Refactor marine ensemble recentering script and move to GW from GDASApp

.gitignore

@@ -143,7 +143,6 @@ sorc/ocnicepost.fd
 #------------------------------
 # jobs symlinks
 # scripts symlinks
-scripts/exgdas_global_marine_analysis_ecen.py
 scripts/exglobal_prep_ocean_obs.py
 # ush symlinks
 ush/bufr2ioda_insitu_profile_argo.py

dev/jobs/ocnanalecen.sh → dev/jobs/marineanlecen.sh

@@ -10,7 +10,7 @@ if [[ ${status} -ne 0 ]]; then
     exit "${status}"
 fi
 
-export job="ocnanalecen"
+export job="marineanlecen"
 export jobid="${job}.$$"
 
 ###############################################################
@@ -20,6 +20,6 @@ export PYTHONPATH
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_ANALYSIS_ECEN
 status=$?
 exit "${status}"

dev/parm/config/gcafs/config.resources

@@ -28,7 +28,7 @@ if (( $# != 1 )); then
     echo "waveinit waveprep wavepostsbs wavepostbndpnt wavepostbndpntbll wavepostpnt"
     echo "wavegempak waveawipsbulls waveawipsgridded"
     echo "postsnd awips gempak npoess"
-    echo "marineanlinit prepoceanobs marinebmat marineanlvar ocnanalecen marineanalletkf marineanlchkpt marineanlfinal ocnanalvrfy"
+    echo "marineanlinit prepoceanobs marinebmat marineanlvar marineanlecen marineanalletkf marineanlchkpt marineanlfinal ocnanalvrfy"
     exit 1
 
 fi
@@ -590,7 +590,7 @@ case ${step} in
     tasks_per_node=$(( max_tasks_per_node / 2 ))
     ;;
 
-  "ocnanalecen")
+  "marineanlecen")
     ntasks=16
     case ${OCNRES} in
       "025")

dev/parm/config/gfs/config.marineanl.j2

@@ -7,6 +7,7 @@ echo "BEGIN: config.marineanl"
 
 export JEDI_CONFIG_YAML_BMAT="${PARMgfs}/gdas/soca_bmat_jedi_config.yaml.j2"
 export JEDI_CONFIG_YAML_ANALYSIS="${PARMgfs}/gdas/soca_analysis_jedi_config.yaml.j2"
+export JEDI_CONFIG_YAML_ECEN="${PARMgfs}/gdas/soca/soca_ecen_jedi_config.yaml.j2"
 export JCB_ALGO_YAML_VAR="{{ JCB_ALGO_YAML_VAR }}"
 
 export MARINE_OBS_YAML_DIR="${PARMgfs}/gdas/soca/obs/config"
@@ -19,9 +20,12 @@ export SOCA_ENS_BKG_STAGE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_ens_bkg_stage.yam
 export SOCA_FIX_YAML_TMPL="${PARMgfs}/gdas/soca/soca_fix_stage_${OCNRES}.yaml.j2"
 export MARINE_UTILITY_YAML_TMPL="${PARMgfs}/gdas/soca/soca_utils_stage.yaml.j2"
 export MARINE_ENSDA_STAGE_BKG_YAML_TMPL="${PARMgfs}/gdas/soca/ensda/stage_ens_mem.yaml.j2"
+export MARINE_BMAT_FINALIZE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_bmat_finalize.yaml.j2"
 export MARINE_DET_STAGE_BKG_YAML_TMPL="${PARMgfs}/gdas/soca/soca_det_bkg_stage.yaml.j2"
 export MARINE_DET_STAGE_FILES_YAML_TMPL="${PARMgfs}/gdas/soca/soca_det_files_stage.yaml.j2"
 export MARINE_DET_FINALIZE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_det_finalize.yaml.j2"
+export MARINE_ECEN_STAGE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_ecen_stage.yaml.j2"
+export MARINE_ECEN_FINALIZE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_ecen_finalize.yaml.j2"
 export MARINE_JCB_GDAS_ALGO="${PARMgfs}/gdas/jcb-gdas/algorithm/marine"
 export MARINE_JCB_GDAS_OBS="${PARMgfs}/gdas/jcb-gdas/observations/marine"
 

dev/parm/config/gfs/config.marineanlecen

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+########## config.marineanlecen ##########
+# Ocn Analysis specific
+
+echo "BEGIN: config.marineanlecen"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" marineanlecen
+
+echo "END: config.marineanlecen"

dev/parm/config/gfs/config.resources

@@ -26,7 +26,7 @@ if (( $# != 1 )); then
     echo "waveinit waveprep wavepostsbs wavepostbndpnt wavepostbndpntbll wavepostpnt"
     echo "wavegempak waveawipsbulls waveawipsgridded"
     echo "postsnd awips gempak npoess"
-    echo "marineanlinit prepoceanobs marinebmatinit marinebmat marineanlvar ocnanalecen marineanalletkf marineanlchkpt marineanlfinal ocnanalvrfy"
+    echo "marineanlinit prepoceanobs marinebmatinit marinebmat marineanlvar marineanlecen marineanalletkf marineanlchkpt marineanlfinal ocnanalvrfy"
     exit 1
 
 fi
@@ -568,7 +568,7 @@ case ${step} in
     tasks_per_node=$(( max_tasks_per_node / 2 ))
     ;;
 
