Convert IC staging job into a proper j-job

jobs/JGLOBAL_STAGE_IC

@@ -0,0 +1,16 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage_ic"
+
+
+# Execute the Script
+"${HOMEgfs}/scripts/exglobal_stage_ic.sh"
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || (echo "${DATAROOT} does not exist. ABORT!"; exit 1)
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
+exit 0

jobs/rocoto/stage_ic.sh

@@ -0,0 +1,18 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+# Source FV3GFS workflow modules
+. "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+[[ "${status}" -ne 0 ]] && exit "${status}"
+
+export job="stage_ic"
+export jobid="${job}.$$"
+
+# Execute the JJOB
+"${HOMEgfs}"/jobs/JGLOBAL_STAGE_IC
+status=$?
+
+
+exit "${status}"

jobs/rocoto/coupled_ic.sh → scripts/exglobal_stage_ic.sh

@@ -7,12 +7,12 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit ${status}
 
-export job="coupled_ic"
+export job="stage_ic"
 export jobid="${job}.$$"
 
 # Execute the JJOB
 
-source "${HOMEgfs}/ush/jjob_header.sh" -e "coupled_ic" -c "base coupled_ic"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage_ic"
 
 # Locally scoped variables and functions
 GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
@@ -36,16 +36,16 @@ source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/gfs_ctrl.
 target="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
 ${NCP} "${source}" "${target}"
 rc=$?
-[[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-err=$((err + rc))
+(( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+(( err = err + rc ))
 for ftype in gfs_data sfc_data; do
   for tt in $(seq 1 6); do
     source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/${ftype}.tile${tt}.nc"
     target="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
     ${NCP} "${source}" "${target}"
     rc=$?
-    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-    err=$((err + rc))
+    (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+    (( err = err + rc ))
   done
 done
 
@@ -57,8 +57,8 @@ if [[ "${DO_OCN:-}" = "YES" ]]; then
   target="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res.nc"
   ${NCP} "${source}" "${target}"
   rc=$?
-  [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-  err=$((err + rc))
+  (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+  (( err = err + rc ))
   case "${OCNRES}" in
     "500" | "100")  # Only 5 degree or 1 degree ocean does not have MOM.res_[1-4].nc files
     ;;
@@ -69,15 +69,15 @@ if [[ "${DO_OCN:-}" = "YES" ]]; then
           target="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
           ${NCP} "${source}" "${target}"
           rc=$?
-          [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-          err=$((err + rc))
+          (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+          (( err = err + rc ))
         fi
       done
     ;;
     *)
       echo "FATAL ERROR: Unsupported ocean resolution ${OCNRES}"
       rc=1
-      err=$((err + rc))
+      (( err = err + rc ))
     ;;
   esac
 fi
@@ -91,8 +91,8 @@ if [[ "${DO_ICE:-}" = "YES" ]]; then
   target="${COM_ICE_RESTART}/${PDY}.${cyc}0000.cice_model.res.nc"
   ${NCP} "${source}" "${target}"
   rc=$?
-  [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-  err=$((err + rc))
+  (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+  (( err = err + rc ))
 fi
 
 # Stage the WW3 initial conditions to ROTDIR (warm start; TODO: these should be placed in $RUN.$gPDY/$gcyc)
@@ -104,8 +104,8 @@ if [[ "${DO_WAVE:-}" = "YES" ]]; then
     target="${COM_WAVE_RESTART}/${PDY}.${cyc}0000.restart.${grdID}"
     ${NCP} "${source}" "${target}"
     rc=$?
-    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-    err=$((err + rc))
+    (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+    (( err = err + rc ))
   done
 fi
 

workflow/applications/gfs_forecast_only.py

@@ -15,7 +15,7 @@ def _get_app_configs(self):
         Returns the config_files that are involved in the forecast-only app
         """
 
-        configs = ['coupled_ic', 'fcst', 'arch']
+        configs = ['stage_ic', 'fcst', 'arch']
 
         if self.do_atm:
             configs += ['post', 'vrfy']
@@ -65,7 +65,7 @@ def get_task_names(self):
         This is the place where that order is set.
         """
 
-        tasks = ['coupled_ic']
+        tasks = ['stage_ic']
 
         if self.do_aero:
             tasks += ['aerosol_init']

workflow/rocoto/gfs_tasks.py

@@ -15,9 +15,9 @@ def _is_this_a_gdas_task(cdump, task_name):
             raise TypeError(f'{task_name} must be part of the "enkfgdas" cycle and not {cdump}')
 
     # Specific Tasks begin here
-    def coupled_ic(self):
+    def stage_ic(self):
 
-        cpl_ic = self._configs['coupled_ic']
+        cpl_ic = self._configs['stage_ic']
 
         deps = []
 
@@ -72,8 +72,8 @@ def coupled_ic(self):
 
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
-        resources = self.get_resource('coupled_ic')
-        task = create_wf_task('coupled_ic', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+        resources = self.get_resource('stage_ic')
+        task = create_wf_task('stage_ic', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
 
         return task
 
@@ -472,7 +472,7 @@ def fcst(self):
     def _fcst_forecast_only(self):
         dependencies = []
 
-        dep_dict = {'type': 'task', 'name': f'{self.cdump}coupled_ic'}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}stage_ic'}
         dependencies.append(rocoto.add_dependency(dep_dict))
 
         if self.app_config.do_wave and self.cdump in self.app_config.wave_cdumps:

workflow/rocoto/tasks.py

@@ -10,7 +10,7 @@
 
 class Tasks:
     SERVICE_TASKS = ['arch', 'earc']
-    VALID_TASKS = ['aerosol_init', 'coupled_ic',
+    VALID_TASKS = ['aerosol_init', 'stage_ic',
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch',
                    'atmanlinit', 'atmanlrun', 'atmanlfinal',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',