Merge branch 'NOAA-EMC:develop' into develop

kayeekayee · Jan 29, 2024 · f4c8e00 · f4c8e00
2 parents 61975cf + d5bee38
commit f4c8e00
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Showing 26 changed files with 115 additions and 66 deletions.
diff --git a/ci/cases/pr/C48_ATM.yaml b/ci/cases/pr/C48_ATM.yaml
@@ -10,4 +10,4 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C48_S2SW.yaml b/ci/cases/pr/C48_S2SW.yaml
@@ -11,4 +11,4 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C48_S2SWA_gefs.yaml b/ci/cases/pr/C48_S2SWA_gefs.yaml
@@ -15,4 +15,4 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: {{ HOMEgfs }}/ci/platforms/gefs_ci_defaults.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_ci_defaults.yaml
diff --git a/ci/cases/pr/C96C48_hybatmDA.yaml b/ci/cases/pr/C96C48_hybatmDA.yaml
@@ -16,4 +16,4 @@ arguments:
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C96_atm3DVar.yaml b/ci/cases/pr/C96_atm3DVar.yaml
@@ -14,4 +14,4 @@ arguments:
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/pr/C96_atmsnowDA.yaml b/ci/cases/pr/C96_atmsnowDA.yaml
@@ -0,0 +1,21 @@
+experiment:
+  system: gfs
+  mode: cycled
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: ATM
+  resdetatmos: 96
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  idate: 2021122012
+  edate: 2021122100
+  nens: 0
+  gfs_cyc: 1
+  start: cold
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/atmsnowDA_defaults_ci.yaml
+
+skip_ci_on_hosts:
+  - orion
+  - hercules
diff --git a/ci/cases/weekly/C384C192_hybatmda.yaml b/ci/cases/weekly/C384C192_hybatmda.yaml
@@ -16,4 +16,4 @@ arguments:
   nens: 2
   gfs_cyc: 1
   start: cold
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384_S2SWA.yaml b/ci/cases/weekly/C384_S2SWA.yaml
@@ -11,4 +11,4 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2016070100
   edate: 2016070100
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/weekly/C384_atm3DVar.yaml b/ci/cases/weekly/C384_atm3DVar.yaml
@@ -16,4 +16,4 @@ arguments:
   nens: 0
   gfs_cyc: 1
   start: cold
-  yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/ci/cases/yamls/atmsnowDA_defaults_ci.yaml b/ci/cases/yamls/atmsnowDA_defaults_ci.yaml
@@ -0,0 +1,6 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+base:
+  DOIAU: "NO"
+  DO_JEDILANDDA: "YES"
+  ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}
diff --git a/ci/platforms/gefs_ci_defaults.yaml → ci/cases/yamls/gefs_ci_defaults.yaml b/ci/platforms/gefs_ci_defaults.yaml → ci/cases/yamls/gefs_ci_defaults.yaml
diff --git a/ci/platforms/gfs_defaults_ci.yaml → ci/cases/yamls/gfs_defaults_ci.yaml b/ci/platforms/gfs_defaults_ci.yaml → ci/cases/yamls/gfs_defaults_ci.yaml
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -10,7 +10,7 @@ Status
 ======
 
 * State of develop (HEAD) branch: GFSv17+ development
-* State of operations (dev/gfs.v16 branch): GFS v16.3.12 `tag: [gfs.v16.3.12] <https://github.com/NOAA-EMC/global-workflow/releases/tag/gfs.v16.3.12>`_
+* State of operations (dev/gfs.v16 branch): GFS v16.3.13 `tag: [gfs.v16.3.13] <https://github.com/NOAA-EMC/global-workflow/releases/tag/gfs.v16.3.13>`_
 
 =============
 Code managers

diff --git a/jobs/JGLOBAL_LAND_ANALYSIS b/jobs/JGLOBAL_LAND_ANALYSIS
@@ -1,6 +1,7 @@
 #! /usr/bin/env bash
 
 source "${HOMEgfs}/ush/preamble.sh"
+export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
 source "${HOMEgfs}/ush/jjob_header.sh" -e "landanl" -c "base landanl"
 
