Merge remote-tracking branch 'emc/develop' into feature/multi-app

.github/workflows/pw_aws_ci.yaml

@@ -72,9 +72,9 @@ jobs:
       id: get-branch
       run: |
         pr_number=${{ github.event.inputs.pr_number }}
+        repo=${{ github.repository }}
         if [ "$pr_number" -eq "0" ]; then
           branch=${{ github.event.inputs.ref }}
-          repo=${{ github.repository }}
         else
           branch=$(gh pr view $pr_number --repo $repo --json headRefName --jq '.headRefName')
           repo_owner=$(gh pr view $pr_number --repo $repo --json headRepositoryOwner --jq '.headRepositoryOwner.login')

env/HERA.env

@@ -52,10 +52,6 @@ if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
     export sys_tp="HERA"
     export launcher_PREP="srun --hint=nomultithread"
 
-elif [[ "${step}" = "prepsnowobs" ]]; then
-
-    export APRUN_CALCFIMS="${APRUN_default}"
-
 elif [[ "${step}" = "prep_emissions" ]]; then
 
     export APRUN="${APRUN_default}"
@@ -116,6 +112,8 @@ elif [[ "${step}" = "prepobsaero" ]]; then
 
 elif [[ "${step}" = "snowanl" ]]; then
 
+    export APRUN_CALCFIMS="${launcher} -n 1"
+
     export NTHREADS_SNOWANL=${NTHREADSmax}
     export APRUN_SNOWANL="${APRUN_default} --cpus-per-task=${NTHREADS_SNOWANL}"
 

env/HERCULES.env

@@ -50,10 +50,6 @@ case ${step} in
     export sys_tp="HERCULES"
     export launcher_PREP="srun --hint=nomultithread"
  ;;
- "prepsnowobs")
-
-    export APRUN_CALCFIMS="${APRUN_default}"
- ;;
  "prep_emissions")
 
     export APRUN="${APRUN_default}"
@@ -115,6 +111,8 @@ case ${step} in
 ;;
  "snowanl")
 
+    export APRUN_CALCFIMS="${launcher} -n 1"
+
     export NTHREADS_SNOWANL=${NTHREADSmax}
     export APRUN_SNOWANL="${APRUN_default} --cpus-per-task=${NTHREADS_SNOWANL}"
 

env/JET.env

@@ -40,10 +40,6 @@ if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
     export sys_tp="JET"
     export launcher_PREP="srun"
 
-elif [[ "${step}" = "prepsnowobs" ]]; then
-
-    export APRUN_CALCFIMS="${launcher} -n 1"
-
 elif [[ "${step}" = "prep_emissions" ]]; then
 
     export APRUN="${launcher} -n 1"
@@ -99,6 +95,8 @@ elif [[ "${step}" = "prepobsaero" ]]; then
 
 elif [[ "${step}" = "snowanl" ]]; then
 
+    export APRUN_CALCFIMS="${launcher} -n 1"
+
     export NTHREADS_SNOWANL=${NTHREADSmax}
     export APRUN_SNOWANL="${APRUN_default}"
 

env/ORION.env

@@ -47,10 +47,6 @@ if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
     export sys_tp="ORION"
     export launcher_PREP="srun --hint=nomultithread"
 
-elif [[ "${step}" = "prepsnowobs" ]]; then
-
-    export APRUN_CALCFIMS="${launcher} -n 1"
-
 elif [[ "${step}" = "prep_emissions" ]]; then
 
     export APRUN="${launcher} -n 1"
@@ -106,6 +102,8 @@ elif [[ "${step}" = "prepobsaero" ]]; then
 
 elif [[ "${step}" = "snowanl" ]]; then
 
+    export APRUN_CALCFIMS="${launcher} -n 1"
+
     export NTHREADS_SNOWANL=${NTHREADSmax}
     export APRUN_SNOWANL="${APRUN_default} --cpus-per-task=${NTHREADS_SNOWANL}"
 

env/S4.env

@@ -40,10 +40,6 @@ if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
     export sys_tp="S4"
     export launcher_PREP="srun"
 