-  "ocnanalecen")
+  "marineanlecen")
     ntasks=16
     walltime="00:10:00"
     case ${OCNRES} in

dev/parm/config/gfs/config.resources.GAEAC6

@@ -76,7 +76,7 @@ case ${step} in
     esac
     ;;
 
-  "ocnanalecen")
+  "marineanlecen")
     case ${OCNRES} in
       "025")
         ntasks=288

dev/workflow/applications/gfs_cycled.py

@@ -119,7 +119,7 @@ def _get_app_configs(self, run):
             if options['do_letkf_ocn']:
                 configs += ['marineanlletkf']
             if options['do_hybvar']:
-                configs += ['ocnanalecen']
+                configs += ['marineanlecen']
             configs += ['marineanlchkpt', 'marineanlfinal']
 
         if options['do_ocean'] or options['do_ice']:
@@ -255,12 +255,7 @@ def get_task_names(self):
                     task_names[run] += ['anal', 'analcalc']
 
                 if options['do_jediocnvar']:
-                    task_names[run] += ['prepoceanobs', 'marineanlinit', 'marinebmatinit', 'marinebmat', 'marineanlvar']
-                    if options['do_letkf_ocn']:
-                        task_names[run] += ['marineanlletkf']
-                    if options['do_hybvar']:
-                        task_names[run] += ['ocnanalecen']
-                    task_names[run] += ['marineanlchkpt', 'marineanlfinal']
+                    task_names[run] += ['prepoceanobs', 'marineanlinit', 'marinebmatinit', 'marinebmat', 'marineanlvar', 'marineanlchkpt', 'marineanlfinal']
 
                 task_names[run] += ['sfcanl']
 
@@ -398,6 +393,12 @@ def get_task_names(self):
                     task_names[run].append('echgres') if 'gdas' in run else 0
                     task_names[run] += ['ediag']
 
+                if options['do_jediocnvar']:
+                    if options['do_letkf_ocn']:
+                        task_names[run] += ['marineanlletkf']
+                    if options['do_hybvar']:
+                        task_names[run] += ['marineanlecen']
+
                 task_names[run].append('esnowanl') if options['do_jedisnowda'] else 0
                 task_names[run].append('efcs') if 'gdas' in run else 0
                 task_names[run].append('epos') if 'gdas' in run else 0

dev/workflow/rocoto/gfs_tasks.py

@@ -705,9 +705,9 @@ def prepoceanobs(self):
     def marineanlletkf(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.run}_prepoceanobs'}
+        dep_dict = {'type': 'task', 'name': f"{self.run.replace('enkf','')}_prepoceanobs"}
         deps.append(rocoto.add_dependency(dep_dict))
-        dep_dict = {'type': 'task', 'name': f'{self.run}_marinebmat'}
+        dep_dict = {'type': 'task', 'name': f"{self.run.replace('enkf','')}_marinebmat"}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
@@ -834,22 +834,22 @@ def marineanlvar(self):
 
         return task
 
-    def ocnanalecen(self):
+    def marineanlecen(self):
 
         # can run in parallel with marinebmat
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.run}_marinebmatinit'}
+        dep_dict = {'type': 'task', 'name': f"{self.run.replace('enkf','')}_marinebmatinit"}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)
 
