Add a job to prepare ioda format dumps for use in atmospheric UFS-DA

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.sh}
+${EXSCRIPT} "${PDY}${cyc}" "${CDUMP}" "${DMPDIR}" "${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 +1,18 @@
+#! /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}.$$"
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_ATM_PREP_IODA_OBS"
+status=$?
+exit "${status}"

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.sh"
+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

sorc/link_workflow.sh

@@ -203,6 +203,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   cd "${HOMEgfs}/ush" || exit 1
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda"                              .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py"                     .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.sh"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
 fi
 

workflow/applications/gfs_cycled.py

@@ -37,7 +37,7 @@ def _get_app_configs(self):
         configs = ['prep']
 
         if self.do_jediatmvar:
-            configs += ['atmanlinit', 'atmanlrun', 'atmanlfinal']
+            configs += ['prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             configs += ['anal', 'analdiag']
 
@@ -109,7 +109,7 @@ def get_task_names(self):
         gdas_gfs_common_cleanup_tasks = ['arch']
 
         if self.do_jediatmvar:
-            gdas_gfs_common_tasks_before_fcst += ['atmanlinit', 'atmanlrun', 'atmanlfinal']
+            gdas_gfs_common_tasks_before_fcst += ['prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal']
         else:
             gdas_gfs_common_tasks_before_fcst += ['anal']
 

workflow/rocoto/gfs_tasks.py

@@ -245,11 +245,23 @@ def analdiag(self):
 
         return task
 
-    def atmanlinit(self):
+    def prepatmiodaobs(self):
 
         deps = []
         dep_dict = {'type': 'task', 'name': f'{self.cdump}prep'}
         deps.append(rocoto.add_dependency(dep_dict))
+        dependencies = rocoto.create_dependency(dep=deps)
+
+        resources = self.get_resource('prepatmiodaobs')
+        task = create_wf_task('prepatmiodaobs', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+
+        return task
+
+    def atmanlinit(self):
+
+        deps = []
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}prepatmiodaobs'}
+        deps.append(rocoto.add_dependency(dep_dict))
         if self.app_config.do_hybvar:
             dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
             deps.append(rocoto.add_dependency(dep_dict))
@@ -993,7 +1005,7 @@ def eupd(self):
 
     def atmensanlinit(self):
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.cdump.replace("enkf","")}prep'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump.replace("enkf","")}prepatmiodaobs'}
         deps.append(rocoto.add_dependency(dep_dict))
         dep_dict = {'type': 'metatask', 'name': 'enkfgdasepmn', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))

workflow/rocoto/tasks.py

@@ -12,7 +12,7 @@ class Tasks:
     SERVICE_TASKS = ['arch', 'earc']
     VALID_TASKS = ['aerosol_init', 'coupled_ic',
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch',
-                   'atmanlinit', 'atmanlrun', 'atmanlfinal',
+                   'prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',