Merge remote-tracking branch 'upstream/develop' into feature/move_jcb

* upstream/develop: Parameterize some things in config.atmanl and config.atmensanl (NOAA-EMC#2661) Add links to the ocean insitu obs processing tools (NOAA-EMC#2644) Update S4 point of contact in docs (NOAA-EMC#2660) Enable wcoss2 ufsda build and module load (NOAA-EMC#2620)
danholdaway · Jun 6, 2024 · b71d285 · b71d285
2 parents a5db89e + acf3aaa
commit b71d285
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diff --git a/ci/cases/pr/C96C48_ufs_hybatmDA.yaml b/ci/cases/pr/C96C48_ufs_hybatmDA.yaml
@@ -21,5 +21,4 @@ skip_ci_on_hosts:
   - hera
   - orion
   - hercules
-  - wcoss2
 
diff --git a/ci/scripts/clone-build_ci.sh b/ci/scripts/clone-build_ci.sh
@@ -74,7 +74,7 @@ set +e
 source "${HOMEgfs}/ush/module-setup.sh"
 export BUILD_JOBS=8
 rm -rf log.build
-./build_all.sh -gk  >> log.build 2>&1
+./build_all.sh -guk  >> log.build 2>&1
 build_status=$?
 
 DATE=$(date +'%D %r')

diff --git a/docs/source/hpc.rst b/docs/source/hpc.rst
@@ -22,7 +22,7 @@ HPC helpdesks
 * Hercules:  [email protected]
 * HPSS: [email protected]
 * Gaea: [email protected]
-* S4: david.huber@noaa.gov
+* S4: innocent.souopgui@noaa.gov
 * Jet: [email protected]
 * Cloud: [email protected]
 
@@ -48,7 +48,7 @@ https://aim.rdhpcs.noaa.gov/
 Optimizing the global workflow on S4
 ====================================
 
-The S4 cluster is relatively small and so optimizations are recommended to improve cycled runtimes. Please contact David Huber (david.huber@noaa.gov) if you are planning on running a cycled experiment on this system to obtain optimized configuration files.
+The S4 cluster is relatively small and so optimizations are recommended to improve cycled runtimes. Please contact Innocent Souopgui (innocent.souopgui@noaa.gov) if you are planning on running a cycled experiment on this system to obtain optimized configuration files.
 
 ============
 Git settings

diff --git a/docs/source/init.rst b/docs/source/init.rst
@@ -315,7 +315,7 @@ Manual Generation
 *****************
 
 .. note::
-   Initial conditions cannot be generated on S4. These must be generated on another supported platform then pushed to S4. If you do not have access to a supported system or need assistance, please contact David Huber (david.huber@noaa.gov).
+   Initial conditions cannot be generated on S4. These must be generated on another supported platform then pushed to S4. If you do not have access to a supported system or need assistance, please contact Innocent Souopgui (innocent.souopgui@noaa.gov).
 
 .. _coldstarts:
 

diff --git a/parm/config/gfs/config.atmanl b/parm/config/gfs/config.atmanl
@@ -6,9 +6,9 @@
 echo "BEGIN: config.atmanl"
 
 export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
-export JCB_ALGO_YAML="${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2"
+export JCB_ALGO_YAML=@JCB_ALGO_YAML@
 
-export STATICB_TYPE="gsibec"
+export STATICB_TYPE=@STATICB_TYPE@
 export LOCALIZATION_TYPE="bump"
 export INTERP_METHOD='barycentric'
 

diff --git a/parm/config/gfs/config.atmensanl b/parm/config/gfs/config.atmensanl
@@ -6,7 +6,7 @@
 echo "BEGIN: config.atmensanl"
 
 export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
-export JCB_ALGO_YAML="${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
+export JCB_ALGO_YAML=@JCB_ALGO_YAML@
 
 export INTERP_METHOD='barycentric'
 

diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
@@ -20,12 +20,15 @@ base:
   FHMAX_ENKF_GFS: 12
 
 atmanl:
+  JCB_ALGO_YAML: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2" 
+  STATICB_TYPE: "gsibec"  
   LAYOUT_X_ATMANL: 8
   LAYOUT_Y_ATMANL: 8
   IO_LAYOUT_X: 1
   IO_LAYOUT_Y: 1
 
 atmensanl:
+  JCB_ALGO_YAML: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
   LAYOUT_X_ATMENSANL: 8
   LAYOUT_Y_ATMENSANL: 8
   IO_LAYOUT_X: 1

diff --git a/sorc/build_all.sh b/sorc/build_all.sh
@@ -145,7 +145,7 @@ build_opts["ww3prepost"]="${_wave_opt} ${_verbose_opt} ${_build_ufs_opt} ${_buil
 
 # Optional DA builds
 if [[ "${_build_ufsda}" == "YES" ]]; then
-   if [[ "${MACHINE_ID}" != "orion" && "${MACHINE_ID}" != "hera" && "${MACHINE_ID}" != "hercules" ]]; then
+   if [[ "${MACHINE_ID}" != "orion" && "${MACHINE_ID}" != "hera" && "${MACHINE_ID}" != "hercules" && "${MACHINE_ID}" != "wcoss2" ]]; then
       echo "NOTE: The GDAS App is not supported on ${MACHINE_ID}.  Disabling build."
    else
       build_jobs["gdas"]=8

diff --git a/sorc/gsi_utils.fd b/sorc/gsi_utils.fd
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
@@ -261,6 +261,14 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_yaml.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
+  declare -a gdasapp_ocn_insitu_profile_platforms=("argo" "bathy" "glider" "marinemammal" "tesac" "xbtctd")
+  for platform in "${gdasapp_ocn_insitu_profile_platforms[@]}"; do
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/marine/bufr2ioda_insitu_profile_${platform}.py" .
+  done
+  declare -a gdasapp_ocn_insitu_sfc_platforms=("altkob" "trkob")
+  for platform in "${gdasapp_ocn_insitu_sfc_platforms[@]}"; do
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/marine/bufr2ioda_insitu_surface_${platform}.py" .
+  done
 fi
 
 

diff --git a/ush/load_ufsda_modules.sh b/ush/load_ufsda_modules.sh
@@ -34,13 +34,13 @@ source "${HOMEgfs}/ush/module-setup.sh"
 module use "${HOMEgfs}/sorc/gdas.cd/modulefiles"
 
 case "${MACHINE_ID}" in
-  ("hera" | "orion" | "hercules")
+  ("hera" | "orion" | "hercules" | "wcoss2")
     module load "${MODS}/${MACHINE_ID}"
     ncdump=$( command -v ncdump )
     NETCDF=$( echo "${ncdump}" | cut -d " " -f 3 )
     export NETCDF
     ;;
-  ("wcoss2" | "acorn" | "jet" | "gaea" | "s4")
+  ("jet" | "gaea" | "s4" | "acorn")
     echo WARNING: UFSDA NOT SUPPORTED ON THIS PLATFORM
     ;;  
   *)