-elif [[ "${step}" = "prepsnowobs" ]]; then
-
-    export APRUN_CALCFIMS="${APRUN_default}"
-
 elif [[ "${step}" = "prep_emissions" ]]; then
 
     export APRUN="${APRUN_default}"
@@ -99,6 +95,8 @@ elif [[ "${step}" = "prepobsaero" ]]; then
 
 elif [[ "${step}" = "snowanl" ]]; then
 
+    export APRUN_CALCFIMS="${launcher} -n 1"
+
     export NTHREADS_SNOWANL=${NTHREADSmax}
     export APRUN_SNOWANL="${APRUN_default}"
 

env/WCOSS2.env

@@ -34,10 +34,6 @@ if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
     export sys_tp="wcoss2"
     export launcher_PREP="mpiexec"
 
-elif [[ "${step}" = "prepsnowobs" ]]; then
-
-    export APRUN_CALCFIMS="${APRUN_default}"
-
 elif [[ "${step}" = "prep_emissions" ]]; then
 
     export APRUN="${APRUN_default}"
@@ -92,6 +88,8 @@ elif [[ "${step}" = "prepobsaero" ]]; then
 
 elif [[ "${step}" = "snowanl" ]]; then
 
+    export APRUN_CALCFIMS="${launcher} -n 1"
+
     export NTHREADS_SNOWANL=${NTHREADSmax}
     export APRUN_SNOWANL="${APRUN_default}"
 

jobs/JGDAS_ENKF_ECEN

@@ -29,13 +29,13 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export GPREFIX_ENS="${GDUMP_ENS}.t${gcyc}z."
 
 RUN=${RUN/enkf} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-  COM_ATMOS_ANALYSIS_DET:COM_ATMOS_ANALYSIS_TMPL
+  COMIN_ATMOS_ANALYSIS_DET:COM_ATMOS_ANALYSIS_TMPL
 
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-  COM_ATMOS_ANALYSIS_STAT:COM_ATMOS_ANALYSIS_TMPL
+  COMOUT_ATMOS_ANALYSIS_STAT:COM_ATMOS_ANALYSIS_TMPL
 
 MEMDIR="ensstat" RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-  COM_ATMOS_HISTORY_STAT_PREV:COM_ATMOS_HISTORY_TMPL
+  COMIN_ATMOS_HISTORY_STAT_PREV:COM_ATMOS_HISTORY_TMPL
 
 
 ###############################################################

jobs/rocoto/snowanl.sh

@@ -11,6 +11,14 @@ status=$?
 export job="snowanl"
 export jobid="${job}.$$"
 
+###############################################################
+# setup python path for ioda utilities
+# shellcheck disable=SC2311
+pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python$(detect_py_ver)/"
+gdasappPATH="${HOMEgfs}/sorc/gdas.cd/sorc/iodaconv/src:${pyiodaPATH}"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}:${gdasappPATH}"
+export PYTHONPATH
+
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_SNOW_ANALYSIS"

parm/config/gfs/config.resources

@@ -12,7 +12,7 @@ if (( $# != 1 )); then
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
     echo "stage_ic aerosol_init"
-    echo "prep prepsnowobs prepatmiodaobs"
+    echo "prep prepatmiodaobs"
     echo "atmanlinit atmanlvar atmanlfv3inc atmanlfinal"
     echo "atmensanlinit atmensanlobs atmensanlsol atmensanlletkf atmensanlfv3inc atmensanlfinal"
     echo "snowanl esnowrecen"
@@ -152,13 +152,6 @@ case ${step} in
     memory="${mem_node_max}"
     ;;
 
