[uwtools_integration] Integrate ics/lbcs

parm/wflow/coldstart.yaml

@@ -102,7 +102,16 @@ metatask_run_ensemble:
     mem: '{% if global.DO_ENSEMBLE %}{%- for m in range(1, global.NUM_ENS_MEMBERS+1) -%}{{ "%03d "%m }}{%- endfor -%} {% else %}{{ "000"|string }}{% endif %}'
   task_make_ics_mem#mem#:
     <<: *default_task
-    command: '&LOAD_MODULES_RUN_TASK; "make_ics" "&JOBSdir;/JREGIONAL_MAKE_ICS"'
+    command: 
+      cyclestr:
+        value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} ; &SCRIPTSdir;/chgres_cube.py
+          -c &GLOBAL_VAR_DEFNS_FP;
+          --cycle @Y-@m-@dT@H:@M:@S
+          --key-path task_make_ics
+          --mem #mem#'
+    join:
+      cyclestr:
+        value: '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     envars:
       <<: *default_vars
       SLASH_ENSMEM_SUBDIR: '&SLASH_ENSMEM_SUBDIR;'
@@ -111,7 +120,7 @@ metatask_run_ensemble:
       cyclestr:
         value: '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     nodes: '{{ task_make_ics.chgres_cube.execution.batchargs.nodes }}:ppn={{ task_make_ics.chgres_cube.execution.batchargs.tasks_per_node }}'
-    walltime: '{{ task_make_ics.chgres_cube.execution.batchargs.walltime }}'
+    walltime: '{{ task_make_ics.chgres_cube.execution.batchargs.walltime }}' 
     dependency:
       and: &make_ics_deps
         taskdep_get_extrn:
@@ -144,7 +153,16 @@ metatask_run_ensemble:
 
   task_make_lbcs_mem#mem#:
     <<: *default_task
-    command: '&LOAD_MODULES_RUN_TASK; "make_lbcs" "&JOBSdir;/JREGIONAL_MAKE_LBCS"'
+    command: 
+      cyclestr:
+        value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE }} ; &SCRIPTSdir;/chgres_cube.py
+          -c &GLOBAL_VAR_DEFNS_FP;
+          --cycle @Y-@m-@dT@H:@M:@S
+          --key-path task_make_lbcs
+          --mem #mem#'
+    join:
+      cyclestr:
+        value: '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     envars:
       <<: *default_vars
       SLASH_ENSMEM_SUBDIR: '&SLASH_ENSMEM_SUBDIR;'
@@ -155,7 +173,7 @@ metatask_run_ensemble:
       cyclestr:
         value: '&LOGDIR;/{{ jobname }}_@Y@m@d@H&LOGEXT;'
     nodes: '{{ task_make_lbcs.chgres_cube.execution.batchargs.nodes }}:ppn={{ task_make_lbcs.chgres_cube.execution.batchargs.tasks_per_node }}'
-    walltime: '{{ task_make_lbcs.chgres_cube.execution.batchargs.walltime }}'
+    walltime: '{{ task_make_lbcs.chgres_cube.execution.batchargs.walltime }}' 
     dependency:
       and:
         <<: *make_ics_deps

parm/wflow/post.yaml

@@ -12,7 +12,7 @@ metatask_run_ens_post:
         maxtries: '2'
       command:
         cyclestr:
-          value: 'source &USHdir;/load_modules_wflow.sh hera ; &SCRIPTSdir;/upp.py
+          value: 'source &USHdir;/load_modules_wflow.sh {{ user.MACHINE  }} ; &SCRIPTSdir;/upp.py
             -c &GLOBAL_VAR_DEFNS_FP;
             --cycle @Y-@m-@dT@H:@M:@S
             --leadtime #fhr#:00:00

