Vivarium Cluster Tools Documentation
Vivarium cluster tools is a python package that makes running vivarium
simulations at scale on a Slurm cluster easy.
- Installation
- Running simulations in parallel
- YAML Basics
- The Branches File
- Logging
- API Reference
- vivarium_cluster_tools
- 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
Keyspace
calculate_input_draws()
calculate_random_seeds()
calculate_keyspace()
load_branch_configuration()
expand_branch_templates()
validate_artifact_path()
- psimulate CLI
- Environment Variables
EnvVariable
- psimulate Jobs
JobParameters
build_job_list()
already_complete()
- Model specification management
parse()
persist()
- File Path Management
InputPaths
OutputPaths
- 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()
NativeSpecification
submit_worker_jobs()
- redis_dbs
- Redis DB CLI options
- Redis Database Initialization
launch_redis_processes()
- Redis Queue and Registry Management
QueueManager
RegistryManager
- 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
- Glossary