Marine DA updates (NOAA-EMC#2802)

Companion PR to GDASApp#1226

Addresses a few issues described in:

- GDASApp#1219
- GDASApp#1217
- GDASApp#1232

ci/cases/gfsv17/ocnanal.yaml

@@ -17,7 +17,7 @@ base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
 
 ocnanal:
-  SOCA_INPUT_FIX_DIR: {{ FIXgfs }}/gdas/soca/1440x1080x75/soca
+  SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca
   SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
   SOCA_NINNER: 100
 

jobs/rocoto/prepoceanobs.sh

@@ -14,8 +14,10 @@ export jobid="${job}.$$"
 
 ###############################################################
 # setup python path for class defs and utils
-
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush"
+# shellcheck disable=SC2311
+pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python$(detect_py_ver)/"
+PYTHONPATH="${pyiodaPATH}:${PYTHONPATH}"
+export PYTHONPATH
 
 ###############################################################
 # Execute the JJOB

parm/config/gfs/config.resources

@@ -580,7 +580,7 @@ case ${step} in
     case ${OCNRES} in
       "025")
         memory="128GB"
-        ntasks=40;;
+        ntasks=16;;
       "050")
         memory="32GB"
         ntasks=16;;

ush/python/pygfs/task/marine_bmat.py

@@ -43,7 +43,7 @@ def __init__(self, config):
                 'MARINE_WINDOW_END': _window_end,
                 'MARINE_WINDOW_MIDDLE': self.task_config.current_cycle,
                 'BERROR_YAML_DIR': os.path.join(_home_gdas, 'parm', 'soca', 'berror'),
-                'GRID_GEN_YAML': os.path.join(_home_gdas, 'parm', 'soca', 'gridgen', 'gridgen.yaml'),
+                'UTILITY_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'soca_utils_stage.yaml.j2'),
                 'MARINE_ENSDA_STAGE_BKG_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'ensda', 'stage_ens_mem.yaml.j2'),
                 'MARINE_DET_STAGE_BKG_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'soca_det_bkg_stage.yaml.j2'),
                 'ENSPERT_RELPATH': _enspert_relpath,
@@ -82,12 +82,11 @@ def initialize(self: Task) -> None:
         # TODO(G): Check ocean backgrounds dates for consistency
         bkg_list = parse_j2yaml(self.task_config.MARINE_DET_STAGE_BKG_YAML_TMPL, self.task_config)
         FileHandler(bkg_list).sync()
-        for cice_fname in ['./INPUT/cice.res.nc', './bkg/ice.bkg.f006.nc', './bkg/ice.bkg.f009.nc']:
-            mdau.cice_hist2fms(cice_fname, cice_fname)
 
-        # stage the grid generation yaml
-        FileHandler({'copy': [[self.task_config.GRID_GEN_YAML,
-                               os.path.join(self.task_config.DATA, 'gridgen.yaml')]]}).sync()
+        # stage the soca utility yamls (gridgen, fields and ufo mapping yamls)
+        logger.info(f"Staging SOCA utility yaml files from {self.task_config.HOMEgfs}/parm/gdas/soca")
+        soca_utility_list = parse_j2yaml(self.task_config.UTILITY_YAML_TMPL, self.task_config)
+        FileHandler(soca_utility_list).sync()
 
         # generate the variance partitioning YAML file
         logger.debug("Generate variance partitioning YAML file")

ush/python/pygfs/utils/marine_da_utils.py

@@ -61,29 +61,6 @@ def prep_input_nml(task_config: AttrDict) -> None:
         nml.write('mom_input.nml')
 
 
-@logit(logger)
-def cice_hist2fms(input_filename: str, output_filename: str) -> None:
-    """ Reformat the CICE history file so it can be read by SOCA/FMS
-    Simple reformatting utility to allow soca/fms to read the CICE history files
-    """
-
-    # open the CICE history file
-    ds = xr.open_dataset(input_filename)
-
-    if 'aicen' in ds.variables and 'hicen' in ds.variables and 'hsnon' in ds.variables:
-        logger.info(f"*** Already reformatted, skipping.")
-        return
-
-    # rename the dimensions to xaxis_1 and yaxis_1
-    ds = ds.rename({'ni': 'xaxis_1', 'nj': 'yaxis_1'})
-
-    # rename the variables
-    ds = ds.rename({'aice_h': 'aicen', 'hi_h': 'hicen', 'hs_h': 'hsnon'})
-
-    # Save the new netCDF file
-    ds.to_netcdf(output_filename, mode='w')
-
-
 @logit(logger)
 def stage_ens_mem(task_config: AttrDict) -> None:
     """ Copy the ensemble members to the DATA directory

versions/fix.ver

@@ -9,7 +9,7 @@ export cpl_ver=20230526
 export datm_ver=20220805
 export gdas_crtm_ver=20220805
 export gdas_fv3jedi_ver=20220805
-export gdas_soca_ver=20240624
+export gdas_soca_ver=20240802
 export gdas_gsibec_ver=20240416
 export gdas_obs_ver=20240213
 export glwu_ver=20220805