 ##############################################

diff --git a/jobs/JGLOBAL_PREP_LAND_OBS b/jobs/JGLOBAL_PREP_LAND_OBS
@@ -1,6 +1,7 @@
 #! /usr/bin/env bash
 
 source "${HOMEgfs}/ush/preamble.sh"
+export DATA=${DATA:-${DATAROOT}/${RUN}landanl_${cyc}}
 source "${HOMEgfs}/ush/jjob_header.sh" -e "preplandobs" -c "base preplandobs"
 
 ##############################################

diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
@@ -7,7 +7,7 @@ echo "BEGIN: config.prepoceanobs"
 export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
-export OBSPROC_YAML=@OBSPROC_YAML@
+export OBSPREP_YAML=@OBSPREP_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@
 [[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
 export OBS_YAML=${OBS_LIST}

diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
@@ -60,6 +60,9 @@ case ${machine} in
     export PARTITION_BATCH="compute"
     npe_node_max=40
     ;;
+  "CONTAINER")
+    npe_node_max=1
+    ;;
   *)
     echo "FATAL ERROR: Unknown machine encountered by ${BASH_SOURCE[0]}"
     exit 2
@@ -810,15 +813,15 @@ case ${step} in
     export npe_cleanup=1
     export npe_node_cleanup=1
     export nth_cleanup=1
-    export memory_cleanu="4096M"
+    export memory_cleanup="4096M"
     ;;
 
   "stage_ic")
     export wtime_stage_ic="00:15:00"
     export npe_stage_ic=1
     export npe_node_stage_ic=1
     export nth_stage_ic=1
-    export is_exclusive=Tue
+    export is_exclusive=True
     ;;
 
   "atmensanlinit")
@@ -953,7 +956,7 @@ case ${step} in
     export npe_node_esfc=$(( npe_node_max / nth_esfc ))
     export nth_cycle=${nth_esfc}
     export npe_node_cycle=$(( npe_node_max / nth_cycle ))
-    export memory_esfc="8GB"
+    export memory_esfc="80GB"
     ;;
 
   "epos")
@@ -983,15 +986,15 @@ case ${step} in
     export npe_awips=1
     export npe_node_awips=1
     export nth_awips=1
-    export memory_awip="3GB"
+    export memory_awips="3GB"
     ;;
 
   "npoess")
     export wtime_npoess="03:30:00"
     export npe_npoess=1
     export npe_node_npoess=1
     export nth_npoess=1
-    export memory_npoes="3GB"
+    export memory_npoess="3GB"
     ;;
 
   "gempak")
@@ -1012,7 +1015,7 @@ case ${step} in
     export nth_mos_stn_prep=1
     export memory_mos_stn_prep="5GB"
     export NTASK="${npe_mos_stn_prep}"
-    export PTILE="${npe_node_mos_stn_pep}"
+    export PTILE="${npe_node_mos_stn_prep}"
     ;;
 
   "mos_grd_prep")
@@ -1022,7 +1025,7 @@ case ${step} in
     export nth_mos_grd_prep=1
     export memory_mos_grd_prep="16GB"
     export NTASK="${npe_mos_grd_prep}"
-    export PTILE="${npe_node_mos_grd_pep}"
+    export PTILE="${npe_node_mos_grd_prep}"
     ;;
 
   "mos_ext_stn_prep")
@@ -1032,7 +1035,7 @@ case ${step} in
     export nth_mos_ext_stn_prep=1
     export memory_mos_ext_stn_prep="5GB"
     export NTASK="${npe_mos_ext_stn_prep}"
-    export PTILE="${npe_node_mos_ext_stn_pep}"
+    export PTILE="${npe_node_mos_ext_stn_prep}"
     ;;
 
   "mos_ext_grd_prep")
@@ -1042,7 +1045,7 @@ case ${step} in
     export nth_mos_ext_grd_prep=1
     export memory_mos_ext_grd_prep="3GB"
     export NTASK="${npe_mos_ext_grd_prep}"
-    export PTILE="${npe_node_mos_ext_grd_pep}"
+    export PTILE="${npe_node_mos_ext_grd_prep}"
     ;;
 
   "mos_stn_fcst")
@@ -1052,7 +1055,7 @@ case ${step} in
     export nth_mos_stn_fcst=1
     export memory_mos_stn_fcst="40GB"
     export NTASK="${npe_mos_stn_fcst}"
-    export PTILE="${npe_node_mos_stn_fst}"
+    export PTILE="${npe_node_mos_stn_fcst}"
     ;;
 
