Add LETKF suite and initial tasks.

src/swell/configuration/jedi/interfaces/geos_atmosphere/task_questions.yaml

@@ -32,6 +32,9 @@ clean_patterns:
   - '*.txt'
   - logfile.*.out
 
+ensemble_num_members:
+  default_value: 10
+
 geos_background_restart_offset:
   default_value: TODO
 
@@ -153,6 +156,9 @@ observations:
   - omi_aura
   - ompsnm_npp
 
+path_to_ensemble:
+  default_value: /discover/nobackup/drholdaw/SwellTestData/letk/ensemble/Y%Y/M%m/D%d/H%H
+
 path_to_geos_adas_background:
   default_value: /discover/nobackup/drholdaw/SwellTestData/geosadas/bkg/*bkg_clcv_rst*
 

src/swell/deployment/prep_suite.py

@@ -123,6 +123,7 @@ def prepare_cylc_suite_jinja2(logger, swell_suite_path, exp_suite_path, experime
         'BuildGeos',
         'GenerateBClimatology',
         'RunJediHofxExecutable',
+        'RunJediLetkfExecutable',
         'RunJediVariationalExecutable',
         'RunJediUfoTestsExecutable',
         'RunGeosExecutable',

src/swell/suites/letkf/flow.cylc

@@ -0,0 +1,155 @@
+# (C) Copyright 2021- United States Government as represented by the Administrator of the
+# National Aeronautics and Space Administration. All Rights Reserved.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+# --------------------------------------------------------------------------------------------------
+
+# Cylc suite for executing JEDI-based h(x)
+
+# --------------------------------------------------------------------------------------------------
+
+[scheduler]
+    UTC mode = True
+    allow implicit tasks = False
+
+# --------------------------------------------------------------------------------------------------
+
+[scheduling]
+
+    initial cycle point = {{start_cycle_point}}
+    final cycle point = {{final_cycle_point}}
+    runahead limit = {{runahead_limit}}
+
+    [[graph]]
+        R1 = """
+            # Triggers for non cycle time dependent tasks
+            # -------------------------------------------
+            # Clone JEDI source code
+            CloneJedi
+
+            # Build JEDI source code by linking
+            CloneJedi => BuildJediByLinking?
+
+            # If not able to link to build create the build
+            BuildJediByLinking:fail? => BuildJedi
+
+            {% for model_component in model_components %}
+            # Stage JEDI static files
+            CloneJedi => StageJedi-{{model_component}}
+            {% endfor %}
+        """
+
+        {% for cycle_time in cycle_times %}
+        {{cycle_time.cycle_time}} = """
+        {% for model_component in model_components %}
+        {% if cycle_time[model_component] %}
+            # Task triggers for: {{model_component}}
+            # ------------------
+            # Get ensemble
+            GetEnsemble-{{model_component}}
+
+            # Get observations
+            GetObservations-{{model_component}}
+
+            # Perform staging that is cycle dependent
+            StageJediCycle-{{model_component}}
+
+            # Run Jedi hofx executable
+            BuildJediByLinking[^]? | BuildJedi[^]  => RunJediLetkfExecutable-{{model_component}}
+            StageJedi-{{model_component}}[^] => RunJediLetkfExecutable-{{model_component}}
+            StageJediCycle-{{model_component}} => RunJediLetkfExecutable-{{model_component}}
+            GetEnsemble-{{model_component}} => RunJediLetkfExecutable-{{model_component}}
+            GetObservations-{{model_component}} => RunJediLetkfExecutable-{{model_component}}
+
+            # EvaObservations
+            RunJediLetkfExecutable-{{model_component}} => EvaObservations-{{model_component}}
+
+            # Save observations
+            RunJediLetkfExecutable-{{model_component}} => SaveObsDiags-{{model_component}}
+
+            # Clean up large files
+            EvaObservations-{{model_component}} & SaveObsDiags-{{model_component}} =>
+            CleanCycle-{{model_component}}
+
+        {% endif %}
+        {% endfor %}
+        """
+        {% endfor %}
+
+# --------------------------------------------------------------------------------------------------
+
+[runtime]
+
+    # Task defaults
+    # -------------
+    [[root]]
+        pre-script = "source $CYLC_SUITE_DEF_PATH/modules"
+
+        [[[environment]]]
+            datetime = $CYLC_TASK_CYCLE_POINT
+            config   = $CYLC_SUITE_DEF_PATH/experiment.yaml
+
+    # Tasks
+    # -----
+    [[CloneJedi]]
+        script = "swell_task CloneJedi $config"
+
+    [[BuildJediByLinking]]
+        script = "swell_task BuildJediByLinking $config"
+
+    [[BuildJedi]]
+        script = "swell_task BuildJedi $config"
+        platform = {{platform}}
+        execution time limit = {{scheduling["BuildJedi"]["execution_time_limit"]}}
+        [[[directives]]]
+            --account = {{scheduling["BuildJedi"]["account"]}}
+            --qos = {{scheduling["BuildJedi"]["qos"]}}
+            --job-name = BuildJedi
+            --nodes={{scheduling["BuildJedi"]["nodes"]}}
+            --ntasks-per-node={{scheduling["BuildJedi"]["ntasks_per_node"]}}
+            --constraint={{scheduling["BuildJedi"]["constraint"]}}
+            {% if scheduling["BuildJedi"]["partition"] %}
+            --partition={{scheduling["BuildJedi"]["partition"]}}
+            {% endif %}
+
+    {% for model_component in model_components %}
+    [[StageJedi-{{model_component}}]]
+        script = "swell_task StageJedi $config -m {{model_component}}"
+
+    [[StageJediCycle-{{model_component}}]]
+        script = "swell_task StageJedi $config -d $datetime -m {{model_component}}"
+
+    [[ GetEnsemble-{{model_component}} ]]
+        script = "swell_task GetEnsemble $config -d $datetime -m {{model_component}}"
+
+    [[GetObservations-{{model_component}}]]
+        script = "swell_task GetObservations $config -d $datetime -m {{model_component}}"
+
+    [[RunJediLetkfExecutable-{{model_component}}]]
+        script = "swell_task RunJediLetkfExecutable $config -d $datetime -m {{model_component}}"
+        platform = {{platform}}
+        execution time limit = {{scheduling["RunJediLetkfExecutable"]["execution_time_limit"]}}
+        [[[directives]]]
+            --account = {{scheduling["RunJediLetkfExecutable"]["account"]}}
+            --qos = {{scheduling["RunJediLetkfExecutable"]["qos"]}}
+            --job-name = RunJediLetkfExecutable
+            --nodes={{scheduling["RunJediLetkfExecutable"]["nodes"]}}
+            --ntasks-per-node={{scheduling["RunJediLetkfExecutable"]["ntasks_per_node"]}}
+            --constraint={{scheduling["RunJediLetkfExecutable"]["constraint"]}}
+            {% if scheduling["RunJediLetkfExecutable"]["partition"] %}
+            --partition={{scheduling["RunJediLetkfExecutable"]["partition"]}}
+            {% endif %}
+
+    [[EvaObservations-{{model_component}}]]
+        script = "swell_task EvaObservations $config -d $datetime -m {{model_component}}"
+
+    [[SaveObsDiags-{{model_component}}]]
+        script = "swell_task SaveObsDiags $config -d $datetime -m {{model_component}}"
+
+    [[CleanCycle-{{model_component}}]]
+        script = "swell_task CleanCycle $config -d $datetime -m {{model_component}}"
+    {% endfor %}
+
+# --------------------------------------------------------------------------------------------------

