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Add the suite file and task shell for running a forecast of GEOS (#150)
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
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13 files changed

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‎src/swell/deployment/prep_suite.py‎

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Original file line numberDiff line numberDiff line change
@@ -56,18 +56,31 @@ def prepare_cylc_suite_jinja2(logger, swell_suite_path, exp_suite_path, experime
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render_dictionary['scheduling']['RunJediHofxExecutable']['execution_time_limit'] = 'PT2H'
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render_dictionary['scheduling']['RunJediHofxExecutable']['account'] = 'g0613'
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render_dictionary['scheduling']['RunJediHofxExecutable']['qos'] = 'allnccs'
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render_dictionary['scheduling']['RunJediHofxExecutable']['constraint'] = 'hasw'
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render_dictionary['scheduling']['RunJediHofxExecutable']['nodes'] = 1
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render_dictionary['scheduling']['RunJediHofxExecutable']['ntasks_per_node'] = 24
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render_dictionary['scheduling'] = {}
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render_dictionary['scheduling']['RunGeosExecutable'] = {}
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render_dictionary['scheduling']['RunGeosExecutable']['execution_time_limit'] = 'PT2H'
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render_dictionary['scheduling']['RunGeosExecutable']['account'] = 'g0613'
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render_dictionary['scheduling']['RunGeosExecutable']['qos'] = 'allnccs'
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render_dictionary['scheduling']['RunGeosExecutable']['nodes'] = 1
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render_dictionary['scheduling']['RunGeosExecutable']['ntasks_per_node'] = 24
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render_dictionary['scheduling']['BuildJedi'] = {}
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render_dictionary['scheduling']['BuildJedi']['execution_time_limit'] = 'PT4H'
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render_dictionary['scheduling']['BuildJedi']['account'] = 'g0613'
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render_dictionary['scheduling']['BuildJedi']['qos'] = 'allnccs'
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render_dictionary['scheduling']['BuildJedi']['constraint'] = 'hasw'
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render_dictionary['scheduling']['BuildJedi']['nodes'] = 1
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render_dictionary['scheduling']['BuildJedi']['ntasks_per_node'] = 24
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render_dictionary['scheduling']['BuildGeos'] = {}
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render_dictionary['scheduling']['BuildGeos']['execution_time_limit'] = 'PT1H'
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render_dictionary['scheduling']['BuildGeos']['account'] = 'g0613'
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render_dictionary['scheduling']['BuildGeos']['qos'] = 'allnccs'
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render_dictionary['scheduling']['BuildGeos']['nodes'] = 1
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render_dictionary['scheduling']['BuildGeos']['ntasks_per_node'] = 24
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# Render the template
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# -------------------
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new_suite_file = template_string_jinja2(logger, suite_file, render_dictionary)

