Index

Symbols

--add-draws psimulate-expand command line option --add-seeds psimulate-expand command line option --artifact_path psimulate-run command line option --backup-freq psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --branch-configuration psimulate-run command line option --csv vipin command line option --hardware psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --hdf vipin command line option --max-attempts psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --max-runtime psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --max-workers psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --model-specification psimulate-run command line option --num-workers psimulate-test command line option --pdb psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --peak-memory psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --project psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --queue psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option --result-directory psimulate-run command line option psimulate-test command line option vipin command line option --results-root psimulate-expand command line option psimulate-restart command line option

--run-config psimulate-expand command line option psimulate-restart command line option psimulate-run command line option --sim-verbosity psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -B psimulate-run command line option -c psimulate-expand command line option psimulate-restart command line option psimulate-run command line option -h psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -i psimulate-run command line option -M psimulate-run command line option -m psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -n psimulate-test command line option -o psimulate-run command line option psimulate-test command line option vipin command line option -P psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -q psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -R psimulate-expand command line option psimulate-restart command line option -r psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -s psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option -v psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option vipin command line option -w psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test command line option

A

add_draws() (vivarium_cluster_tools.psimulate.branches.Keyspace method) add_logging_sink() (in module vivarium_cluster_tools.logs) add_seeds() (vivarium_cluster_tools.psimulate.branches.Keyspace method) already_complete() (in module vivarium_cluster_tools.psimulate.jobs)

append_child_job_data() (in module vivarium_cluster_tools.psimulate.performance_logger) append_perf_data_to_central_logs() (in module vivarium_cluster_tools.psimulate.performance_logger) artifact (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) artifact_name (vivarium_cluster_tools.psimulate.paths.OutputPaths property)

B

backoff_and_retry() (in module vivarium_cluster_tools.utilities) backup_configuration (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) backup_dir (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) backup_metadata_path (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) Branch Configuration

branch_configuration (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) BRANCH_CONFIGURATION_POS psimulate-run command line option branches (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) build_job_list() (in module vivarium_cluster_tools.psimulate.jobs)

C

calculate_input_draws() (in module vivarium_cluster_tools.psimulate.branches) calculate_keyspace() (in module vivarium_cluster_tools.psimulate.branches) calculate_random_seeds() (in module vivarium_cluster_tools.psimulate.branches) clean_perf_logs() (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary method) coerce_to_full_path() (in module vivarium_cluster_tools.cli_tools)

collect_metadata() (in module vivarium_cluster_tools.psimulate.results.writing) Configuration Parameter configure_main_process_logging_to_file() (in module vivarium_cluster_tools.logs) configure_main_process_logging_to_terminal() (in module vivarium_cluster_tools.logs) convert() (vivarium_cluster_tools.cli_tools.MinutesOrNone method) CounterSnapshot (class in vivarium_cluster_tools.vipin.perf_counters)

D

do_sim_epilogue() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse)

E

environment_file (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) EnvVariable (class in vivarium_cluster_tools.psimulate.environment)

errors (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary attribute) expand_branch_templates() (in module vivarium_cluster_tools.psimulate.branches) extras (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute)

F

for_load_test() (vivarium_cluster_tools.psimulate.branches.Keyspace class method) from_branch_configuration() (vivarium_cluster_tools.psimulate.branches.Keyspace class method) from_entry_point_args() (vivarium_cluster_tools.psimulate.branches.Keyspace class method) (vivarium_cluster_tools.psimulate.paths.InputPaths class method) (vivarium_cluster_tools.psimulate.paths.OutputPaths class method)

from_previous_run() (vivarium_cluster_tools.psimulate.branches.Keyspace class method)

G

generate_runner_job_data() (in module vivarium_cluster_tools.psimulate.performance_logger) generate_task_id() (in module vivarium_cluster_tools.psimulate.jobs) get_backup() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) get_cluster_name() (in module vivarium_cluster_tools.utilities) get_completed_task_ids() (in module vivarium_cluster_tools.psimulate.results.writing)

get_psimulate_test_dict() (in module vivarium_cluster_tools.psimulate.worker.load_test_work_horse) get_sim_from_backup() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) get_sim_results() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) get_summaries() (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary method) get_workflow_timeout_seconds() (in module vivarium_cluster_tools.psimulate.cluster.interface)

H

hardware (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute)

I

initialize_new_sim() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) Input Draw

input_draw (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) InputPaths (class in vivarium_cluster_tools.psimulate.paths)

J

job_name (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute)

job_specific (vivarium_cluster_tools.psimulate.jobs.JobParameters property) JobParameters (class in vivarium_cluster_tools.psimulate.jobs)

