Update global-workflow and subcomponents to Hera/Rocky 8 partition (N…

…OAA-EMC#2421)

This PR addresses issue NOAA-EMC#2329. The following is accomplished:

- All submodule RDHPCS Hera stacks are updated to be compatible with the
Rocky-8 distro spack-stack;
- The global-workflow version files `versions/build.hera.ver` and
`versions/run.hera.ver` are updated for Rocky-8;
- All submodule hashes have been updated to be compliant with the
Rocky-8 distro spack-stack (see the reference PRs below);
- Update to `parm/config/config.base` is made for not yet compliant
packages;
- Relevant updates are made to `modulefiles/module_base.hera.lua` and
`modulefiles/module_gwsetup.lua`.

  Resolves NOAA-EMC#2329
  Refs: [NOAA-EMC#958](NOAA-EMC/GDASApp#958)
           [NOAA-EMC#49](NOAA-EMC/gfs-utils#49)
           [NOAA-EMC#124](NOAA-EMC/GSI-Monitor#124)
           [NOAA-EMC#31](NOAA-EMC/GSI-utils#31)
[NOAA-EMC#2167](ufs-community/ufs-weather-model#2167)
[NOAA-EMC#2143](ufs-community/ufs-weather-model#2143)
           [NOAA-EMC#913](ufs-community/UFS_UTILS#913)

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>

.gitmodules

@@ -26,3 +26,6 @@
 [submodule "sorc/gsi_monitor.fd"]
   path = sorc/gsi_monitor.fd
   url = https://github.com/NOAA-EMC/GSI-Monitor.git
+[submodule "sorc/upp.fd"]
+  path = sorc/upp.fd
+  url = https://github.com/NOAA-EMC/UPP.git

ci/cases/pr/C48_S2SWA_gefs.yaml

@@ -16,3 +16,6 @@ arguments:
   idate: 2021032312
   edate: 2021032312
   yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_ci_defaults.yaml
+
+skip_ci_on_hosts:
+  - hera

ci/cases/pr/C48mx500_3DVarAOWCDA.yaml

@@ -19,4 +19,5 @@ arguments:
 
 skip_ci_on_hosts:
   - orion
+  - hera
   - hercules

modulefiles/module_base.hera.lua

@@ -42,7 +42,7 @@ setenv("WGRIB2","wgrib2")
 setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 
 --prepend_path("MODULEPATH", pathJoin("/scratch1/NCEPDEV/global/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
-prepend_path("MODULEPATH", pathJoin("/scratch1/NCEPDEV/global/glopara/git/prepobs/feature-GFSv17_com_reorg_log_update/modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/scratch1/NCEPDEV/global/glopara/git/prepobs/dev-gfsv17/modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
 prepend_path("MODULEPATH", pathJoin("/scratch1/NCEPDEV/global/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))

modulefiles/module_gwci.hera.lua

@@ -2,7 +2,7 @@ help([[
 Load environment to run GFS workflow setup scripts on Hera
 ]])
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev-rocky8/install/modulefiles/Core")
 
 load(pathJoin("stack-intel", os.getenv("2021.5.0")))
 load(pathJoin("stack-intel-oneapi-mpi", os.getenv("2021.5.1")))

modulefiles/module_gwsetup.hera.lua

@@ -4,7 +4,7 @@ Load environment to run GFS workflow setup scripts on Hera
 
 load(pathJoin("rocoto"))
 
-prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev-rocky8/install/modulefiles/Core")
 
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 local python_ver=os.getenv("python_ver") or "3.11.6"

parm/config/gfs/config.base

@@ -384,11 +384,14 @@ export FITSARC="YES"
 export FHMAX_FITS=132
 [[ "${FHMAX_FITS}" -gt "${FHMAX_GFS}" ]] && export FHMAX_FITS=${FHMAX_GFS}
 
-# The monitor jobs are not yet supported for JEDIATMVAR
+# The monitor jobs are not yet supported for JEDIATMVAR.
 if [[ ${DO_JEDIATMVAR} = "YES" ]]; then
    export DO_VERFOZN="NO"     # Ozone data assimilation monitoring
    export DO_VERFRAD="NO"     # Radiance data assimilation monitoring
    export DO_VMINMON="NO"     # GSI minimization monitoring
+# The minimization monitor is not yet supported on RDHPCS Hera for Rocky-8
+elif [[ ${machine} = "HERA" ]]; then
+   export DO_VMINMON="NO"     # GSI minimization monitoring
 fi
 
 echo "END: config.base"

sorc/build_upp.sh

@@ -26,6 +26,6 @@ if [[ ! -d "../exec" ]]; then
   mkdir -p ../exec
 fi
 
-cd ufs_model.fd/FV3/upp/tests
+cd upp.fd/tests
 # shellcheck disable=SC2086
 BUILD_JOBS=${BUILD_JOBS:-8} ./compile_upp.sh ${_opts}

sorc/link_workflow.sh

@@ -352,10 +352,11 @@ fi
 #--link source code directories
 #------------------------------
 cd "${HOMEgfs}/sorc" || exit 8
-if [[ -d ufs_model.fd ]]; then
-  [[ -d upp.fd ]] && rm -rf upp.fd
-  ${LINK} ufs_model.fd/FV3/upp upp.fd
-fi
+# TODO: Commenting out until UPP is up-to-date with Rocky-8.
+#if [[ -d ufs_model.fd ]]; then
+#  [[ -d upp.fd ]] && rm -rf upp.fd
+#  ${LINK} ufs_model.fd/FV3/upp upp.fd
+#fi
 
 if [[ -d gsi_enkf.fd ]]; then
   [[ -d gsi.fd ]] && rm -rf gsi.fd

versions/build.hera.ver

@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.1
-export spack_env=gsi-addon-dev
+export spack_env=gsi-addon-dev-rocky8
 source "${HOMEgfs:-}/versions/build.spack.ver"
 export spack_mod_path="/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"

versions/run.hera.ver

@@ -1,6 +1,6 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.1
-export spack_env=gsi-addon-dev
+export spack_env=gsi-addon-dev-rocky8
 
 export hpss_ver=hpss
 export ncl_ver=6.6.2