-  "prepsnowobs")
-    walltime="00:05:00"
-    ntasks=1
-    threads_per_task=1
-    tasks_per_node=1
-    ;;
-
   "prepatmiodaobs")
     walltime="00:30:00"
     ntasks=1

parm/config/gfs/config.snowanl

@@ -19,6 +19,12 @@ export JEDIYAML="${PARMgfs}/gdas/snow/letkfoi/letkfoi.yaml.j2"
 export SNOWDEPTHVAR="snodl"
 export BESTDDEV="30."  # Background Error Std. Dev. for LETKFOI
 
+# Process IMS snowcover into snow depth
+export IMS_OBS_LIST="${PARMgfs}/gdas/snow/prep/prep_ims.yaml.j2"
+export CALCFIMSEXE="${EXECgfs}/calcfIMS.exe"
+export FIMS_NML_TMPL="${PARMgfs}/gdas/snow/prep/fims.nml.j2"
+export IMS2IODACONV="${USHgfs}/imsfv3_scf2ioda.py"
+
 # Name of the executable that applies increment to bkg and its namelist template
 export APPLY_INCR_EXE="${EXECgfs}/apply_incr.exe"
 export APPLY_INCR_NML_TMPL="${PARMgfs}/gdas/snow/letkfoi/apply_incr_nml.j2"

scripts/exgdas_enkf_ecen.sh

@@ -117,37 +117,37 @@ for imem in $(seq 1 $NMEM_ENS); do
    memchar="mem"$(printf %03i $imem)
 
    MEMDIR=${memchar} YMD=${PDY} HH=${cyc} declare_from_tmpl -x \
-      COM_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL
+      COMOUT_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL
 
    MEMDIR=${gmemchar} RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -x \
-      COM_ATMOS_HISTORY_MEM_PREV:COM_ATMOS_HISTORY_TMPL
+      COMIN_ATMOS_HISTORY_MEM_PREV:COM_ATMOS_HISTORY_TMPL
 
-   ${NLN} "${COM_ATMOS_HISTORY_MEM_PREV}/${GPREFIX_ENS}atmf00${FHR}${ENKF_SUFFIX}.nc" "./atmges_${memchar}"
+   ${NLN} "${COMIN_ATMOS_HISTORY_MEM_PREV}/${GPREFIX_ENS}atmf00${FHR}${ENKF_SUFFIX}.nc" "./atmges_${memchar}"
    if [ $DO_CALC_INCREMENT = "YES" ]; then
       if [ $FHR -eq 6 ]; then
-         ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atmanl.nc" "./atmanl_${memchar}"
+         ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atmanl.nc" "./atmanl_${memchar}"
       else
-         ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atma00${FHR}.nc" "./atmanl_${memchar}"
+         ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atma00${FHR}.nc" "./atmanl_${memchar}"
       fi
    fi
-   mkdir -p "${COM_ATMOS_ANALYSIS_MEM}"
+   mkdir -p "${COMOUT_ATMOS_ANALYSIS_MEM}"
    if [ $FHR -eq 6 ]; then
-      ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atminc.nc" "./atminc_${memchar}"
+      ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atminc.nc" "./atminc_${memchar}"
    else
-      ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atmi00${FHR}.nc" "./atminc_${memchar}"
+      ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}atmi00${FHR}.nc" "./atminc_${memchar}"
    fi
    if [[ $RECENTER_ENKF = "YES" ]]; then
       if [ $DO_CALC_INCREMENT = "YES" ]; then
          if [ $FHR -eq 6 ]; then
-            ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratmanl.nc" "./ratmanl_${memchar}"
+            ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratmanl.nc" "./ratmanl_${memchar}"
          else
-            ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratma00${FHR}.nc" "./ratmanl_${memchar}"
+            ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratma00${FHR}.nc" "./ratmanl_${memchar}"
          fi
      else
          if [ $FHR -eq 6 ]; then
-            ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratminc.nc" "./ratminc_${memchar}"
+            ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratminc.nc" "./ratminc_${memchar}"
          else
-            ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratmi00${FHR}.nc" "./ratminc_${memchar}"
+            ${NLN} "${COMOUT_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}ratmi00${FHR}.nc" "./ratminc_${memchar}"
          fi
      fi
    fi
@@ -156,9 +156,9 @@ done
 if [ $DO_CALC_INCREMENT = "YES" ]; then
    # Link ensemble mean analysis
    if [ $FHR -eq 6 ]; then
-      ${NLN} "${COM_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atmanl.ensmean.nc" "./atmanl_ensmean"
+      ${NLN} "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atmanl.ensmean.nc" "./atmanl_ensmean"
    else
-      ${NLN} "${COM_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atma00${FHR}.ensmean.nc" "./atmanl_ensmean"
+      ${NLN} "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atma00${FHR}.ensmean.nc" "./atmanl_ensmean"
    fi
 