scripts/chgres_cube.py

@@ -0,0 +1,218 @@
+#!/usr/bin/env python
+"""
+The run script for chgres_cube
+"""
+
+import datetime as dt
+import logging
+import os
+import sys
+from argparse import ArgumentParser
+from copy import deepcopy
+from pathlib import Path
+
+from uwtools.api.chgres_cube import ChgresCube
+from uwtools.api.config import get_yaml_config
+from uwtools.api.fs import link as uwlink
+from uwtools.api.logging import use_uwtools_logger
+
+
+def _walk_key_path(config, key_path):
+    """
+    Navigate to the sub-config at the end of the path of given keys.
+    """
+    keys = []
+    pathstr = "<unknown>"
+    for key in key_path:
+        keys.append(key)
+        pathstr = " -> ".join(keys)
+        try:
+            subconfig = config[key]
+        except KeyError:
+            logging.error(f"Bad config path: {pathstr}")
+            raise
+        if not isinstance(subconfig, dict):
+            logging.error(f"Value at {pathstr} must be a dictionary")
+            sys.exit(1)
+        config = subconfig
+    return config
+
+
+def parse_args(argv):
+    """
+    Parse arguments for the script.
+    """
+    parser = ArgumentParser(
+        description="Script that runs chgres_cube via uwtools API",
+    )
+    parser.add_argument(
+        "-c",
+        "--config-file",
+        metavar="PATH",
+        required=True,
+        help="Path to experiment config file.",
+        type=Path,
+    )
+    parser.add_argument(
+        "--cycle",
+        help="The cycle in ISO8601 format (e.g. 2024-07-15T18)",
+        required=True,
+        type=dt.datetime.fromisoformat,
+    )
+    parser.add_argument(
+        "--key-path",
+        help="Dot-separated path of keys leading through the config to the driver's YAML block",
+        metavar="KEY[.KEY...]",
+        required=True,
+        type=lambda s: s.split("."),
+    )
+    parser.add_argument(
+        "--member",
+        default="000",
+        help="The 3-digit ensemble member number.",
+    )
+    return parser.parse_args(argv)
+
+
+# pylint: disable-next=too-many-locals, too-many-statements
+def run_chgres_cube(config_file, cycle, key_path, member):
+    """
+    Setup and run the chgres_cube Driver.
+    """
+    expt_config = get_yaml_config(config_file)
+
+    # The experiment config will have {{ CRES | env }} expressions in it that need to be
+    # dereferenced during driver initialization
+    cres = expt_config["workflow"]["CRES"]
+    os.environ["CRES"] = cres
+    os.environ["MEMBER"] = member
+    expt_config.dereference(
+        context={
+            "cycle": cycle,
+            **os.environ,
+            **expt_config,
+        }
+    )
+    chgres_cube_driver = ChgresCube(
+        config=config_file,
+        cycle=cycle,
+        key_path=key_path,
+    )
+    rundir = Path(chgres_cube_driver.config["rundir"])
+    logging.info(f"Will run in {rundir}")
+
+    chgres_cube_config = _walk_key_path(expt_config, key_path)
+    input_type = chgres_cube_config["chgres_cube"]["namelist"]["update_values"][
+        "config"
+    ].get("input_type")
+
+    varsfilepath = chgres_cube_config["input_files_metadata_path"]
+    external_config = get_yaml_config(varsfilepath)
+    external_config_fns = external_config["external_model_fns"]
+    external_config_fhrs = external_config["external_model_fhrs"]
+
+    # update config for ics task, run and stage data
+    if "task_make_ics" in key_path:
+        if input_type == "grib2":
+            os.environ["fn_grib2"] = external_config_fns[0]
+        else:
+            os.environ["fn_atm"] = external_config_fns[0]
+            os.environ["fn_sfc"] = external_config_fns[1]
+        # reinstantiate driver
+        expt_config_cp = get_yaml_config(deepcopy(expt_config.data))
+        expt_config_cp.dereference(
+            context={
+                "cycle": cycle,
+                **os.environ,
+                **expt_config_cp,
+            }
+        )
+        chgres_cube_driver = ChgresCube(
+            config=expt_config_cp,
+            cycle=cycle,
+            key_path=key_path,
+        )
+        chgres_cube_driver.run()
+
+        # Deliver output data to a common location above the rundir.
+        links = {}
+
+        output_dir = os.path.join(rundir.parent, "INPUT")
+        os.makedirs(output_dir, exist_ok=True)
+        task_get_block = _walk_key_path(expt_config_cp, {"task_get_extrn_ics"})
+        task_make_block = _walk_key_path(expt_config_cp, key_path)
+        for i, output_fn in enumerate(task_make_block["output_file_labels"]):
+            input_fn = task_get_block["output_file_labels"][i]
+            links[output_fn] = str(rundir / input_fn)
+
+        uwlink(target_dir=output_dir, config=links)
+
+    #  update config for lbcs task, loop run and stage data
+    else:
+        num_fhrs = len(external_config_fhrs)
+
+        bcgrp10 = 0
+        bcgrpnum10 = 1
+        for ii in range(bcgrp10, num_fhrs, bcgrpnum10):
+            i = ii + bcgrp10
+            if i < num_fhrs:
+                print(f"group {bcgrp10} processes member {i}")
+                if input_type == "grib2":
+                    os.environ["fn_grib2"] = external_config_fns[i]
+                else:
+                    os.environ["fn_atm"] = external_config_fns[i]
+
+                lbc_spec_fhrs = external_config_fhrs[i]
+                lbc_offset_fhrs = expt_config["task_get_extrn_lbcs"]["envvars"][
+                    "EXTRN_MDL_LBCS_OFFSET_HRS"
+                ]
+                fcst_hhh = int(lbc_spec_fhrs) - int(lbc_offset_fhrs)
+                os.environ["fcst_hhh_FV3LAM"] = f"{fcst_hhh:03d}"
+
+                # reinstantiate driver
+                expt_config_cp = get_yaml_config(deepcopy(expt_config.data))
+                expt_config_cp.dereference(
+                    context={
+                        "cycle": cycle,
+                        **os.environ,
+                        **expt_config_cp,
+                    }
+                )
+                chgres_cube_driver = ChgresCube(
+                    config=expt_config_cp,
+                    cycle=cycle,
+                    key_path=key_path,
+                )
+                chgres_cube_driver.run()
+
+                # Deliver output data to a common location above the rundir.
+                links = {}
+
+                task_get_block = _walk_key_path(expt_config_cp, {"task_get_extrn_lbcs"})
+                task_make_block = _walk_key_path(expt_config_cp, key_path)
+
+                output_dir = os.path.join(rundir.parent, "INPUT")
+                os.makedirs(output_dir, exist_ok=True)
+
+                lbc_input_fn = task_get_block["output_file_labels"][0]
+                lbc_output_fn = task_make_block["output_file_labels"][0]
+                links[lbc_output_fn] = str(rundir / lbc_input_fn)
+                uwlink(target_dir=output_dir, config=links)
+
+    # error message
+    if not (rundir / "runscript.chgres_cube.done").is_file():
+        print("Error occurred running chgres_cube. Please see component error logs.")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+
+    use_uwtools_logger()
+
+    args = parse_args(sys.argv[1:])
+    run_chgres_cube(
+        config_file=args.config_file,
+        cycle=args.cycle,
+        key_path=args.key_path,
+        member=args.member,
+    )

