgEnv_intel_ver))

regression/regression_param.sh

@@ -36,11 +36,6 @@ case $machine in
     ;;
 	Discover)
 	   sub_cmd="sub_discover"
-    ;;
-	Cheyenne)
-           sub_cmd="sub_cheyenne"
-           memnode=128
-           numcore=36
     ;;
     *) # EXIT out for unresolved machine
         echo "unknown $machine"
@@ -73,9 +68,6 @@ case $regtest in
         elif [[ "$machine" = "Discover" ]]; then
            topts[1]="0:30:00" ; popts[1]="48/2"  ; ropts[1]="/1"
            topts[2]="0:30:00" ; popts[2]="60/3"  ; ropts[2]="/2"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:10:00" ; popts[1]="12/8/" ; ropts[1]="/1"
-           topts[2]="0:10:00" ; popts[2]="12/10/" ; ropts[2]="/2"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:10:00" ; popts[1]="18/8/" ; ropts[1]="/1"
            topts[2]="0:10:00" ; popts[2]="18/10/" ; ropts[2]="/2"
@@ -106,9 +98,6 @@ case $regtest in
         elif [[ "$machine" = "Jet" ]]; then
            topts[1]="0:15:00" ; popts[1]="20/1/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="20/2/"  ; ropts[2]="/1"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/" ; ropts[2]="/2"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:15:00" ; popts[1]="18/1/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="18/2/"  ; ropts[2]="/1"
@@ -139,9 +128,6 @@ case $regtest in
         elif [[ "$machine" = "Jet" ]]; then
            topts[1]="0:15:00" ; popts[1]="20/1/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="20/2/"  ; ropts[2]="/1"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/" ; ropts[2]="/2"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:15:00" ; popts[1]="18/1/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="18/2/"  ; ropts[2]="/1"
@@ -171,9 +157,6 @@ case $regtest in
         elif [[ "$machine" = "Jet" ]]; then
            topts[1]="0:15:00" ; popts[1]="20/1/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="20/2/"  ; ropts[2]="/1"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:15:00" ; popts[1]="20/1/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="20/2/" ; ropts[2]="/2"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:15:00" ; popts[1]="18/1/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="18/2/"  ; ropts[2]="/1"
@@ -204,9 +187,6 @@ case $regtest in
         elif [[ "$machine" = "Jet" ]]; then
            topts[1]="0:15:00" ; popts[1]="4/4/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="6/6/"  ; ropts[2]="/1"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:15:00" ; popts[1]="4/4/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="6/6/" ; ropts[2]="/2"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:15:00" ; popts[1]="4/4/"  ; ropts[1]="/1"
            topts[2]="0:15:00" ; popts[2]="6/6/"  ; ropts[2]="/1"
@@ -237,9 +217,6 @@ case $regtest in
         elif [[ "$machine" = "Jet" ]]; then
            topts[1]="0:30:00" ; popts[1]="6/12/"  ; ropts[1]="/1"
            topts[2]="0:30:00" ; popts[2]="8/12/"  ; ropts[2]="/1"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:30:00" ; popts[1]="6/12/"  ; ropts[1]="/1"
-           topts[2]="0:30:00" ; popts[2]="8/12/"  ; ropts[2]="/1"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:30:00" ; popts[1]="8/6/"  ; ropts[1]="/1"
            topts[2]="0:30:00" ; popts[2]="8/8/"  ; ropts[2]="/1"
@@ -270,9 +247,6 @@ case $regtest in
         elif [[ "$machine" = "Jet" ]]; then
            topts[1]="0:10:00" ; popts[1]="12/3/" ; ropts[1]="/1"
            topts[2]="0:10:00" ; popts[2]="12/5/" ; ropts[2]="/2"
-        elif [[ "$machine" = "Cheyenne" ]]; then
-           topts[1]="0:15:00" ; popts[1]="12/3/" ; ropts[1]="/1"
-           topts[2]="0:15:00" ; popts[2]="12/5/" ; ropts[2]="/2"
         elif [[ "$machine" = "Gaea" ]]; then
            topts[1]="0:10:00" ; popts[1]="12/3/" ; ropts[1]="/1"
            topts[2]="0:10:00" ; popts[2]="12/5/" ; ropts[2]="/2"
@@ -342,12 +316,6 @@ elif [[ "$machine" = "Gaea" ]]; then
    export MPI_BUFS_PER_HOST=256
    export MPI_GROUP_MAX=256
    export APRUN="srun --export=ALL --mpi=pmi2 -n \$ntasks"
-elif [[ "$machine" = "Cheyenne" ]]; then
-   export OMP_STACKSIZE=1024M
-   export MPI_BUFS_PER_PROC=256
-   export MPI_BUFS_PER_HOST=256
-   export MPI_GROUP_MAX=256
-   export APRUN="mpirun -v -np \$ntasks"
 elif [[ "$machine" = "wcoss2" ]]; then
    export OMP_PLACES=cores
    export OMP_STACKSIZE=2G

regression/regression_var.sh

@@ -30,9 +30,7 @@ else
 fi
 
 # Determine the machine
-if [[ -d /glade ]]; then # Cheyenne
-  export machine="Cheyenne"
-elif [[ -d /scratch1 ]]; then # Hera
+if [[ -d /scratch1 ]]; then # Hera
   export machine="Hera"
 elif [[ -d /mnt/lfs4 || -d /jetmon || -d /mnt/lfs1 ]]; then # Jet
   export machine="Jet"
@@ -66,20 +64,6 @@ case $machine in
     export check_resource="no"
     export accnt="nggps_emc"
   ;;
-  Cheyenne)
-    export queue="regular"
-    export noscrub="/glade/scratch/$LOGNAME/noscrub"
-    export group="global"
-    if [[ "$cmaketest" = "false" ]]; then
-      export basedir="/glade/scratch/$LOGNAME"
-    fi
-    export ptmp="/glade/scratch/$LOGNAME/$ptmpName"
-
-    export casesdir="/glade/work/epicufsrt/contrib/GSI_data/CASES/regtest"
-
-    export check_resource="no"
-    export accnt="NRAL0032"
-  ;;
   wcoss2)
       export local_or_default="${local_or_default:-/lfs/h2/emc/da/noscrub/$LOGNAME}"
       if [ -d $local_or_default ]; then

ush/module-setup.sh

@@ -40,13 +40,6 @@ elif [[ $MACHINE_ID = wcoss2 ]]; then
     # We are on WCOSS2
     module reset
 
-elif [[ $MACHINE_ID = cheyenne* ]] ; then
-    # We are on NCAR Cheyenne
-    if ( ! eval module help > /dev/null 2>&1 ) ; then
-        source /glade/u/apps/ch/modulefiles/default/localinit/localinit.sh
-    fi
-    module purge
-
 elif [[ $MACHINE_ID = stampede* ]] ; then
     # We are on TACC Stampede
     if ( ! eval module help > /dev/null 2>&1 ) ; then