    # Compute ensemble mean analysis
@@ -176,9 +176,9 @@ if [ $DO_CALC_INCREMENT = "YES" ]; then
 else
    # Link ensemble mean increment
    if [ $FHR -eq 6 ]; then
-      ${NLN} "${COM_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atminc.ensmean.nc" "./atminc_ensmean"
+      ${NLN} "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atminc.ensmean.nc" "./atminc_ensmean"
    else
-      ${NLN} "${COM_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atmi00${FHR}.ensmean.nc" "./atminc_ensmean"
+      ${NLN} "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX_ENS}atmi00${FHR}.ensmean.nc" "./atminc_ensmean"
    fi
 
    # Compute ensemble mean increment
@@ -195,8 +195,8 @@ else
    export err=$?; err_chk
 
    # If available, link to ensemble mean guess.  Otherwise, compute ensemble mean guess
-   if [[ -s "${COM_ATMOS_HISTORY_STAT_PREV}/${GPREFIX_ENS}atmf00${FHR}.ensmean.nc" ]]; then
-       ${NLN} "${COM_ATMOS_HISTORY_STAT_PREV}/${GPREFIX_ENS}atmf00${FHR}.ensmean.nc" "./atmges_ensmean"
+   if [[ -s "${COMIN_ATMOS_HISTORY_STAT_PREV}/${GPREFIX_ENS}atmf00${FHR}.ensmean.nc" ]]; then
+       ${NLN} "${COMIN_ATMOS_HISTORY_STAT_PREV}/${GPREFIX_ENS}atmf00${FHR}.ensmean.nc" "./atmges_ensmean"
    else
        DATAPATH="./"
        ATMGESNAME="atmges"
@@ -231,11 +231,11 @@ if [ $RECENTER_ENKF = "YES" ]; then
 
    # GSI EnVar analysis
    if [ $FHR -eq 6 ]; then
-     ATMANL_GSI="${COM_ATMOS_ANALYSIS_DET}/${APREFIX}atmanl.nc"
-     ATMANL_GSI_ENSRES="${COM_ATMOS_ANALYSIS_DET}/${APREFIX}atmanl.ensres.nc"
+     ATMANL_GSI="${COMIN_ATMOS_ANALYSIS_DET}/${APREFIX}atmanl.nc"
+     ATMANL_GSI_ENSRES="${COMIN_ATMOS_ANALYSIS_DET}/${APREFIX}atmanl.ensres.nc"
    else
-     ATMANL_GSI="${COM_ATMOS_ANALYSIS_DET}/${APREFIX}atma00${FHR}.nc"
-     ATMANL_GSI_ENSRES="${COM_ATMOS_ANALYSIS_DET}/${APREFIX}atma00${FHR}.ensres.nc"
+     ATMANL_GSI="${COMIN_ATMOS_ANALYSIS_DET}/${APREFIX}atma00${FHR}.nc"
+     ATMANL_GSI_ENSRES="${COMIN_ATMOS_ANALYSIS_DET}/${APREFIX}atma00${FHR}.ensres.nc"
    fi
 
    # if we already have a ensemble resolution GSI analysis then just link to it