polaris.tasks.ocean.analysis.analysis_step.AnalysisStep

class polaris.tasks.ocean.analysis.analysis_step.AnalysisStep(component, name, subdir, start_year, end_year, **kwargs)

A step of the ocean analysis suite

Every analysis step covers a range of simulation years and reads some of the simulation’s output, so both live here rather than being repeated by each product.

Variables:

• start_year (int) – The first year of the range this step covers, inclusive

• end_year (int) – The last year of the range this step covers, inclusive

• input_filenames (list of str) – The local names of the simulation files symlinked into the step’s work directory, in the order they were added

• manifest (polaris.analysis.manifest.Manifest) – The products this step has described so far, written to manifest.json in the step’s work directory as they are added. Steps add to it through add_product() rather than directly.

__init__(component, name, subdir, start_year, end_year, **kwargs)

Create a new analysis step

Parameters:

• component (polaris.tasks.ocean.Ocean) – The ocean component the step belongs to

• name (str) – The name of the step

• subdir (str) – The subdirectory for the step, which ends in the range key so that a step covering a different range is a different step

• start_year (int) – The first year of the range this step covers, inclusive

• end_year (int) – The last year of the range this step covers, inclusive

• kwargs – Keyword arguments passed on to polaris.ocean.model.OceanIOStep

Methods

__init__(component, name, subdir, ...)	Create a new analysis step
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_horiz_mesh_input_file(**kwargs)	Add the horizontal-mesh input file using a placeholder that is resolved to the configured filename at process_inputs_and_outputs() time.
add_init_input_file(**kwargs)	Add the initial-condition input file using a placeholder that is resolved to the configured filename at process_inputs_and_outputs() time.
add_input_file([filename, target, database, ...])	Add an input file to the step (but not necessarily to the MPAS model).
add_output_file(filename[, validate_vars, ...])	Add an output file, optionally resolving validate_class to a pre-defined list of variables from the Ocean component.
add_output_files_for_ocean_model_input([...])	Register output files that will be consumed by the ocean model as inputs (horizontal mesh, initial condition, and model-specific files).
add_produced_file(filename)	Register a file the step has just written as one of its outputs
add_product(plot, group, gallery, title[, data])	Describe one product this step has just made, and update the fragment
add_property_check(filename, check_properties)	Add a single conservation comparison for an output file
add_sim_input_file(path[, filename])	Symlink one file of simulation output into the step's work directory
add_sim_input_files(sim_files)	Symlink a list of simulation files into the step's work directory
add_vert_coord_input_file([filename])	Add the vertical-coordinate input file.
check_properties()	Check conservation properties of the output files of this step.
constrain_resources(available_resources)	Constrain cpus_per_task and ntasks based on the number of cores available to this step
get_horiz_mesh_filename()	Get the configured local filename for the horizontal mesh file.
get_init_filename()	Get the configured local filename for the initial-condition file.
get_sim_files()	Get the simulation's files, reporting where each path came from
get_vert_coord_filename()	Get the configured local filename for the vertical coordinate file.
log_inputs()	Report the simulation files this step reads
map_from_native_model_vars(ds)	If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)	If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename[, config, ...])	Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
open_vert_coord_dataset(ds_init[, ...])	Return the dataset containing vertical-coordinate variables (bottomDepth, minLevelCell, maxLevelCell, vertCoordMovementWeights and either restingThickness or RefPseudoThickness).
process_inputs_and_outputs()	Resolve <<<placeholder>>> filenames to configured names and drop <<<vert_coord>>> entries for MPAS-Ocean before delegating to the base Step processing.
run()	Run the step.
runtime_setup()	Write the empty manifest fragment before the step runs
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()	Set up the task in the work directory, including downloading any dependencies.
validate_baselines()	Compare variables between output files in this step and in the same step from a baseline run if one was provided.
work_path(*filenames)	Get the absolute path to a file or directory in the step's work directory
write_horiz_mesh_dataset(ds, filename, config)	Write a horizontal mesh dataset, validating that all expected mesh variables are present before writing.
write_initial_state_dataset(ds, filename, config)	Write an initial-state dataset, converting the tracers to the convention the model expects and omitting horizontal mesh fields and (for Omega) vertical coordinate fields.
write_model_dataset(ds, filename, config)	Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
write_vert_coord_dataset(ds, filename, config)	Write a vertical-coordinate dataset for Omega's InitialVertCoord stream.

Attributes

cores	the number of cores this step needs, in total
gpus	the number of GPUs this step needs, in total
makes_products	Whether this step makes products for the published gallery, and so writes a manifest fragment describing them.
may_span_nodes	whether this step's cores and GPUs may come from several nodes
min_cores	the number of cores this step needs in order to run at all
min_gpus	the number of GPUs this step requires, in total
component
config
input_data
logger