Merge branch 'NOAA-EMC:develop' into enablepio_cycle_uglo15km

.github/workflows/docs.yaml

@@ -42,14 +42,14 @@ jobs:
         ./.github/scripts/build_docs.sh
 
     - name: Upload documentation (on success)
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: always()
       with:
         name: documentation
         path: artifact/documentation
 
     - name: Upload warnings (on failure)
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       if: failure()
       with:
         name: documentation_warnings.log

.github/workflows/linters.yaml

@@ -31,7 +31,7 @@ jobs:
 
       - if: ${{ always() }}
         name: Upload artifact with ShellCheck defects in SARIF format
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Differential ShellCheck SARIF
           path: ${{ steps.ShellCheck.outputs.sarif }}

ci/cases/yamls/gefs_defaults_ci.yaml

@@ -4,7 +4,6 @@ base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
   SFS_POST: "NO"
   FHOUT_GFS: 6
-stage_ic:
   USE_OCN_ENS_PERTURB_FILES: "NO"
   USE_ATM_ENS_PERTURB_FILES: "NO"
 ocn:

ci/cases/yamls/sfs_defaults.yaml

@@ -7,7 +7,7 @@ base:
   DO_BUFRSND: "NO"
   DO_GEMPAK: "NO"
   DO_AWIPS: "NO"
-  KEEPDATA: "YES"
+  KEEPDATA: "NO"
   DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 2976
   FHMAX_HF_GFS: 0
@@ -17,6 +17,8 @@ base:
   FHOUT_ICE_GFS: 24
   FCST_BREAKPOINTS: ""
   REPLAY_ICS: "NO"
+  USE_OCN_ENS_PERTURB_FILES: "YES"
+  USE_ATM_ENS_PERTURB_FILES: "YES"
   HPSSARCH: "NO"
   LOCALARCH: "NO"
   SFS_POST: "YES"
@@ -26,8 +28,5 @@ fcst:
   MONO: "mono"
   reforecast: "YES"
   FHZER: 24
-stage_ic:
-  USE_OCN_ENS_PERTURB_FILES: "YES"
-  USE_ATM_ENS_PERTURB_FILES: "YES"
 ocn:
   MOM6_INTERP_ICS: "YES"

env/WCOSS2.env

@@ -123,7 +123,7 @@ elif [[ "${step}" = "marineanlchkpt" ]]; then
 elif [[ "${step}" = "ocnanalecen" ]]; then
 
     export NTHREADS_OCNANALECEN=${NTHREADSmax}
-    export APRUN_OCNANALECEN="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANALECEN}"
+    export APRUN_OCNANALECEN="${APRUN_default}"
 
 elif [[ "${step}" = "marineanlletkf" ]]; then
 

parm/config/gefs/config.base

@@ -227,8 +227,13 @@ export SDATE_GFS=@SDATE_GFS@
 export REPLAY_ICS=@REPLAY_ICS@
 if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
     export OFFSET_START_HOUR=$(( assim_freq / 2 ))
+    echo "WARNING: Replay ICs require perturbation files, ignoring any previous settings"
+    export USE_OCN_ENS_PERTURB_FILES="YES"
+    export USE_ATM_ENS_PERTURB_FILES="YES"
 else
     export OFFSET_START_HOUR=0
+    export USE_OCN_ENS_PERTURB_FILES=@USE_OCN_ENS_PERTURB_FILES@
+    export USE_ATM_ENS_PERTURB_FILES=@USE_ATM_ENS_PERTURB_FILES@
 fi
 
 # GFS output and frequency

parm/config/gefs/config.efcs

@@ -57,7 +57,7 @@ if (( OCNRES <= 100 )); then
     export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
 fi
 
-if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
+if [[ "${USE_OCN_ENS_PERTURB_FILES:-NO}" == "YES" ]]; then
     export ODA_INCUPD="True"
     export ODA_TEMPINC_VAR='t_pert'
     export ODA_SALTINC_VAR='s_pert'

parm/config/gefs/config.fcst

@@ -192,14 +192,14 @@ case ${imp_physics} in
 
         export hord_mt_nh_nonmono=5
         export hord_xx_nh_nonmono=5
+        export hord_dp_nh_nonmono=-5
         export vtdm4_nh_nonmono=0.02
         export nord=2
         if [[ "${TYPE}" == "nh"* ]]; then
             export dddmp=0.1
         else
             export dddmp=0.
 	    fi
-        export dddmp=0.1
         export d4_bg=0.12
         ;;
     11) # GFDL
@@ -216,6 +216,7 @@ case ${imp_physics} in
 
         export hord_mt_nh_nonmono=5
         export hord_xx_nh_nonmono=5
+        export hord_dp_nh_nonmono=-5
         export vtdm4_nh_nonmono=0.02
         export nord=2
         export d4_bg=0.12

parm/config/gefs/config.nsst

@@ -12,10 +12,6 @@ export NST_MODEL=2
 
 # nstf_name(2) : NST_SPINUP : 0 = OFF, 1 = ON,
 export NST_SPINUP=0
-cdate="${PDY}${cyc}"
-if (( cdate < 2017072000 )); then
-    export NST_SPINUP=1
-fi
 
