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

.gitignore

@@ -144,6 +144,7 @@ ush/make_tif.sh
 ush/month_name.sh
 ush/imsfv3_scf2ioda.py
 ush/atparse.bash
+ush/run_bufr2ioda.py
 
 # version files
 versions/build.ver

Externals.cfg

@@ -15,7 +15,7 @@ protocol = git
 required = True
 
 [gfs-utils]
-hash = 8965258
+hash = a283262
 local_path = sorc/gfs_utils.fd
 repo_url = https://github.com/NOAA-EMC/gfs-utils
 protocol = git
@@ -57,7 +57,7 @@ protocol = git
 required = False
 
 [GDASApp]
-hash = 2774a10
+hash = ac8fdb1
 local_path = sorc/gdas.cd
 repo_url = https://github.com/NOAA-EMC/GDASApp.git
 protocol = git

jobs/JGLOBAL_ATM_PREP_IODA_OBS

@@ -0,0 +1,36 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "prepatmiodaobs" -c "base prepatmiodaobs"
+
+##############################################
+# Set variables used in the script
+##############################################
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
+
+
+###############################################################
+# Run relevant script
+EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.py}
+${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
+status=$?
+[[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/rocoto/prepatmiodaobs.sh

@@ -0,0 +1,25 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="prepatmobs"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow and ioda utilities
+wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
+PYIODALIB="${HOMEgfs}/sorc/gdas.cd/build/lib/python3.7"
+PYTHONPATH="${PYIODALIB}:${wxflowPATH}:${PYTHONPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATM_PREP_IODA_OBS"
+status=$?
+exit "${status}"

parm/config/gfs/config.coupled_ic

@@ -21,7 +21,7 @@ case "${CASE}" in
     export CPL_WAVIC=GEFSwave20210528v2
     ;;
   "C768")
-    export CPL_ATMIC=HR1
+    export CPL_ATMIC=HR2
     export CPL_ICEIC=HR1
     export CPL_OCNIC=HR1
     export CPL_WAVIC=HR1

parm/config/gfs/config.prepatmiodaobs

@@ -0,0 +1,14 @@
+#! /usr/bin/env bash
+
+########## config.prepatmiodaobs ##########
+# Atm Obs Prep specific
+
+echo "BEGIN: config.prepatmiodaobs"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" prepatmiodaobs
+
+export BUFR2IODASH="${HOMEgfs}/ush/run_bufr2ioda.py"
+export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"
+
+echo "END: config.prepatmiodaobs"

parm/config/gfs/config.resources

@@ -9,7 +9,7 @@ if [[ $# -ne 1 ]]; then
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
     echo "coupled_ic aerosol_init"
-    echo "prep preplandobs"
+    echo "prep preplandobs prepatmiodaobs"
     echo "atmanlinit atmanlrun atmanlfinal"
     echo "atmensanlinit atmensanlrun atmensanlfinal"
     echo "landanl"
@@ -73,6 +73,13 @@ elif [[ "${step}" = "preplandobs" ]]; then
     npe_node_preplandobs=1
     export npe_node_preplandobs
 
+elif [[ "${step}" = "prepatmiodaobs" ]]; then
+    export wtime_prepatmiodaobs="00:10:00"
+    export npe_prepatmiodaobs=1
+    export nth_prepatmiodaobs=1
+    npe_node_prepatmiodaobs=$(echo "${npe_node_max} / ${nth_prepatmiodaobs}" | bc)
+    export npe_node_prepatmiodaobs
+
 elif [[ "${step}" = "aerosol_init" ]]; then
     export wtime_aerosol_init="00:05:00"
     export npe_aerosol_init=1
@@ -249,18 +256,23 @@ elif [[ "${step}" = "aeroanlinit" ]]; then
 
    # below lines are for creating JEDI YAML
    case ${CASE} in
-     C768)
+      C768)
         layout_x=8
         layout_y=8
         ;;
       C384)
         layout_x=8
         layout_y=8
         ;;
-     C192 | C96 | C48)
+      C192 | C96)
         layout_x=8
         layout_y=8
         ;;
+      C48 )
+        # this case is for testing only
+        layout_x=1
+        layout_y=1
+        ;;
       *)
           echo "FATAL ERROR: Resolution not supported for aerosol analysis'"
           exit 1
@@ -279,18 +291,23 @@ elif [[ "${step}" = "aeroanlinit" ]]; then
 elif [[ "${step}" = "aeroanlrun" ]]; then
 
    case ${CASE} in
-     C768)
+      C768)
         layout_x=8
         layout_y=8
         ;;
       C384)
         layout_x=8
         layout_y=8
         ;;
-     C192 | C96 | C48)
+      C192 | C96)
         layout_x=8
         layout_y=8
         ;;
+      C48 )
+        # this case is for testing only
+        layout_x=1
+        layout_y=1
+        ;;
       *)
           echo "FATAL ERROR: Resolution ${CASE} is not supported, ABORT!"
           exit 1

parm/config/gfs/config.ufs

@@ -171,7 +171,7 @@ case "${fv3_res}" in
         export WRITE_GROUP=2
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
         export WRITE_GROUP_GFS=4
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20
+        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20 #Note this should be 10 for WCOSS2
         ;;
     "C1152")
         export DELTIM=120