From c6e32621a71e71d250c64c5349d9249cfeec2cf4 Mon Sep 17 00:00:00 2001 From: Jiarui Dong Date: Thu, 19 Sep 2024 12:43:21 -0400 Subject: [PATCH] Remove the GTS BUFR2IODA part of the snow obs prep job (#2900) This PR removed the GTS BUFR2IODA part of the snow obs prep job, and replaced it with a direct read from BUFR snow data at runtime by the JEDI executable. Depends on NOAA-EMC/GDASApp#1276 --------- Co-authored-by: Cory Martin --- parm/config/gfs/config.prepsnowobs | 3 - parm/config/gfs/config.snowanl | 1 + scripts/exglobal_prep_snow_obs.py | 1 - sorc/gdas.cd | 2 +- ush/python/pygfs/task/snow_analysis.py | 84 ++------------------------ 5 files changed, 8 insertions(+), 83 deletions(-) diff --git a/parm/config/gfs/config.prepsnowobs b/parm/config/gfs/config.prepsnowobs index 60ca16ce9e..20bdd89ddf 100644 --- a/parm/config/gfs/config.prepsnowobs +++ b/parm/config/gfs/config.prepsnowobs @@ -8,11 +8,8 @@ echo "BEGIN: config.prepsnowobs" # Get task specific resources . "${EXPDIR}/config.resources" prepsnowobs -export GTS_OBS_LIST="${PARMgfs}/gdas/snow/prep/prep_gts.yaml.j2" export IMS_OBS_LIST="${PARMgfs}/gdas/snow/prep/prep_ims.yaml.j2" -export BUFR2IODAX="${EXECgfs}/bufr2ioda.x" - export CALCFIMSEXE="${EXECgfs}/calcfIMS.exe" export FIMS_NML_TMPL="${PARMgfs}/gdas/snow/prep/fims.nml.j2" diff --git a/parm/config/gfs/config.snowanl b/parm/config/gfs/config.snowanl index a2984f190b..b1460dfa67 100644 --- a/parm/config/gfs/config.snowanl +++ b/parm/config/gfs/config.snowanl @@ -9,6 +9,7 @@ echo "BEGIN: config.snowanl" source "${EXPDIR}/config.resources" snowanl export OBS_LIST="${PARMgfs}/gdas/snow/obs/lists/gdas_snow.yaml.j2" +export GTS_SNOW_STAGE_YAML="${PARMgfs}/gdas/snow/obs/config/bufr2ioda_mapping.yaml.j2" # Name of the JEDI executable and its yaml template export JEDIEXE="${EXECgfs}/gdas.x" diff --git a/scripts/exglobal_prep_snow_obs.py b/scripts/exglobal_prep_snow_obs.py index a6a9070151..aa1eb1bb7d 100755 --- a/scripts/exglobal_prep_snow_obs.py +++ b/scripts/exglobal_prep_snow_obs.py @@ -20,6 +20,5 @@ # Instantiate the snow prepare task SnowAnl = SnowAnalysis(config) - SnowAnl.prepare_GTS() if SnowAnl.task_config.cyc == 0: SnowAnl.prepare_IMS() diff --git a/sorc/gdas.cd b/sorc/gdas.cd index faa95efb18..7c1c181359 160000 --- a/sorc/gdas.cd +++ b/sorc/gdas.cd @@ -1 +1 @@ -Subproject commit faa95efb18f0f52acab2cf09b17f78406f9b48b1 +Subproject commit 7c1c181359c2c1952bab3dc1c481bbdb361aa472 diff --git a/ush/python/pygfs/task/snow_analysis.py b/ush/python/pygfs/task/snow_analysis.py index 9656b00a8e..4b991d2b34 100644 --- a/ush/python/pygfs/task/snow_analysis.py +++ b/ush/python/pygfs/task/snow_analysis.py @@ -54,83 +54,6 @@ def __init__(self, config): # Extend task_config with local_dict self.task_config = AttrDict(**self.task_config, **local_dict) - @logit(logger) - def prepare_GTS(self) -> None: - """Prepare the GTS data for a global snow analysis - - This method will prepare GTS data for a global snow analysis using JEDI. - This includes: - - processing GTS bufr snow depth observation data to IODA format - - Parameters - ---------- - Analysis: parent class for GDAS task - - Returns - ---------- - None - """ - - # create a temporary dict of all keys needed in this method - localconf = AttrDict() - keys = ['HOMEgfs', 'DATA', 'current_cycle', 'COM_OBS', 'COM_ATMOS_RESTART_PREV', - 'OPREFIX', 'CASE', 'OCNRES', 'ntiles'] - for key in keys: - localconf[key] = self.task_config[key] - - # Read and render the GTS_OBS_LIST yaml - logger.info(f"Reading {self.task_config.GTS_OBS_LIST}") - prep_gts_config = parse_j2yaml(self.task_config.GTS_OBS_LIST, localconf) - logger.debug(f"{self.task_config.GTS_OBS_LIST}:\n{pformat(prep_gts_config)}") - - # copy the GTS obs files from COM_OBS to DATA/obs - logger.info("Copying GTS obs for bufr2ioda.x") - FileHandler(prep_gts_config.gtsbufr).sync() - - logger.info("Link BUFR2IODAX into DATA/") - exe_src = self.task_config.BUFR2IODAX - exe_dest = os.path.join(localconf.DATA, os.path.basename(exe_src)) - if os.path.exists(exe_dest): - rm_p(exe_dest) - os.symlink(exe_src, exe_dest) - - # Create executable instance - exe = Executable(self.task_config.BUFR2IODAX) - - def _gtsbufr2iodax(exe, yaml_file): - if not os.path.isfile(yaml_file): - logger.exception(f"FATAL ERROR: {yaml_file} not found") - raise FileNotFoundError(yaml_file) - - logger.info(f"Executing {exe}") - try: - exe(yaml_file) - except OSError: - raise OSError(f"Failed to execute {exe} {yaml_file}") - except Exception: - raise WorkflowException(f"An error occured during execution of {exe} {yaml_file}") - - # Loop over entries in prep_gts_config.bufr2ioda keys - # 1. generate bufr2ioda YAML files - # 2. execute bufr2ioda.x - for name in prep_gts_config.bufr2ioda.keys(): - gts_yaml = os.path.join(self.task_config.DATA, f"bufr_{name}_snow.yaml") - logger.info(f"Generate BUFR2IODA YAML file: {gts_yaml}") - temp_yaml = parse_j2yaml(prep_gts_config.bufr2ioda[name], localconf) - save_as_yaml(temp_yaml, gts_yaml) - logger.info(f"Wrote bufr2ioda YAML to: {gts_yaml}") - - # execute BUFR2IODAX to convert {name} bufr data into IODA format - _gtsbufr2iodax(exe, gts_yaml) - - # Ensure the IODA snow depth GTS file is produced by the IODA converter - # If so, copy to COM_OBS/ - try: - FileHandler(prep_gts_config.gtsioda).sync() - except OSError as err: - logger.exception(f"{self.task_config.BUFR2IODAX} failed to produce GTS ioda files") - raise OSError(err) - @logit(logger) def prepare_IMS(self) -> None: """Prepare the IMS data for a global snow analysis @@ -248,7 +171,7 @@ def initialize(self) -> None: # create a temporary dict of all keys needed in this method localconf = AttrDict() - keys = ['DATA', 'current_cycle', 'COM_OBS', 'COM_ATMOS_RESTART_PREV', + keys = ['PARMgfs', 'DATA', 'current_cycle', 'COM_OBS', 'COM_ATMOS_RESTART_PREV', 'OPREFIX', 'CASE', 'OCNRES', 'ntiles'] for key in keys: localconf[key] = self.task_config[key] @@ -268,6 +191,11 @@ def initialize(self) -> None: logger.info("Staging ensemble backgrounds") FileHandler(self.get_ens_bkg_dict(localconf)).sync() + # stage GTS bufr2ioda mapping YAML files + logger.info(f"Staging GTS bufr2ioda mapping YAML files from {self.task_config.GTS_SNOW_STAGE_YAML}") + gts_mapping_list = parse_j2yaml(self.task_config.GTS_SNOW_STAGE_YAML, localconf) + FileHandler(gts_mapping_list).sync() + # Write out letkfoi YAML file save_as_yaml(self.task_config.jedi_config, self.task_config.jedi_yaml) logger.info(f"Wrote letkfoi YAML to: {self.task_config.jedi_yaml}")