 # nstf_name(3) : NST_RESV (Reserved, NSST Analysis) : 0 = OFF, 1 = ON
 export NST_RESV=0

parm/config/gefs/config.resources

@@ -219,7 +219,7 @@ case ${step} in
 
     case "${CASE}" in
       "C48" | "C96" | "C192")
-        declare -x "walltime"="03:00:00"
+        declare -x "walltime"="04:00:00"
         ;;
       "C384" | "C768" | "C1152")
         declare -x "walltime"="06:00:00"

parm/config/gefs/config.stage_ic

@@ -32,8 +32,4 @@ if [[ -z "${ICSDIR}" ]] ; then
 
 fi
 
-#use of perturbations files for ensembles
-export USE_OCN_ENS_PERTURB_FILES=@USE_OCN_ENS_PERTURB_FILES@
-export USE_ATM_ENS_PERTURB_FILES=@USE_ATM_ENS_PERTURB_FILES@
-
 echo "END: config.stage_ic"

parm/config/gefs/config.ufs

@@ -99,8 +99,8 @@ case "${fv3_res}" in
         export DELTIM=600
         export layout_x=2
         export layout_y=2
-        export layout_x_gfs=4
-        export layout_y_gfs=4
+        export layout_x_gfs=6
+        export layout_y_gfs=8
         export nthreads_fv3=1
         export nthreads_fv3_gfs=1
         export nthreads_ufs=1

parm/config/gefs/yaml/defaults.yaml

@@ -14,22 +14,20 @@ base:
   FHOUT_HF_GFS: 1
   FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
-  USE_OCN_PERTURB_FILES: "false"
   FHOUT_GFS: 6
   FHOUT_OCN_GFS: 6
   FHOUT_ICE_GFS: 6
   HPSSARCH: "NO"
   LOCALARCH: "NO"
   SFS_POST: "NO"
+  USE_OCN_ENS_PERTURB_FILES: "NO"
+  USE_ATM_ENS_PERTURB_FILES: "NO"
   DO_TEST_MODE: "NO"
 fcst:
   reforecast: "NO"
   FHZER: 6
   TYPE: "nh"
   MONO: "non-mono"
-stage_ic:
-  USE_OCN_ENS_PERTURB_FILES: "NO"
-  USE_ATM_ENS_PERTURB_FILES: "NO"
 ocn:
   MOM6_INTERP_ICS: "NO"
 # config.aero has just a system-specific path to add.

parm/config/gfs/config.fcst

@@ -203,6 +203,7 @@ case ${imp_physics} in
 
         export hord_mt_nh_nonmono=5
         export hord_xx_nh_nonmono=5
+        export hord_dp_nh_nonmono=-5
         export vtdm4_nh_nonmono=0.02
         export nord=2
         export dddmp=0.1
@@ -236,6 +237,7 @@ case ${imp_physics} in
 
         export hord_mt_nh_nonmono=5
         export hord_xx_nh_nonmono=5
+        export hord_dp_nh_nonmono=-5
         export vtdm4_nh_nonmono=0.02
         export nord=2
         export d4_bg=0.12

parm/config/gfs/config.resources

@@ -324,7 +324,7 @@ case ${step} in
   "snowanl")
     # below lines are for creating JEDI YAML
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         layout_x=6
         layout_y=6
         ;;
@@ -353,7 +353,7 @@ case ${step} in
   "esnowanl")
     # below lines are for creating JEDI YAML
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         layout_x=6
         layout_y=6
         ;;
@@ -390,7 +390,7 @@ case ${step} in
   "aeroanlinit")
     # below lines are for creating JEDI YAML
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         layout_x=8
         layout_y=8
         ;;
@@ -423,7 +423,7 @@ case ${step} in
 
   "aeroanlvar")
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         layout_x=8
         layout_y=8
         ;;
@@ -457,7 +457,7 @@ case ${step} in
 