-        resources = self.get_resource('ocnanalecen')
-        task_name = f'{self.run}_ocnanalecen'
+        resources = self.get_resource('marineanlecen')
+        task_name = f'{self.run}_marineanlecen'
         task_dict = {'task_name': task_name,
                      'resources': resources,
                      'dependency': dependencies,
                      'envars': self.envars,
                      'cycledef': self.run.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/dev/jobs/ocnanalecen.sh',
+                     'command': f'{self.HOMEgfs}/dev/jobs/marineanlecen.sh',
                      'job_name': f'{self.pslot}_{task_name}_@H',
                      'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
                      'maxtries': '&MAXTRIES;'
@@ -865,7 +865,7 @@ def marineanlchkpt(self):
         dep_dict = {'type': 'task', 'name': f'{self.run}_marineanlvar'}
         deps.append(rocoto.add_dependency(dep_dict))
         if self.options['do_hybvar_ocn']:
-            dep_dict = {'type': 'task', 'name': f'{self.run}_ocnanalecen'}
+            dep_dict = {'type': 'task', 'name': f'enkf{self.run}_marineanlecen'}
             deps.append(rocoto.add_dependency(dep_dict))
         if self.options['do_mergensst']:
             data = f'&ROTDIR;/{self.run}.@Y@m@d/@H/atmos/{self.run}.t@Hz.sfcanl.nc'
@@ -2780,7 +2780,7 @@ def efcs(self):
         dep_dict = {'type': 'task', 'name': f'{self.run}_esfc'}
         deps.append(rocoto.add_dependency(dep_dict))
         if self.options['do_hybvar_ocn']:
-            dep_dict = {'type': 'task', 'name': f'{self.run.replace("enkf", "")}_ocnanalecen'}
+            dep_dict = {'type': 'task', 'name': f'{self.run}_marineanlecen'}
             deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
         dep_dict = {'type': 'task', 'name': f'{self.run}_stage_ic'}
@@ -2964,7 +2964,7 @@ def earc_tars(self):
             dep_dict = {'type': 'metatask', 'name': f'{self.run}_ecmn'}
             deps.append(rocoto.add_dependency(dep_dict))
             if self._base.get('DOHYBVAR_OCN', True):
-                dep_dict = {'type': 'task', 'name': f'gfs_ocnanalecen'}
+                dep_dict = {'type': 'task', 'name': f'enkfgfs_marineanlecen'}
                 deps.append(rocoto.add_dependency(dep_dict))
                 dep_dict = {'type': 'task', 'name': f'gfs_marineanlfinal'}
                 deps.append(rocoto.add_dependency(dep_dict))

dev/workflow/rocoto/tasks.py

@@ -19,7 +19,7 @@ class Tasks:
                    'prepatmiodaobs', 'atmanlinit', 'atmanlvar', 'atmanlfv3inc', 'atmanlfinal',
                    'prep_emissions', 'prepoceanobs',
                    'marineanlinit', 'marineanlletkf', 'marinebmatinit', 'marinebmat', 'marineanlvar',
-                   'ocnanalecen', 'marineanlchkpt', 'marineanlfinal', 'ocnanalvrfy',
+                   'marineanlecen', 'marineanlchkpt', 'marineanlfinal', 'ocnanalvrfy',
                    'eobs', 'epos', 'esfc', 'eupd',
                    'earc_vrfy', 'earc_tars', 'ecen', 'echgres', 'ediag', 'efcs',
                    'atmensanlinit', 'atmensanlobs', 'atmensanlsol', 'atmensanlletkf', 'atmensanlfv3inc', 'atmensanlfinal', 'atmos_ensstat',

env/GAEAC5.env

@@ -135,9 +135,9 @@ case ${step} in
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEANLVAR="${APRUN_default}"
  ;;
- "ocnanalecen")
+ "marineanlecen")
 
-    export APRUN_OCNANALECEN="${APRUN_default}"
+    export APRUN_MARINEANLECEN="${APRUN_default}"
  ;;
  "marineanlchkpt")
 

env/GAEAC6.env

@@ -135,9 +135,9 @@ case ${step} in
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEANLVAR="${APRUN_default}"
  ;;
- "ocnanalecen")
+ "marineanlecen")
 
-    export APRUN_OCNANALECEN="${APRUN_default}"
+    export APRUN_MARINEANLECEN="${APRUN_default}"
  ;;
  "marineanlchkpt")
 

env/HERA.env

@@ -154,10 +154,10 @@ elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUN_MARINEANLOBSSTATS="${launcher} -n 1"
 
-elif [[ "${step}" = "ocnanalecen" ]]; then
+elif [[ "${step}" = "marineanlecen" ]]; then
 
-    export NTHREADS_OCNANALECEN=${NTHREADSmax}
-    export APRUN_OCNANALECEN="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANALECEN}"
+    export NTHREADS_MARINEANLECEN=${NTHREADSmax}
+    export APRUN_MARINEANLECEN="${APRUN_default} --cpus-per-task=${NTHREADS_MARINEANLECEN}"
 
 elif [[ "${step}" = "marineanlletkf" ]]; then
 

env/HERCULES.env

@@ -141,9 +141,9 @@ case ${step} in
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEANLVAR="${APRUN_default}"
  ;;
- "ocnanalecen")
+ "marineanlecen")
 