src/swell/suites/letkf/suite_questions.yaml

@@ -0,0 +1,26 @@
+start_cycle_point:
+  ask_question: True
+  default_value: '2021-12-12T00:00:00Z'
+  prompt: What is the time of the first cycle (middle of the window)?
+  type: iso-datetime
+
+final_cycle_point:
+  ask_question: True
+  default_value: '2021-12-12T06:00:00Z'
+  prompt: What is the time of the final cycle (middle of the window)?
+  type: iso-datetime
+
+runahead_limit:
+  ask_question: True
+  default_value: 'P4'
+  prompt: Since this suite is non-cycling choose how many hours the workflow can run ahead?
+  type: string
+
+cycle_times:
+  ask_question: True
+  default_value: defer_to_model
+  options: defer_to_model
+  models:
+  - all
+  prompt: Enter the cycle times for this model.
+  type: string-check-list

src/swell/tasks/base/task_registry.py

@@ -18,6 +18,7 @@
   'GenerateBClimatology',
   'GetBackgroundGeosExperiment',
   'GetBackground',
+  'GetEnsemble',
   'GetGeosAdasBackground',
   'GetGeosRestart',
   'GetGeovals',
@@ -35,6 +36,7 @@
   'RemoveForecastDir',
   'RunGeosExecutable',
   'RunJediHofxExecutable',
+  'RunJediLetkfExecutable',
   'RunJediUfoTestsExecutable',
   'RunJediVariationalExecutable',
   'SaveObsDiags',

src/swell/tasks/get_ensemble.py

@@ -0,0 +1,69 @@
+# (C) Copyright 2021- United States Government as represented by the Administrator of the
+# National Aeronautics and Space Administration. All Rights Reserved.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+import datetime
+import glob
+import os
+import re
+
+from swell.tasks.base.task_base import taskBase
+
+
+# --------------------------------------------------------------------------------------------------
+
+
+class GetEnsemble(taskBase):
+
+    def execute(self):
+
+        # Get the path and pattern for the background files
+        # -------------------------------------------------
+        ensemble_path = self.config.path_to_ensemble()
+
+        # Fetch list of ensemble members
+        # --------------------------------
+        ensemble_members = glob.glob(ensemble_path)
+
+        # Assert at least one ensemble member was found
+        # -----------------------------------------------
+        self.logger.assert_abort(len(ensemble_members) != 0, f'No ensemble member ' +
+                                 f'files found in the source directory ' +
+                                 f'\'{ensemble_path}\'')
+
+        # Loop over all the ensemble members found
+        # -----------------------------------------
+        for ensemble_member in ensemble_members:
+
+            # Get filename from full path
+            member_file = os.path.basename(ensemble_member)
+
+            # Extract the datetime part from the string
+            datetime_part = re.search(r"\d{8}_\d{4}\w", member_file).group()
+
+            # Get datetime for the file from the filename
+            member_file_datetime = datetime.datetime.strptime(datetime_part, '%Y%m%d_%H%Mz')
+
+            # Create target filename using the datetime format
+            member_file_target = member_file_datetime.strftime('geos.mem001.%Y%m%d_%H%M%Sz.nc4')
+
+            # Target path and filename
+            ensemble_path_file_target = os.path.join(self.cycle_dir(), member_file_target)
+
+            # Remove target file if it exists (might be a link)
+            if os.path.exists(ensemble_path_file_target):
+                os.remove(ensemble_path_file_target)
+
+            # Create symlink from target to source
+            self.logger.info(f'Creating sym link from {ensemble_member} to '
+                             f'{ensemble_path_file_target}')
+            os.symlink(ensemble_member, ensemble_path_file_target)
+
+
+# --------------------------------------------------------------------------------------------------