From 1842c22f4f4afe945e32382dec6f48a2b2830123 Mon Sep 17 00:00:00 2001
From: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com>
Date: Tue, 12 Sep 2023 09:21:11 -0400
Subject: [PATCH] Convert IC staging job into a proper j-job (#1806)

---
 jobs/JGLOBAL_STAGE_IC                         | 16 ++++++++++++
 jobs/rocoto/stage_ic.sh                       | 18 +++++++++++++
 parm/config/gfs/config.resources              | 12 ++++-----
 .../{config.coupled_ic => config.stage_ic}    |  8 +++---
 .../exglobal_stage_ic.sh                      | 25 ++++++-------------
 workflow/applications/gfs_forecast_only.py    |  4 +--
 workflow/rocoto/gfs_tasks.py                  | 10 ++++----
 workflow/rocoto/tasks.py                      |  2 +-
 8 files changed, 59 insertions(+), 36 deletions(-)
 create mode 100755 jobs/JGLOBAL_STAGE_IC
 create mode 100755 jobs/rocoto/stage_ic.sh
 rename parm/config/gfs/{config.coupled_ic => config.stage_ic} (79%)
 rename jobs/rocoto/coupled_ic.sh => scripts/exglobal_stage_ic.sh (83%)

diff --git a/jobs/JGLOBAL_STAGE_IC b/jobs/JGLOBAL_STAGE_IC
new file mode 100755
index 0000000000..437c8f40a0
--- /dev/null
+++ b/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
diff --git a/jobs/rocoto/stage_ic.sh b/jobs/rocoto/stage_ic.sh
new file mode 100755
index 0000000000..5e7b3395d2
--- /dev/null
+++ b/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}"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 17a1423589..a73d702eac 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -8,7 +8,7 @@ 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 "stage_ic aerosol_init"
     echo "prep preplandobs prepatmiodaobs"
     echo "atmanlinit atmanlrun atmanlfinal"
     echo "atmensanlinit atmensanlrun atmensanlfinal"
@@ -772,12 +772,12 @@ elif [[ ${step} = "arch" || ${step} = "earc" || ${step} = "getic" ]]; then
       eval "export memory_${step}=50GB"
     fi
 
-elif [[ ${step} = "coupled_ic" ]]; then
+elif [[ ${step} = "stage_ic" ]]; then
 
-    export wtime_coupled_ic="00:15:00"
-    export npe_coupled_ic=1
-    export npe_node_coupled_ic=1
-    export nth_coupled_ic=1
+    export wtime_stage_ic="00:15:00"
+    export npe_stage_ic=1
+    export npe_node_stage_ic=1
+    export nth_stage_ic=1
     export is_exclusive=True
 
 elif [[ "${step}" = "atmensanlinit" ]]; then
diff --git a/parm/config/gfs/config.coupled_ic b/parm/config/gfs/config.stage_ic
similarity index 79%
rename from parm/config/gfs/config.coupled_ic
rename to parm/config/gfs/config.stage_ic
index bafd4e111d..4e29c3306e 100644
--- a/parm/config/gfs/config.coupled_ic
+++ b/parm/config/gfs/config.stage_ic
@@ -1,11 +1,11 @@
 #! /usr/bin/env bash
 
-########## config.coupled_ic ##########
+########## config.stage_ic ##########
 
-echo "BEGIN: config.coupled_ic"
+echo "BEGIN: config.stage_ic"
 
 # Get task specific resources
-source "${EXPDIR}/config.resources" coupled_ic
+source "${EXPDIR}/config.resources" stage_ic
 
 case "${CASE}" in
   "C48" | "C96")
@@ -32,4 +32,4 @@ case "${CASE}" in
     ;;
 esac
 
-echo "END: config.coupled_ic"
+echo "END: config.stage_ic"
diff --git a/jobs/rocoto/coupled_ic.sh b/scripts/exglobal_stage_ic.sh
similarity index 83%
rename from jobs/rocoto/coupled_ic.sh
rename to scripts/exglobal_stage_ic.sh
index 8b0088834d..7ea48fe599 100755
--- a/jobs/rocoto/coupled_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -2,19 +2,8 @@
 
 source "${HOMEgfs}/ush/preamble.sh"
 
-# Source FV3GFS workflow modules
-. ${HOMEgfs}/ush/load_fv3gfs_modules.sh
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
-
-export job="coupled_ic"
-export jobid="${job}.$$"
-
-# Execute the JJOB
-
-source "${HOMEgfs}/ush/jjob_header.sh" -e "coupled_ic" -c "base coupled_ic"
-
 # Locally scoped variables and functions
+# shellcheck disable=SC2153
 GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
 gPDY="${GDATE:0:8}"
 gcyc="${GDATE:8:2}"
@@ -36,7 +25,7 @@ source="${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}"
+(( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
 err=$((err + rc))
 for ftype in gfs_data sfc_data; do
   for tt in $(seq 1 6); do
@@ -44,7 +33,7 @@ for ftype in gfs_data sfc_data; do
     target="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
     ${NCP} "${source}" "${target}"
     rc=$?
-    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+    (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
     err=$((err + rc))
   done
 done
@@ -57,7 +46,7 @@ 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}"
+  (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
   err=$((err + rc))
   case "${OCNRES}" in
     "500" | "100")  # Only 5 degree or 1 degree ocean does not have MOM.res_[1-4].nc files
@@ -69,7 +58,7 @@ if [[ "${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}"
+          (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
           err=$((err + rc))
         fi
       done
@@ -91,7 +80,7 @@ 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}"
+  (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
   err=$((err + rc))
 fi
 
@@ -104,7 +93,7 @@ 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}"
+    (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
     err=$((err + rc))
   done
 fi
diff --git a/workflow/applications/gfs_forecast_only.py b/workflow/applications/gfs_forecast_only.py
index de01caa6e2..e6d1ab35a2 100644
--- a/workflow/applications/gfs_forecast_only.py
+++ b/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']
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index 8f91abae75..b9ba4a29ed 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/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
 
@@ -484,7 +484,7 @@ 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:
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index 1eba5a2652..b9716c938e 100644
--- a/workflow/rocoto/tasks.py
+++ b/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',
                    'prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',