K

Keyspace (class in vivarium_cluster_tools.psimulate.branches)

keyspace (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute)

L

large_results_test() (in module vivarium_cluster_tools.psimulate.worker.load_test_work_horse) load_branch_configuration() (in module vivarium_cluster_tools.psimulate.branches) load_run_config() (in module vivarium_cluster_tools.cli_tools) log_dir (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary attribute)

logging_root (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) logging_to_central_results_directory (vivarium_cluster_tools.psimulate.paths.OutputPaths property) LOGS_DIRECTORY vipin command line option

M

main() (in module vivarium_cluster_tools.psimulate.runner) (in module vivarium_cluster_tools.psimulate.worker.task_runner) max_runtime (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute) metadata_dir (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) MinutesOrNone (class in vivarium_cluster_tools.cli_tools) mkdir() (in module vivarium_cluster_tools.utilities) Model Specification model_specification (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) MODEL_SPECIFICATION_POS psimulate-run command line option module vivarium_cluster_tools vivarium_cluster_tools.cli_tools vivarium_cluster_tools.logs vivarium_cluster_tools.psimulate vivarium_cluster_tools.psimulate.branches vivarium_cluster_tools.psimulate.cli vivarium_cluster_tools.psimulate.cluster vivarium_cluster_tools.psimulate.cluster.cli_options vivarium_cluster_tools.psimulate.cluster.interface vivarium_cluster_tools.psimulate.environment vivarium_cluster_tools.psimulate.jobs vivarium_cluster_tools.psimulate.model_specification vivarium_cluster_tools.psimulate.paths vivarium_cluster_tools.psimulate.performance_logger vivarium_cluster_tools.psimulate.pip_env vivarium_cluster_tools.psimulate.results vivarium_cluster_tools.psimulate.results.cli_options vivarium_cluster_tools.psimulate.results.writing vivarium_cluster_tools.psimulate.runner vivarium_cluster_tools.psimulate.worker vivarium_cluster_tools.psimulate.worker.load_test_work_horse vivarium_cluster_tools.psimulate.worker.task_runner vivarium_cluster_tools.psimulate.worker.vivarium_work_horse vivarium_cluster_tools.utilities vivarium_cluster_tools.vipin vivarium_cluster_tools.vipin.cli vivarium_cluster_tools.vipin.perf_counters vivarium_cluster_tools.vipin.perf_report

N

name (vivarium_cluster_tools.cli_tools.MinutesOrNone attribute) (vivarium_cluster_tools.psimulate.environment.EnvVariable property)

NativeSpecification (class in vivarium_cluster_tools.psimulate.cluster.interface) NUM_THREADS (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute)

O

original_run_date (vivarium_cluster_tools.psimulate.paths.OutputPaths property)

OutputPaths (class in vivarium_cluster_tools.psimulate.paths)

P

ParallelSimulationContext (class in vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) Parameter Uncertainty parse() (in module vivarium_cluster_tools.psimulate.model_specification) parse_args() (in module vivarium_cluster_tools.psimulate.worker.task_runner) pass_shared_options() (in module vivarium_cluster_tools.cli_tools) peak_memory (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute) PERF_LOG_PATTERN (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary attribute) PerformanceSummary (class in vivarium_cluster_tools.vipin.perf_report) persist() (in module vivarium_cluster_tools.psimulate.model_specification) (vivarium_cluster_tools.psimulate.branches.Keyspace method) print_stat_report() (in module vivarium_cluster_tools.vipin.perf_report) project (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute) project_name (vivarium_cluster_tools.psimulate.paths.OutputPaths property) psimulate-expand command line option --add-draws --add-seeds --backup-freq --hardware --max-attempts --max-runtime --max-workers --pdb --peak-memory --project --queue --results-root --run-config --sim-verbosity -c -h -m -P -q -R -r -s -v -w RESULTS_ROOT_POS psimulate-restart command line option --backup-freq --hardware --max-attempts --max-runtime --max-workers --pdb --peak-memory --project --queue --results-root --run-config --sim-verbosity -c -h -m -P -q -R -r -s -v -w RESULTS_ROOT_POS

psimulate-run command line option --artifact_path --backup-freq --branch-configuration --hardware --max-attempts --max-runtime --max-workers --model-specification --pdb --peak-memory --project --queue --result-directory --run-config --sim-verbosity -B -c -h -i -M -m -o -P -q -r -s -v -w BRANCH_CONFIGURATION_POS MODEL_SPECIFICATION_POS psimulate-test command line option --backup-freq --hardware --max-attempts --max-runtime --max-workers --num-workers --pdb --peak-memory --project --queue --result-directory --sim-verbosity -h -m -n -o -P -q -r -s -v -w TEST_TYPE

