API Reference

vivarium.cluster_tools

Tools for working with vivarium on compute clusters.

• vivarium.cluster_tools Utilities
• get_cluster_name()
• hash_output_path()
• mkdir()
• backoff_and_retry()
• core
• Shared CLI tools
• with_verbose_and_pdb()
• with_sim_verbosity()
• resolve_sim_verbosity()
• with_slack_channel()
• with_slack_tag()
• with_slack_mute()
• validate_slack_options()
• coerce_to_full_path()
• pass_shared_options()
• MinutesOrNone
  • MinutesOrNone.name
  • MinutesOrNone.convert()
• load_run_config()
• with_run_config()
• with_workflow_config()
• resolve_deprecated_positional()
• Logging Utilities
• configure_main_process_logging_to_terminal()
• configure_main_process_logging_to_file()
• Cluster Interaction
• Cluster CLI options
• with_queue_and_max_runtime()
• Cluster Interface
• NativeSpecification
  • NativeSpecification.job_name
  • NativeSpecification.project
  • NativeSpecification.queue
  • NativeSpecification.peak_memory
  • NativeSpecification.max_runtime
  • NativeSpecification.hardware
  • NativeSpecification.cores
  • NativeSpecification.requires_archive_node
  • NativeSpecification.to_jobmon_spec()
• get_workflow_timeout_seconds()
• dagger
• dagger CLI
  • dagger
• dagger Runner
• run_workflow()
• restart_workflow()
• Workflow Configuration
• Workflow Builder
• STEP_TYPE_API_FNS
• build_workflow_from_config()
• Workflow Configuration
• REQUIRED_WORKFLOW_FIELDS
• DEFAULT_BACKUP_FREQ_SECONDS
• ResourceConfig
  • ResourceConfig.memory_gb
  • ResourceConfig.project
  • ResourceConfig.queue
  • ResourceConfig.runtime
  • ResourceConfig.cores
  • ResourceConfig.hardware
  • ResourceConfig.requires_archive_node
  • ResourceConfig.from_dict()
  • ResourceConfig.to_dict()
  • ResourceConfig.to_native_specification()
• ParsedStep
  • ParsedStep.step_type
  • ParsedStep.name
  • ParsedStep.api_kwargs
• WorkflowConfig
  • WorkflowConfig.name
  • WorkflowConfig.project
  • WorkflowConfig.queue
  • WorkflowConfig.output_directory
  • WorkflowConfig.default_environment
  • WorkflowConfig.steps
  • WorkflowConfig.max_attempts
  • WorkflowConfig.parse_yaml_file()
• Workflow Config Interface
• get_step_resources()
• get_bash_step_tasks()
• get_simulation_step_tasks()
• get_pytest_step_tasks()
• get_python_step_tasks()
• get_notebook_step_tasks()
• Workflow Step Parsing
• resolve_step_type()
• parse_bash_step_from_yaml()
• parse_simulation_step_from_yaml()
• parse_pytest_step_from_yaml()
• parse_python_step_from_yaml()
• parse_notebook_step_from_yaml()
• STEP_TYPE_YAML_PARSERS
• parse_step_from_yaml()
• load_workflow_config()
• Workflow Step Serialization
• serialize_bash_step_to_yaml()
• serialize_simulation_step_to_yaml()
• serialize_pytest_step_to_yaml()
• serialize_python_step_to_yaml()
• serialize_notebook_step_to_yaml()
• STEP_TYPE_YAML_SERIALIZERS
• workflow_config_to_dict()
• Workflow Step Validation
• validate_bash_step()
• validate_simulation_step()
• validate_pytest_step()
• validate_python_step()
• validate_notebook_step()
• psimulate
• Branch and Keyspace Management
• Keyspace
  • Keyspace.from_branch_configuration()
  • Keyspace.from_previous_run()
  • Keyspace.for_load_test()
  • Keyspace.from_entry_point_args()
  • Keyspace.persist()
  • Keyspace.add_draws()
  • Keyspace.add_seeds()
• calculate_input_draws()
• calculate_random_seeds()
• calculate_keyspace()
• load_branch_configuration()
• expand_branch_templates()
• validate_artifact_path()
• psimulate CLI
  • psimulate
• Environment Variables
• EnvVariable
  • EnvVariable.name
  • EnvVariable.value
  • EnvVariable.update()
• psimulate Jobs
• BackupConfiguration
  • BackupConfiguration.backup_dir
  • BackupConfiguration.backup_freq
  • BackupConfiguration.backup_metadata_path
• generate_task_id()
• JobParameters
  • JobParameters.model_specification
  • JobParameters.branch_configuration
  • JobParameters.input_draw
  • JobParameters.random_seed
  • JobParameters.results_path
  • JobParameters.worker_logging_root
  • JobParameters.backup_configuration
  • JobParameters.extras
  • JobParameters.task_id
  • JobParameters.shared
  • JobParameters.job_specific
  • JobParameters.sim_config
  • JobParameters.to_dict()
• build_job_parameters_from_keyspace()
• build_job_list()
• already_complete()
• Model specification management
• parse()
• persist()
• File Path Management
• InputPaths
  • InputPaths.model_specification
  • InputPaths.branch_configuration
  • InputPaths.artifact
  • InputPaths.result_directory
  • InputPaths.from_entry_point_args()
• OutputPaths
  • OutputPaths.root
  • OutputPaths.logging_root
  • OutputPaths.worker_logging_root
  • OutputPaths.metadata_dir
  • OutputPaths.environment_file
  • OutputPaths.model_specification
  • OutputPaths.keyspace
  • OutputPaths.branches
  • OutputPaths.results_dir
  • OutputPaths.backup_dir
  • OutputPaths.backup_metadata_path
  • OutputPaths.artifact_name
  • OutputPaths.run_date
  • OutputPaths.run_type
  • OutputPaths.original_run_date
  • OutputPaths.project_name
  • OutputPaths.root_path
  • OutputPaths.logging_to_central_results_directory
  • OutputPaths.from_entry_point_args()
  • OutputPaths.touch()
• transform_perf_df_for_appending()
• append_child_job_data()
• generate_runner_job_data()
• append_perf_data_to_central_logs()
• Reproducible Programming Environments
• validate()
• psimulate Runner
• report_initial_status()
• try_run_vipin()
• write_backup_metadata()
• write_configuration()
• main()
• Results Management
• Results CLI Options
• Results Writing
• write_metadata()
• write_task_results()
• get_completed_task_ids()
• collect_metadata()
• psimulate Workers
• Load Test Worker
• get_psimulate_test_dict()
• sleep_test()
• large_results_test()
• work_horse()
• Jobmon Task Runner
• parse_args()
• main()
• Vivarium Worker
• ParallelSimulationContext
• work_horse()
• get_backup()
• get_sim_from_backup()
• initialize_new_sim()
• run_simulation()
• get_sim_results()
• do_sim_epilogue()
• remove_backups()
• vipin - Vivarium Performance Log Parser
  • vipin
  • vipin CLI
  • vipin Performance Counters
  • CounterSnapshot
  • Performance Reporting
  • PerformanceSummary
  • set_index_scenario_cols()
  • print_stat_report()
  • report_performance()