-   export APRUN_OCNANALECEN="${APRUN_default}"
+   export APRUN_MARINEANLECEN="${APRUN_default}"
  ;;
  "marineanlchkpt")
 

env/ORION.env

@@ -150,10 +150,10 @@ elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUN_MARINEANLOBSSTATS="${launcher} -n 1"
 
-elif [[ "${step}" = "ocnanalecen" ]]; then
+elif [[ "${step}" = "marineanlecen" ]]; then
 
-    export NTHREADS_OCNANALECEN=${NTHREADSmax}
-    export APRUN_OCNANALECEN="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANALECEN}"
+    export NTHREADS_MARINEANLECEN=${NTHREADSmax}
+    export APRUN_MARINEANLECEN="${APRUN_default} --cpus-per-task=${NTHREADS_MARINEANLECEN}"
 
 elif [[ "${step}" = "marineanlletkf" ]]; then
 

env/WCOSS2.env

@@ -126,10 +126,10 @@ elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUN_MARINEANLOBSSTATS="${launcher} -n 1"
 
-elif [[ "${step}" = "ocnanalecen" ]]; then
+elif [[ "${step}" = "marineanlecen" ]]; then
 
-    export NTHREADS_OCNANALECEN=${NTHREADSmax}
-    export APRUN_OCNANALECEN="${APRUN_default}"
+    export NTHREADS_MARINEANLECEN=${NTHREADSmax}
+    export APRUN_MARINEANLECEN="${APRUN_default}"
 
 elif [[ "${step}" = "marineanlletkf" ]]; then
 

jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT

@@ -1,8 +1,8 @@
 #!/bin/bash
 export WIPE_DATA="NO"
-export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATAjob="${DATAROOT}/marineanalysis.${PDY:-}${cyc}"
 export DATAens="${DATAjob}/ensdata"
-export DATA="${DATAjob}/marinevariational"
+export DATA="${DATAjob}/marineanlvar"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlchkpt" -c "base marineanl marineanlchkpt"
 
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN → jobs/JGLOBAL_MARINE_ANALYSIS_ECEN

@@ -1,10 +1,10 @@
 #!/bin/bash
 
-export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
-export DATA="${DATAjob}/${jobid}"
+export DATAjob="${DATAROOT/enkf}/marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marineanlecen"
 export DATAens="${DATAjob}/ensdata"
 
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalecen" -c "base marineanl ocnanalecen"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlecen" -c "base marineanl marineanlecen"
 
 ##############################################
 # Set variables used in the script
@@ -15,17 +15,16 @@ GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 export gPDY=${GDATE:0:8}
 export gcyc=${GDATE:8:2}
 export GDUMP="gdas"
-export GDUMP_ENS="enkf${GDUMP}"
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
    COMIN_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
    COMIN_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL
 
-RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
     COMIN_OCEAN_HISTORY_ENS_PREV:COM_OCEAN_HISTORY_TMPL \
     COMIN_ICE_HISTORY_ENS_PREV:COM_ICE_HISTORY_TMPL
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
    COMOUT_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \
    COMIN_ICE_RESTART:COM_ICE_RESTART_TMPL \
    COMOUT_ICE_ANALYSIS:COM_ICE_ANALYSIS_TMPL
@@ -42,7 +41,7 @@ fi
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNCENPY:-${HOMEgfs}/scripts/exgdas_global_marine_analysis_ecen.py}
+EXSCRIPT=${GDASOCNCENPY:-${HOMEgfs}/scripts/exglobal_marine_analysis_ecen.py}
 ${EXSCRIPT} && true
 export err=$?
 if [[ ${err} -ne 0 ]]; then
@@ -63,14 +62,10 @@ fi
 ##########################################
 # Remove the Temporary working directory
 ##########################################
-cd "${DATAROOT}" && true
+cd "${DATAROOT/enkf}" && true
 export err=$?
 if [[ ${err} -ne 0 ]]; then
     err_exit
 fi
 
-if [[ "${KEEPDATA}" == "NO" ]]; then
-    rm -rf "${DATA}"
-fi
-
 exit 0

jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE

@@ -1,8 +1,8 @@
 #!/bin/bash
 export WIPE_DATA="NO"
-export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATAjob="${DATAROOT}/marineanalysis.${PDY:-}${cyc}"
 export DATAens="${DATAjob}/ensdata"
-export DATA="${DATAjob}/marinevariational"
+export DATA="${DATAjob}/marineanlvar"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlfinal" -c "base marineanl marineanlfinal"
 
 ##############################################
@@ -48,7 +48,7 @@ if [[ ${err} -ne 0 ]]; then
 fi
 
 if [[ "${KEEPDATA}" == "NO" ]]; then
-    rm -rf "${DATA}"
+    rm -rf "${DATAjob}"
 fi
 
 exit 0