Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2451

ci/cases/pr/C96C48_ufs_hybatmDA.yaml

@@ -21,5 +21,4 @@ skip_ci_on_hosts:
   - hera
   - orion
   - hercules
-  - wcoss2
 

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')

docs/source/hpc.rst

@@ -22,7 +22,7 @@ HPC helpdesks
 * Hercules:  rdhpcs.hercules.help@noaa.gov
 * HPSS: rdhpcs.hpss.help@noaa.gov
 * Gaea: oar.gfdl.help@noaa.gov
-* S4: david.huber@noaa.gov
+* S4: innocent.souopgui@noaa.gov
 * Jet: rdhpcs.jet.help@noaa.gov
 * Cloud: rdhpcs.cloud.help@noaa.gov
 
@@ -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

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:
 

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'
 

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'
 

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

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

sorc/link_workflow.sh

@@ -253,6 +253,14 @@ 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
 
 

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
     ;;  
   *)

ush/parsing_namelists_CICE.sh

@@ -59,6 +59,13 @@ local CICE_RUNID="unknown"
 local CICE_USE_RESTART_TIME=${use_restart_time}
 local CICE_RESTART_DIR="./CICE_RESTART/"
 local CICE_RESTART_FILE="cice_model.res"
+local CICE_RESTART_DEFLATE=0
+local CICE_RESTART_CHUNK=0,0
+local CICE_RESTART_STRIDE=-99
+local CICE_RESTART_ROOT=-99
+local CICE_RESTART_REARR="box"
+local CICE_RESTART_IOTASKS=-99
+local CICE_RESTART_FORMAT="pnetcdf2"
 local CICE_DUMPFREQ="y"  # "h","d","m" or "y" for restarts at intervals of "hours", "days", "months" or "years"
 local CICE_DUMPFREQ_N=10000  # Set this to a really large value, as cice, mom6 and cmeps restart interval is controlled by ufs.configure
 local CICE_DIAGFREQ=$(( 86400 / DT_CICE ))  # frequency of diagnostic output in timesteps, recommended for 1x per day
@@ -68,8 +75,16 @@ if [[ "${RUN}" =~ "gdas" ]]; then
 else
   local CICE_HIST_AVG=".true., .true., .true., .true., .true."    # GFS long forecaset wants averaged over CICE_HISTFREQ_N
 fi
+local CICE_HISTORY_FORMAT="pnetcdf2"
 local CICE_HISTORY_DIR="./CICE_OUTPUT/"
 local CICE_INCOND_DIR="./CICE_OUTPUT/"
+local CICE_HISTORY_IOTASKS=-99
+local CICE_HISTORY_REARR="box"
+local CICE_HISTORY_ROOT=-99
+local CICE_HISTORY_STRIDE=-99
+local CICE_HISTORY_CHUNK=0,0
+local CICE_HISTORY_DEFLATE=0
+local CICE_HISTORY_PREC=4
 # grid_nml section
 # CICE_GRID
 # CICE_MASK