‎src/swell/suites/forecast_geos/flow.cylc‎

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# (C) Copyright 2021-2022 United States Government as represented by the Administrator of the
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# National Aeronautics and Space Administration. All Rights Reserved.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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# --------------------------------------------------------------------------------------------------
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# Cylc suite for executing Geos forecast
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# --------------------------------------------------------------------------------------------------
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[scheduler]
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UTC mode = True
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allow implicit tasks = False
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# --------------------------------------------------------------------------------------------------
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[scheduling]
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initial cycle point = {{start_cycle_point}}
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final cycle point = {{final_cycle_point}}
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runahead limit = {{runahead_limit}}
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[[graph]]
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R1 = """
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# Triggers for non cycle time dependent tasks
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# -------------------------------------------
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# Clone Geos source code
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CloneGeos
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# Build Geos source code by linking
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CloneGeos => BuildGeosByLinking?
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# If not able to link to build create the build
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BuildGeosByLinking:fail? => BuildGeos
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"""
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{% for cycle_time in cycle_times %}
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{{cycle_time.cycle_time}} = """
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{% for model_component in model_components %}
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# Task triggers for: {{model_component}}
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# ------------------
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# Get background
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GetRestart-{{model_component}}
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# Run Geos hofx executable
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BuildGeosByLinking[^]? | BuildGeos[^] => PrepGeosRunDir
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GetRestart-{{model_component}} => PrepGeosRunDir
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# Run Geos Executable
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PrepGeosRunDir => RunGeosExecutable
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# Save restart
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RunGeosExecutable => SaveRestart-{{model_component}}
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{% endfor %}
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"""
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{% endfor %}
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# --------------------------------------------------------------------------------------------------
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[runtime]
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# Task defaults
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# -------------
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[[root]]
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pre-script = "source $CYLC_SUITE_DEF_PATH/modules"
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[[[environment]]]
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datetime = $CYLC_TASK_CYCLE_POINT
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config = $CYLC_SUITE_DEF_PATH/experiment.yaml
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# Tasks
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# -----
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[[CloneGeos]]
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script = "swell_task CloneGeos $config"
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[[BuildGeosByLinking]]
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script = "swell_task BuildGeosByLinking $config"
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[[BuildGeos]]
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script = "swell_task BuildGeos $config"
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platform = {{platform}}
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execution time limit = {{scheduling["BuildGeos"]["execution_time_limit"]}}
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[[[directives]]]
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--account = {{scheduling["BuildGeos"]["account"]}}
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--qos = {{scheduling["BuildGeos"]["qos"]}}
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--job-name = BuildGeos
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--nodes={{scheduling["BuildGeos"]["nodes"]}}
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--ntasks-per-node={{scheduling["BuildGeos"]["ntasks_per_node"]}}
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[[PrepGeosRunDir]]
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script = "swell_task PrepGeosRunDir $config"
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{% for model_component in model_components %}
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[[GetRestart-{{model_component}}]]
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script = "swell_task GetRestart $config -d $datetime -m {{model_component}}"
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[[SaveRestart-{{model_component}}]]
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script = "swell_task SaveRestart $config -d $datetime -m {{model_component}}"
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{% endfor %}
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[[RunGeosExecutable]]
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script = "swell_task RunGeosExecutable $config -d $datetime"
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platform = {{platform}}
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execution time limit = {{scheduling["RunGeosExecutable"]["execution_time_limit"]}}
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[[[directives]]]
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--account = {{scheduling["RunGeosExecutable"]["account"]}}
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--qos = {{scheduling["RunGeosExecutable"]["qos"]}}
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--job-name = RunGeosExecutable
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--nodes={{scheduling["RunGeosExecutable"]["nodes"]}}
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--ntasks-per-node={{scheduling["RunGeosExecutable"]["ntasks_per_node"]}}
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# --------------------------------------------------------------------------------------------------

‎src/swell/suites/forecast_geos/geos_atmosphere/suites-forecast_geos-geos_atmosphere.yaml‎

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# Cycle frequency
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cycle_times:
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default_value: ['T00', 'T06', 'T12', 'T18']
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prompt: List all cycle times, by middle of the window?
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options: ['T00', 'T06', 'T12', 'T18']
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type: string-check-list

‎src/swell/suites/forecast_geos/geos_ocean/suites-forecast_geos-geos_ocean.yaml‎

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# Cycle frequency
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cycle_times:
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default_value: ['T00', 'T06', 'T12', 'T18']
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prompt: List all cycle times, by middle of the window?
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options: ['T00', 'T06', 'T12', 'T18']
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type: string-check-list

