Add JEDI atmosphere only CI (#2357)

The PR contains a minimal set of changes to enable JEDI atmospheric DA CI testing. Prototype JEDI atmospheric cycling has begun. The JEDI atmosphere DA CI case provides an automated way to see if future PRs impact JEDI atmospheric cycling. Resolves #2294 Dependency: GDASApp PR [#937](NOAA-EMC/GDASApp#937)
NOAA-EMC · Mar 12, 2024 · ccb1f52 · ccb1f52
1 parent b96f5eb
commit ccb1f52
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Showing 11 changed files with 35 additions and 25 deletions.
diff --git a/ci/cases/pr/C48C48_ufs_hybatmDA.yaml → ci/cases/pr/C96C48_ufs_hybatmDA.yaml b/ci/cases/pr/C48C48_ufs_hybatmDA.yaml → ci/cases/pr/C96C48_ufs_hybatmDA.yaml
@@ -5,12 +5,13 @@ experiment:
 arguments:
   pslot: {{ 'pslot' | getenv }}
   app: ATM
-  resdetatmos: 48
+  resdetatmos: 96
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  idate: 2021032312
-  edate: 2021032400
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  idate: 2024022318
+  edate: 2024022400
   nens: 2
   gfs_cyc: 1
   start: warm

diff --git a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml
@@ -6,11 +6,11 @@ base:
   DO_JEDIATMENS: "YES"
   ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}
 atmanl:
-  LAYOUT_X_ATMANL: 1
-  LAYOUT_Y_ATMANL: 1
+  LAYOUT_X_ATMANL: 4
+  LAYOUT_Y_ATMANL: 4
 atmensanl:
-  LAYOUT_X_ATMENSANL: 1
-  LAYOUT_Y_ATMENSANL: 1
+  LAYOUT_X_ATMENSANL: 4
+  LAYOUT_Y_ATMENSANL: 4
 esfc:
   DONST: "NO"
 nsst:

diff --git a/parm/config/gfs/config.atmanl b/parm/config/gfs/config.atmanl
@@ -5,12 +5,16 @@
 
 echo "BEGIN: config.atmanl"
 
-export CASE_ANL=${CASE}
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/config/
-export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype_3d.yaml
-export ATMVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/variational/3dvar_drpcg.yaml
+if [[ ${DOHYBVAR} = "YES" ]]; then
+    # shellcheck disable=SC2153
+    export CASE_ANL=${CASE_ENS}
+else
+    export CASE_ANL=${CASE}
+fi
+export OBS_LIST="${PARMgfs}/gdas/atm/obs/lists/gdas_prototype_3d.yaml.j2"
+export JEDIYAML="${PARMgfs}/gdas/atm/variational/3dvar_drpcg.yaml.j2"
 export STATICB_TYPE="gsibec"
-export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/berror/staticb_${STATICB_TYPE}.yaml
+export BERROR_YAML="${PARMgfs}/gdas/atm/berror/hybvar_${STATICB_TYPE}.yaml.j2"
 export INTERP_METHOD='barycentric'
 
 export layout_x_atmanl=@LAYOUT_X_ATMANL@

diff --git a/parm/config/gfs/config.atmanlinit b/parm/config/gfs/config.atmanlinit
@@ -7,4 +7,5 @@ echo "BEGIN: config.atmanlinit"
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmanlinit
+
 echo "END: config.atmanlinit"
diff --git a/parm/config/gfs/config.atmensanl b/parm/config/gfs/config.atmensanl
@@ -5,9 +5,8 @@
 
 echo "BEGIN: config.atmensanl"
 
-export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/config/
-export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/atm/obs/lists/lgetkf_prototype.yaml
-export ATMENSYAML=${HOMEgfs}/sorc/gdas.cd/parm/atm/lgetkf/lgetkf.yaml
+export OBS_LIST="${PARMgfs}/gdas/atm/obs/lists/lgetkf_prototype.yaml.j2"
+export JEDIYAML="${PARMgfs}/gdas/atm/lgetkf/lgetkf.yaml.j2"
 export INTERP_METHOD='barycentric'
 