scripts/exregional_get_extrn_mdl_files.sh

@@ -240,9 +240,9 @@ fi
 mkdir -p ${EXTRN_MDL_STAGING_DIR}
 
 if [ $RUN_ENVIR = "nco" ]; then
-    EXTRN_DEFNS="${NET}.${cycle}.${EXTRN_MDL_NAME}.${ICS_OR_LBCS}.${EXTRN_MDL_VAR_DEFNS_FN}.sh"
+    EXTRN_DEFNS="${NET}.${cycle}.${EXTRN_MDL_NAME}.${ICS_OR_LBCS}.${EXTRN_MDL_VAR_DEFNS_FN}.yaml"
 else
-    EXTRN_DEFNS="${EXTRN_MDL_VAR_DEFNS_FN}.sh"
+    EXTRN_DEFNS="${EXTRN_MDL_VAR_DEFNS_FN}.yaml"
 fi
 cmd="
 python3 -u ${USHdir}/retrieve_data.py \

ush/ccpp_suites_defaults.yaml

@@ -1,3 +1,8 @@
+chgres_cube_gsd_defaults: &chgres_cube_gsd_defaults
+  namelist:
+    update_values:
+      config:
+        varmap_file: "{{ user.PARMdir }}/ufs_utils/varmap_tables/GSDphys_var_map.txt"
 
 orog_gsl_defaults: &orog_gsl_defaults
   config:
@@ -19,18 +24,56 @@ orog_gsl_defaults: &orog_gsl_defaults
   rundir: "{{ task_make_orog.rundir }}/orog_gsl"
 
 FV3_RAP:
+  task_make_ics:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+  task_make_lbcs:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
   task_make_orog:
     orog_gsl:
       <<: *orog_gsl_defaults
 FV3_HRRR:
+  task_make_ics:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+  task_make_lbcs:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
   task_make_orog:
     orog_gsl:
       <<: *orog_gsl_defaults
+FV3_WoFS_v0:
+  task_make_ics:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+  task_make_lbcs:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+FV3_RRFS_v1beta:
+  task_make_ics:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+  task_make_lbcs:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
 FV3_GFS_v15_thompson_mynn_lam3km:
+  task_make_ics:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+  task_make_lbcs:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
   task_make_orog:
     orog_gsl:
       <<: *orog_gsl_defaults
 FV3_GFS_v17_p8:
+  task_make_ics:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
+  task_make_lbcs:
+    chgres_cube:
+      <<: *chgres_cube_gsd_defaults
   task_make_orog:
     orog_gsl:
       <<: *orog_gsl_defaults