‎src/swell/suites/forecast_geos/suites-forecast_geos.yaml‎

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# Cycle start point
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start_cycle_point:
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default_value: '2020-12-15T00:00:00Z'
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prompt: What is the time of the first cycle (middle of the window)?
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type: iso-datetime
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# Cycle final point
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final_cycle_point:
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default_value: '2020-12-15T06:00:00Z'
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prompt: What is the time of the final cycle (middle of the window)?
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type: iso-datetime
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# Run ahead limit for workflow
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runahead_limit:
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default_value: 'P4'
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prompt: Since this suite is non-cycling choose how many hours the workflow can run ahead?
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type: string
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# Geos build system
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geos_build_method:
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default_value: use_existing
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prompt: Create a new GEOS build or use an existing build?
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options: ['create', 'use_existing']
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type: string-drop-list
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# Existing Geos bundle directory
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existing_source_directory:
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default_value: {{existing_source_directory}}
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prompt: Provide the path to an existing GEOS bundle directory containing source code repos
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type: string
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depends:
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key: geos_build_method
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value: use_existing
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# Existing GEOS build
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existing_build_directory:
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default_value: {{existing_build_directory}}
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prompt: Provide the path to an existing GEOS build directory
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type: string
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depends:
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key: geos_build_method
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value: use_existing
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# R2D2 Configuration
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r2d2_local_path:
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default_value: {{r2d2_local_path}}
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prompt: Enter the path where R2D2 will store experiment output
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type: string
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# What kind of coupling is needed
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model_coupling_style:
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default_value: uncoupled
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prompt: What kind of coupling would you like to run with?
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options: ['uncoupled', 'coupled']
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type: string-drop-list
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# Models to use
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model_components:
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default_value: ['geos_atmosphere', 'geos_ocean']
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prompt: Select models to use (choose at least one)
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options: use_method
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type: file-check-list
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‎src/swell/tasks/base/task_registry.py‎

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@@ -1,21 +1,28 @@
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# (C) Copyright 2021-2022 United States Government as represented by the Administrator of the
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# (C) Copyright 2021-2023 United States Government as represented by the Administrator of the
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# National Aeronautics and Space Administration. All Rights Reserved.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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valid_tasks = [
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'StageJedi',
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'GetObservations',
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'BuildJedi',
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'BuildGeosByLinking',
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'BuildGeos',
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'BuildJediByLinking',
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'BuildJedi',
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'CleanCycle',
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'CloneGeos',
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'CloneJedi',
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'GetBackground',
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'RunJediHofxExecutable',
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'EvaDriver',
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'GetBackgroundGeosExperiment',
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'StoreBackground',
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'CleanCycle',
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'SaveObsDiags',
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'GetBackground',
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'GetObservations',
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'GetRestart',
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'ObsProcessSetup',
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'PrepGeosRunDir',
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'RunGeosExecutable',
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'RunJediHofxExecutable',
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'SaveObsDiags',
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'SaveRestart',
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'StageJedi',
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'StoreBackground',
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]

‎src/swell/tasks/build_geos.py‎

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# (C) Copyright 2023 United States Government as represented by the Administrator of the
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# National Aeronautics and Space Administration. All Rights Reserved.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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# --------------------------------------------------------------------------------------------------
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from swell.tasks.base.task_base import taskBase
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# --------------------------------------------------------------------------------------------------
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class BuildGeos(taskBase):
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def execute(self):
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self.logger.info('BuildGeos')
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# --------------------------------------------------------------------------------------------------

‎src/swell/tasks/build_geos_by_linking.py‎

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# (C) Copyright 2023 United States Government as represented by the Administrator of the
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# National Aeronautics and Space Administration. All Rights Reserved.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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# --------------------------------------------------------------------------------------------------
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from swell.tasks.base.task_base import taskBase
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# --------------------------------------------------------------------------------------------------
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class BuildGeosByLinking(taskBase):
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def execute(self):
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self.logger.info('BuildGeosByLinking')
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# --------------------------------------------------------------------------------------------------

‎src/swell/tasks/clone_geos.py‎

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# (C) Copyright 2023 United States Government as represented by the Administrator of the
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# National Aeronautics and Space Administration. All Rights Reserved.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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# --------------------------------------------------------------------------------------------------
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from swell.tasks.base.task_base import taskBase
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# --------------------------------------------------------------------------------------------------
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class CloneGeos(taskBase):
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def execute(self):
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self.logger.info('CloneGeos')
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# --------------------------------------------------------------------------------------------------

‎src/swell/tasks/get_restart.py‎

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# (C) Copyright 2023 United States Government as represented by the Administrator of the
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# National Aeronautics and Space Administration. All Rights Reserved.
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#
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# This software is licensed under the terms of the Apache Licence Version 2.0
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# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
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# --------------------------------------------------------------------------------------------------
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from swell.tasks.base.task_base import taskBase
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# --------------------------------------------------------------------------------------------------
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class GetRestart(taskBase):
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def execute(self):
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self.logger.info('GetRestart')
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# --------------------------------------------------------------------------------------------------

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