Q

queue (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute)

R

Random Seed random_seed (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) remove_backups() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) report_initial_status() (in module vivarium_cluster_tools.psimulate.runner) report_performance() (in module vivarium_cluster_tools.vipin.perf_report) resolve_deprecated_positional() (in module vivarium_cluster_tools.cli_tools) result_directory (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) results_dir (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute)

results_path (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) RESULTS_ROOT_POS psimulate-expand command line option psimulate-restart command line option root (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) root_path (vivarium_cluster_tools.psimulate.paths.OutputPaths property) run_date (vivarium_cluster_tools.psimulate.paths.OutputPaths property) run_simulation() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) run_type (vivarium_cluster_tools.psimulate.paths.OutputPaths property)

S

set_index_scenario_cols() (in module vivarium_cluster_tools.vipin.perf_report) shared (vivarium_cluster_tools.psimulate.jobs.JobParameters property)

sim_config (vivarium_cluster_tools.psimulate.jobs.JobParameters property) sleep_test() (in module vivarium_cluster_tools.psimulate.worker.load_test_work_horse) Stochastic Uncertainty

T

task_id (vivarium_cluster_tools.psimulate.jobs.JobParameters property) TELEMETRY_PATTERN (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary attribute) TEST_TYPE psimulate-test command line option to_df() (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary method)

to_dict() (vivarium_cluster_tools.psimulate.jobs.JobParameters method) (vivarium_cluster_tools.vipin.perf_counters.CounterSnapshot method) to_jobmon_spec() (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification method) touch() (vivarium_cluster_tools.psimulate.paths.OutputPaths method) transform_perf_df_for_appending() (in module vivarium_cluster_tools.psimulate.performance_logger) try_run_vipin() (in module vivarium_cluster_tools.psimulate.runner)

U

update() (vivarium_cluster_tools.psimulate.environment.EnvVariable method)

V

validate() (in module vivarium_cluster_tools.psimulate.pip_env) validate_artifact_path() (in module vivarium_cluster_tools.psimulate.branches) validate_cluster_environment() (in module vivarium_cluster_tools.psimulate.cluster.interface) value (vivarium_cluster_tools.psimulate.environment.EnvVariable property) vipin command line option --csv --hdf --result-directory -o -v LOGS_DIRECTORY vivarium_cluster_tools module vivarium_cluster_tools.cli_tools module vivarium_cluster_tools.logs module vivarium_cluster_tools.psimulate module vivarium_cluster_tools.psimulate.branches module vivarium_cluster_tools.psimulate.cli module vivarium_cluster_tools.psimulate.cluster module vivarium_cluster_tools.psimulate.cluster.cli_options module vivarium_cluster_tools.psimulate.cluster.interface module vivarium_cluster_tools.psimulate.environment module vivarium_cluster_tools.psimulate.jobs module

vivarium_cluster_tools.psimulate.model_specification module vivarium_cluster_tools.psimulate.paths module vivarium_cluster_tools.psimulate.performance_logger module vivarium_cluster_tools.psimulate.pip_env module vivarium_cluster_tools.psimulate.results module vivarium_cluster_tools.psimulate.results.cli_options module vivarium_cluster_tools.psimulate.results.writing module vivarium_cluster_tools.psimulate.runner module vivarium_cluster_tools.psimulate.worker module vivarium_cluster_tools.psimulate.worker.load_test_work_horse module vivarium_cluster_tools.psimulate.worker.task_runner module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse module vivarium_cluster_tools.utilities module vivarium_cluster_tools.vipin module vivarium_cluster_tools.vipin.cli module vivarium_cluster_tools.vipin.perf_counters module vivarium_cluster_tools.vipin.perf_report module

W

with_queue_and_max_runtime() (in module vivarium_cluster_tools.psimulate.cluster.cli_options) with_run_config() (in module vivarium_cluster_tools.cli_tools) with_sim_verbosity() (in module vivarium_cluster_tools.cli_tools) with_verbose_and_pdb() (in module vivarium_cluster_tools.cli_tools) work_horse() (in module vivarium_cluster_tools.psimulate.worker.load_test_work_horse) (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse)

worker_logging_root (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) write_backup_metadata() (in module vivarium_cluster_tools.psimulate.runner) write_configuration() (in module vivarium_cluster_tools.psimulate.runner) write_metadata() (in module vivarium_cluster_tools.psimulate.results.writing) write_task_results() (in module vivarium_cluster_tools.psimulate.results.writing)