microbenthos.runners package

Submodules

microbenthos.runners.simulate module

class microbenthos.runners.simulate.SimulationRunner(output_dir=None, resume=False, confirm=False, overwrite=False, model=None, simulation=None, progress=False, progress_tag='evolution', plot=False, video=False, frames=False, budget=False, exporters=None, show_eqns=False)

Bases: object

Class that handles the pipeline of creating and running simulations of models, and generating outputs from it.

This class will:

• check that the model & simulation setup are complete

• check the output path

• create a log file

• export the model definition

• export the run setup

• setup the exporters

• run the simulation evolution

• clean up

property model

The model to run with the simulation. Typically an instance of MicroBenthosModel.

property simulation

The Simulation instance that will run with the model

add_exporter(exptype, name=None, **kwargs)

Add an exporter to the simulation run

Parameters

• exptype (str) – The type of exporter. This should match the _exports_ on the class of the exporter. (See :class:`~microbenthos.exporters.exporter.BaseExporter)

• name (str) – The name to set for the exporter

• **kwargs – passed to the init of the exporter class.

Returns

The name of the exporter created

_create_output_dir()

Create the output directory

Raises

OSError – if output_dir is a file and not a dir

resume_existing_simulation(data_outpath=None)

setup_logfile(mode='a')

Setup log file in the output directory

teardown_logfile()

save_definitions()

Save the model and simulation definition to the output directory

save_run_info()

Save the runner info to output_dir

get_info()

Return a dictionary of info about the runtime environment

check_simulation()

prepare_simulation()

Prepare the simulation by setting up the model

exporters_activated()

A context manager that starts and closes the exporters Returns:

get_data_exporters()

run()

Run the simulation with the stored model and simulation setup.

This performs a sequence of operations:

• shows equations if show_eqns is set

• Announces simulation settings in output

• Runs check_simulation()

• creates output directory

• sets up the logfile

• saves definitions to yaml outputs of simulation & model

• saves the runtime info (library, exporter versions etc)

• prepares the simulation

• activates the exporter context (see exporters_activated())

• iterates over the simulation.evolution() and passes returned state to the exporters

• after that tears down the logfile

Raises

RuntimeError – if no simulation exists

Module contents