   "mos_grd_fcst")
@@ -1062,7 +1065,7 @@ case ${step} in
     export nth_mos_grd_fcst=1
     export memory_mos_grd_fcst="50GB"
     export NTASK="${npe_mos_grd_fcst}"
-    export PTILE="${npe_node_mos_grd_fst}"
+    export PTILE="${npe_node_mos_grd_fcst}"
     ;;
 
   "mos_ext_stn_fcst")
@@ -1083,7 +1086,7 @@ case ${step} in
     export nth_mos_ext_grd_fcst=1
     export memory_mos_ext_grd_fcst="50GB"
     export NTASK="${npe_mos_ext_grd_fcst}"
-    export PTILE="${npe_node_mos_ext_grd_fst}"
+    export PTILE="${npe_node_mos_ext_grd_fcst}"
     ;;
 
   "mos_stn_prdgen")
@@ -1105,7 +1108,7 @@ case ${step} in
     export memory_mos_grd_prdgen="20GB"
     export NTASK="${npe_mos_grd_prdgen}"
     export PTILE="${npe_node_mos_grd_prdgen}"
-    export OMP_NUM_THREADS="${nth_mos_grd_prden}"
+    export OMP_NUM_THREADS="${nth_mos_grd_prdgen}"
     ;;
 
   "mos_ext_stn_prdgen")
@@ -1127,7 +1130,7 @@ case ${step} in
     export memory_mos_ext_grd_prdgen="30GB"
     export NTASK="${npe_mos_ext_grd_prdgen}"
     export PTILE="${npe_node_mos_ext_grd_prdgen}"
-    export OMP_NUM_THREADS="${nth_mos_ext_grd_prden}"
+    export OMP_NUM_THREADS="${nth_mos_ext_grd_prdgen}"
     ;;
 
   "mos_wx_prdgen")
@@ -1138,7 +1141,7 @@ case ${step} in
     export memory_mos_wx_prdgen="10GB"
     export NTASK="${npe_mos_wx_prdgen}"
     export PTILE="${npe_node_mos_wx_prdgen}"
-    export OMP_NUM_THREADS="${nth_mos_wx_prden}"
+    export OMP_NUM_THREADS="${nth_mos_wx_prdgen}"
     ;;
 
   "mos_wx_ext_prdgen")
@@ -1159,4 +1162,4 @@ case ${step} in
 
 esac
 
-echo "END: config.resources"
+echo "END: config.resources"
diff --git a/parm/post/upp.yaml b/parm/post/upp.yaml
@@ -28,7 +28,7 @@ analysis:
 
 forecast:
   config:
-    rdaod: False
+    rdaod: True
   data_in:
     copy:
       {% if forecast_hour == 0 %}
@@ -47,7 +47,7 @@ forecast:
 
 goes:
   config:
-    rdaod: True
+    rdaod: False
   data_in:
     copy:
       {% set crtm_coefficients = [

diff --git a/parm/ufs/gocart/ExtData.other b/parm/ufs/gocart/ExtData.other
@@ -54,10 +54,10 @@ pSO2_OCS NA Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null
 # ---------------
 
 # # VOCs - OFFLINE MEGAN BIOG
-OC_ISOPRENE NA  N Y %y4-%m2-%d2t12:00:00 none none isoprene ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
-OC_LIMO     NA  N Y %y4-%m2-%d2t12:00:00 none none limo     ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
-OC_MTPA     NA  N Y %y4-%m2-%d2t12:00:00 none none mtpa     ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
-OC_MTPO     NA  N Y %y4-%m2-%d2t12:00:00 none none mtpo     ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
+OC_ISOPRENE NA  Y Y %y4-%m2-%d2t12:00:00 none none isoprene ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
+OC_LIMO     NA  Y Y %y4-%m2-%d2t12:00:00 none none limo     ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
+OC_MTPA     NA  Y Y %y4-%m2-%d2t12:00:00 none none mtpa     ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
+OC_MTPO     NA  Y Y %y4-%m2-%d2t12:00:00 none none mtpo     ExtData/nexus/MEGAN_OFFLINE_BVOC/v2021-12/MEGAN_OFFLINE_CLIMO_2000_2022_%m2.nc
 
