polaris.ocean.model.OceanModelStep

class polaris.ocean.model.OceanModelStep(component, name, subdir=None, indir=None, ntasks=None, min_tasks=None, openmp_threads=None, max_memory=None, cached=False, yaml=None, update_pio=True, make_graph=False, mesh_filename=None, partition_graph=True, graph_target=None)

An Omega or MPAS-Ocean step

Variables:

• dynamic_ntasks (bool) – Whether the target and minimum number of MPI tasks (ntasks and min_tasks) are computed dynamically from the number of cells in the mesh

• config_map (dict) – A nested dictionary that maps from MPAS-Ocean to Omega model config options

• graph_target (str) – The name of the graph partition file to link to (relative to the base working directory)

__init__(component, name, subdir=None, indir=None, ntasks=None, min_tasks=None, openmp_threads=None, max_memory=None, cached=False, yaml=None, update_pio=True, make_graph=False, mesh_filename=None, partition_graph=True, graph_target=None)

Make a step for running the model

Parameters:

• component (polaris.Component) – The component the step belongs to

• name (str) – The name of the step

• subdir (str, optional) –

  the subdirectory for the step. If neither this nor indir

  are provided, the directory is the name

• indir (str, optional) – the directory the step is in, to which name will be appended

• ntasks (int, optional) – the target number of tasks the step would ideally use. If too few cores are available on the system to accommodate the number of tasks and the number of cores per task, the step will run on fewer tasks as long as as this is not below min_tasks

• min_tasks (int, optional) – the number of tasks the step requires. If the system has too few cores to accommodate the number of tasks and cores per task, the step will fail

• openmp_threads (int, optional) – the number of OpenMP threads to use

• max_memory (int, optional) – the amount of memory that the step is allowed to use in MB. This is currently just a placeholder for later use with task parallelism

• cached (bool, optional) – Whether to get all of the outputs for the step from the database of cached outputs for this component

• update_pio (bool, optional) – Whether to modify the namelist so the number of PIO tasks and the stride between them is consistent with the number of nodes and cores (one PIO task per node).

• make_graph (bool, optional) – Whether to make a graph file from the given MPAS mesh file. If True, mesh_filename must be given.

• mesh_filename (str, optional) – The name of an MPAS mesh file to use to make the graph file

• partition_graph (bool, optional) – Whether to partition the domain for the requested number of cores. If so, the partitioning executable is taken from the partition option of the [executables] config section.

• graph_target (str, optional) – The graph file name (relative to the base work directory). If none, it will be created.

Methods

__init__(component, name[, subdir, indir, ...])	Make a step for running the model
add_dependency(step[, name])	Add step as a dependency of this step (i.e. this step can't run until the dependency has finished).
add_input_file([filename, target, database, ...])	Add an input file to the step (but not necessarily to the MPAS model).
add_model_config_options(options[, config_model])	Add the replacement model config options to be parsed when generating a namelist or yaml file if and when the step gets set up.
add_namelist_file(package, namelist)	Add a file with updates to namelist options to the step to be parsed when generating a complete namelist file if and when the step gets set up.
add_output_file(filename[, validate_vars])	Add the output file that must be produced by this step and may be made available as an input to steps, perhaps in other tasks.
add_streams_file(package, streams[, ...])	Add a streams file to the step to be parsed when generating a complete streams file if and when the step gets set up.
add_yaml_file(package, yaml[, ...])	Add a file with updates to yaml config options to the step to be parsed when generating a complete yaml file if and when the step gets set up.
compute_cell_count()	Compute the approximate number of cells in the mesh, used to constrain resources
constrain_resources(available_cores)	Update the number of MPI tasks to use based on the estimated mesh size
dynamic_model_config(at_setup)	Add model config options, namelist, streams and yaml files using config options or template replacements that need to be set both during step setup and at runtime
map_yaml_configs(configs, config_model)	A mapping between model sections and config options from MPAS-Ocean to Omega
map_yaml_options(options, config_model)	A mapping between model config options from MPAS-Ocean to Omega
map_yaml_streams(streams, config_model)	A mapping between model streams from different models.
map_yaml_to_namelist(options)	A mapping from yaml model config options to namelist options.
partition([graph_file])	Partition the domain for the requested number of tasks
process_inputs_and_outputs()	Process the model as an input, then call the parent class' version
run()	Run the step.
runtime_setup()	Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])	Update the resources for the step.
set_resources([cpus_per_task, ...])	Update the resources for the subtask.
set_shared_config(config[, link])	Replace the step's config parser with the shared config parser
setup()	Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()	Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()	Compare variables between output files in this step and in the same step from a baseline run if one was provided.