   "aeroanlgenb")
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         layout_x=8
         layout_y=8
         ;;
@@ -668,7 +668,7 @@ case ${step} in
     walltime_gdas="01:20:00"
     walltime_gfs="01:00:00"
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         ntasks_gdas=780
         ntasks_gfs=825
         threads_per_task=5
@@ -704,7 +704,7 @@ case ${step} in
     export threads_per_task_echgres_gfs=12
     export is_exclusive=True
     memory="48GB"
-    if [[ "${CASE}" == "C384" || "${CASE}" == "C768" ]]; then
+    if [[ "${CASE}" == "C384" || "${CASE}" == "C768" || "${CASE}" == "C1152" ]]; then
        memory="${mem_node_max}"
     fi
     ;;
@@ -897,7 +897,7 @@ case ${step} in
         ;;
       "C768" | "C1152")
         # Not valid resolutions for ensembles
-        declare -x "walltime_gdas"="00:40:00"
+        declare -x "walltime_gdas"="00:50:00"
         declare -x "walltime_gfs"="06:00:00"
         ;;
       *)
@@ -923,16 +923,21 @@ case ${step} in
       "C48" | "C96")
         ntasks=${CASE:1}
       ;;
-      "C192" | "C384" | "C768" )
+      "C192" | "C384" | "C768")
         ntasks=120
         memory="${mem_node_max}"
       ;;
+      "C1152")
+        ntasks=200
+        memory="${mem_node_max}"
+      ;;
       *)
         echo "FATAL ERROR: Resources not defined for job ${step} at resolution ${CASE}"
         exit 4
       ;;
     esac
     tasks_per_node=${ntasks}
+    [[ ${CASE} == "C1152" ]] && tasks_per_node=40
 
     threads_per_task=1
 
@@ -1005,7 +1010,7 @@ case ${step} in
     threads_per_task=1
     tasks_per_node=1
     memory="20G"
-    [[ ${CASE} == "C768" ]] && memory="80GB"
+    [[ ${CASE} == "C768" || ${CASE} == "C1152" ]] && memory="80GB"
     ;;
 
   "metp")
@@ -1145,7 +1150,7 @@ case ${step} in
     fi
 
     case ${CASE} in
-      "C768")                 ntasks=200;;
+      "C1152" | "C768")       ntasks=200;;
       "C384")                 ntasks=100;;
       "C192" | "C96" | "C48") ntasks=40;;
       *)
@@ -1178,7 +1183,7 @@ case ${step} in
   "eupd")
     walltime="00:30:00"
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         ntasks=480
         threads_per_task=6
         ;;
@@ -1223,7 +1228,7 @@ case ${step} in
 
   "epos")
     walltime="00:15:00"
-    [[ ${CASE} == "C768" ]] && walltime="00:25:00"
+    [[ ${CASE} == "C768" || ${CASE} == "C1152" ]] && walltime="00:25:00"
     ntasks=80
     threads_per_task=1
     tasks_per_node=$(( max_tasks_per_node / threads_per_task ))

parm/config/gfs/config.resources.GAEA

@@ -12,7 +12,7 @@ case ${step} in
     # The number of tasks and cores used must be the same for eobs
     # See https://github.com/NOAA-EMC/global-workflow/issues/2092 for details
     case ${CASE} in
-      "C768" | "C384")
+      "C1152" | "C768" | "C384")
         export tasks_per_node=50
         ;;
       *)

parm/config/gfs/config.resources.HERA

@@ -32,7 +32,7 @@ case ${step} in
 
   "eupd")
     case ${CASE} in
-      "C768")
+      "C1152" | "C768")
         export ntasks=80
         export threads_per_task=20
         ;;
@@ -49,7 +49,7 @@ case ${step} in
     ;;
 
   "ecen")
-    if [[ "${CASE}" == "C768" ]]; then export threads_per_task=6; fi
+    if [[ "${CASE}" == "C768" || "${CASE}" == "C1152" ]]; then export threads_per_task=6; fi
     export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     ;;
 

parm/config/gfs/config.resources.JET

@@ -40,7 +40,7 @@ case ${step} in
     ;;
 
   "ecen")
-    if [[ "${CASE}" == "C768" ]]; then export threads_per_task=6; fi
+    if [[ "${CASE}" == "C768" || "${CASE}" == "C1152" ]]; then export threads_per_task=6; fi
     export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     ;;
 

parm/config/gfs/config.resources.WCOSS2

@@ -9,7 +9,7 @@ case ${step} in
     ;;
 
   "anal")
-    if [[ "${CASE}" == "C768" ]]; then
+    if [[ "${CASE}" == "C768" || "${CASE}" == "C1152" ]]; then
         export threads_per_task=8
         # Make ntasks a multiple of 16
         export ntasks_gdas=784
@@ -43,7 +43,7 @@ case ${step} in
 
   "eupd")
     case ${CASE} in
-      "C768" | "C384")
+      "C1152" | "C768" | "C384")
         export ntasks=315
         export threads_per_task=14
         ;;
@@ -55,7 +55,7 @@ case ${step} in
 
   "eobs")
     case ${CASE} in
-      "C768" | "C384")
+      "C1152" | "C768" | "C384")
         export tasks_per_node=50
         ;;
       *)