API Reference
vivarium_cluster_tools
Tools for working with vivarium on compute clusters.
- Shared CLI tools
with_verbose_and_pdb()coerce_to_full_path()pass_shared_options()- Logging Utilities
add_logging_sink()configure_main_process_logging_to_terminal()configure_main_process_logging_to_file()- vivarium_cluster_tools Utilities
get_cluster_name()get_drmaa()mkdir()backoff_and_retry()- psimulate
- Branch and Keyspace Management
Keyspacecalculate_input_draws()calculate_random_seeds()calculate_keyspace()load_branch_configuration()expand_branch_templates()validate_artifact_path()- psimulate CLI
- Environment Variables
EnvVariable- psimulate Jobs
JobParametersbuild_job_list()already_complete()- Model specification management
parse()persist()- File Path Management
InputPathsOutputPathsOutputPaths.rootOutputPaths.logging_rootOutputPaths.cluster_logging_rootOutputPaths.worker_logging_rootOutputPaths.worker_settingsOutputPaths.environment_fileOutputPaths.model_specificationOutputPaths.keyspaceOutputPaths.branchesOutputPaths.resultsOutputPaths.artifact_nameOutputPaths.run_dateOutputPaths.run_typeOutputPaths.original_run_dateOutputPaths.project_nameOutputPaths.root_pathOutputPaths.logging_to_central_results_directoryOutputPaths.from_entry_point_args()OutputPaths.touch()
- Reproducible Programming Environments
validate()- psimulate Runner
process_job_results()load_existing_outputs()report_initial_status()try_run_vipin()main()- Cluster Interaction
- Cluster CLI options
with_queue_and_max_runtime()- Cluster Interface
validate_cluster_environment()NativeSpecificationsubmit_worker_jobs()- redis_dbs
- Redis DB CLI options
- Redis Database Initialization
launch_redis_processes()- Redis Queue and Registry Management
QueueManagerRegistryManager- Results Management
- Results Processing CLI Options
- Results Processing
write_results_batch()- psimulate RQ Workers
- Distributed Worker
build_launch_script()- Vivarium Worker
work_horse()setup_sim()do_sim_epilogue()parameter_update_format()- vipin - Vivarium Performance Log Parser