 # Biofuel Source -- Included in AeroCom anthropogenic emissions
 OC_BIOFUEL NA  Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null

diff --git a/sorc/gdas.cd b/sorc/gdas.cd
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
@@ -130,15 +130,21 @@ cd "${HOMEgfs}/parm/ufs" || exit 1
 ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/noahmptable.tbl" .
 
 cd "${HOMEgfs}/parm/post" || exit 1
-for file in postxconfig-NT-GEFS-ANL.txt postxconfig-NT-GEFS-F00.txt postxconfig-NT-GEFS.txt postxconfig-NT-GFS-ANL.txt \
-    postxconfig-NT-GFS-F00-TWO.txt postxconfig-NT-GFS-F00.txt postxconfig-NT-GFS-FLUX-F00.txt postxconfig-NT-GFS-FLUX.txt \
-    postxconfig-NT-GFS-GOES.txt postxconfig-NT-GFS-TWO.txt \
-    postxconfig-NT-GFS.txt postxconfig-NT-gefs-aerosol.txt postxconfig-NT-gefs-chem.txt params_grib2_tbl_new \
-    post_tag_gfs128 post_tag_gfs65 nam_micro_lookup.dat \
-    AEROSOL_LUTS.dat optics_luts_DUST.dat optics_luts_SALT.dat optics_luts_SOOT.dat optics_luts_SUSO.dat optics_luts_WASO.dat
+for file in postxconfig-NT-GEFS-F00.txt postxconfig-NT-GEFS.txt postxconfig-NT-GEFS-WAFS.txt \
+    postxconfig-NT-GEFS-F00-aerosol.txt postxconfig-NT-GEFS-aerosol.txt \
+    postxconfig-NT-GFS-ANL.txt postxconfig-NT-GFS-F00.txt postxconfig-NT-GFS-FLUX-F00.txt \
+    postxconfig-NT-GFS.txt postxconfig-NT-GFS-FLUX.txt postxconfig-NT-GFS-GOES.txt \
+    postxconfig-NT-GFS-F00-TWO.txt postxconfig-NT-GFS-TWO.txt \
+    params_grib2_tbl_new post_tag_gfs128 post_tag_gfs65 nam_micro_lookup.dat 
 do
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${file}" .
 done
+for file in optics_luts_DUST.dat optics_luts_DUST_nasa.dat optics_luts_NITR_nasa.dat \
+    optics_luts_SALT.dat optics_luts_SALT_nasa.dat optics_luts_SOOT.dat optics_luts_SOOT_nasa.dat \
+    optics_luts_SUSO.dat optics_luts_SUSO_nasa.dat optics_luts_WASO.dat optics_luts_WASO_nasa.dat    
+do
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" .
+done
 
 cd "${HOMEgfs}/scripts" || exit 8
 ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_utils.fd/scripts/exemcsfc_global_sfc_prep.sh" .

diff --git a/ush/load_ufsda_modules.sh b/ush/load_ufsda_modules.sh
@@ -44,20 +44,15 @@ elif [[ -d /scratch1 ]] ; then
   # set NETCDF variable based on ncdump location
   NETCDF=$( which ncdump )
   export NETCDF
-  # prod_util stuff, find a better solution later...
-  module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/compiler/intel/2022.1.2/
-  module load prod_util
 elif [[ -d /work ]] ; then
-  # We are on MSU Orion
-  # prod_util stuff, find a better solution later...
-  #module use /apps/contrib/NCEP/hpc-stack/libs/hpc-stack/modulefiles/compiler/intel/2022.1.2/
-  #module load prod_util
-  export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
-  export MDATE=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/mdate
-  export NDATE=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/ndate
-  export NHOUR=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/nhour
-  export FSYNC=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/fsync_file
-  module load "${MODS}/orion"
+  # We are on MSU Orion or Hercules
+  if [[ -d /apps/other ]] ; then
+     # Hercules
+     module load "${MODS}/hercules"
+  else
+     # Orion
+     module load "${MODS}/orion"
+  fi
   # set NETCDF variable based on ncdump location
   ncdump=$( which ncdump )
   NETCDF=$( echo "${ncdump}" | cut -d " " -f 3 )