 export layout_x_atmensanl=@LAYOUT_X_ATMENSANL@

diff --git a/parm/config/gfs/config.atmensanlinit b/parm/config/gfs/config.atmensanlinit
@@ -7,4 +7,5 @@ echo "BEGIN: config.atmensanlinit"
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmensanlinit
+
 echo "END: config.atmensanlinit"
diff --git a/parm/gdas/atm_jedi_fix.yaml b/parm/gdas/atm_jedi_fix.yaml
@@ -1,7 +1,7 @@
 mkdir:
-- $(DATA)/fv3jedi
+- '{{ DATA }}/fv3jedi'
 copy:
-- [$(FIXgfs)/gdas/fv3jedi/fv3files/akbk$(npz).nc4, $(DATA)/fv3jedi/akbk.nc4]
-- [$(FIXgfs)/gdas/fv3jedi/fv3files/fmsmpp.nml, $(DATA)/fv3jedi/fmsmpp.nml]
-- [$(FIXgfs)/gdas/fv3jedi/fv3files/field_table_gfdl, $(DATA)/fv3jedi/field_table]
-- [$(HOMEgfs)/sorc/gdas.cd/parm/io/fv3jedi_fieldmetadata_restart.yaml, $(DATA)/fv3jedi/fv3jedi_fieldmetadata_restart.yaml]
+- ['{{ FIXgfs }}/gdas/fv3jedi/fv3files/akbk{{ npz }}.nc4', '{{ DATA }}/fv3jedi/akbk.nc4']
+- ['{{ FIXgfs }}/gdas/fv3jedi/fv3files/fmsmpp.nml', '{{ DATA }}/fv3jedi/fmsmpp.nml']
+- ['{{ FIXgfs }}/gdas/fv3jedi/fv3files/field_table_gfdl', '{{ DATA }}/fv3jedi/field_table']
+- ['{{ PARMgfs }}/gdas/io/fv3jedi_fieldmetadata_restart.yaml', '{{ DATA }}/fv3jedi/fv3jedi_fieldmetadata_restart.yaml']
diff --git a/sorc/gdas.cd b/sorc/gdas.cd
diff --git a/ush/python/pygfs/task/atm_analysis.py b/ush/python/pygfs/task/atm_analysis.py
@@ -11,7 +11,7 @@
                     FileHandler,
                     add_to_datetime, to_fv3time, to_timedelta, to_YMDH,
                     chdir,
-                    parse_yamltmpl, parse_j2yaml, save_as_yaml,
+                    parse_j2yaml, save_as_yaml,
                     logit,
                     Executable,
                     WorkflowException)
@@ -103,7 +103,7 @@ def initialize(self: Analysis) -> None:
 
         # generate variational YAML file
         logger.debug(f"Generate variational YAML file: {self.task_config.fv3jedi_yaml}")
-        varda_yaml = parse_j2yaml(self.task_config.ATMVARYAML, self.task_config)
+        varda_yaml = parse_j2yaml(self.task_config.JEDIYAML, self.task_config, searchpath=self.gdasapp_j2tmpl_dir)
         save_as_yaml(varda_yaml, self.task_config.fv3jedi_yaml)
         logger.info(f"Wrote variational YAML to: {self.task_config.fv3jedi_yaml}")
 

diff --git a/ush/python/pygfs/task/atmens_analysis.py b/ush/python/pygfs/task/atmens_analysis.py
@@ -11,7 +11,7 @@
                     FileHandler,
                     add_to_datetime, to_fv3time, to_timedelta, to_YMDH, to_YMD,
                     chdir,
-                    parse_yamltmpl, parse_j2yaml, save_as_yaml,
+                    parse_j2yaml, save_as_yaml,
                     logit,
                     Executable,
                     WorkflowException,
@@ -119,7 +119,7 @@ def initialize(self: Analysis) -> None:
 
         # generate ensemble da YAML file
         logger.debug(f"Generate ensemble da YAML file: {self.task_config.fv3jedi_yaml}")
-        ensda_yaml = parse_j2yaml(self.task_config.ATMENSYAML, self.task_config)
+        ensda_yaml = parse_j2yaml(self.task_config.JEDIYAML, self.task_config, searchpath=self.gdasapp_j2tmpl_dir)
         save_as_yaml(ensda_yaml, self.task_config.fv3jedi_yaml)
         logger.info(f"Wrote ensemble da YAML to: {self.task_config.fv3jedi_yaml}")
 

diff --git a/workflow/applications/applications.py b/workflow/applications/applications.py
@@ -145,6 +145,10 @@ def _source_configs(self, conf: Configuration) -> Dict[str, Any]:
                 files += ['config.anal', 'config.eupd']
             elif config in ['efcs']:
                 files += ['config.fcst', 'config.efcs']
+            elif config in ['atmanlinit', 'atmanlrun']:
+                files += ['config.atmanl', f'config.{config}']
+            elif config in ['atmensanlinit', 'atmensanlrun']:
+                files += ['config.atmensanl', f'config.{config}']
             elif 'wave' in config:
                 files += ['config.wave', f'config.{config}']
             else:
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,5 @@ echo "BEGIN: config.atmanlinit"

		# Get task specific resources
		. "${EXPDIR}/config.resources" atmanlinit

		echo "END: config.atmanlinit"
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,5 @@ echo "BEGIN: config.atmensanlinit"

		# Get task specific resources
		. "${EXPDIR}/config.resources" atmensanlinit

		echo "END: config.atmensanlinit"