Index

Symbols

--add-draws psimulate-expand command line option --add-seeds psimulate-expand command line option --artifact_path 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-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 --no-batch psimulate-expand command line option psimulate-restart command line option psimulate-run command line option psimulate-test 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

--redis 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 -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-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 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) add_squid_api_data() (in module vivarium_cluster_tools.vipin.perf_report)

allocate_jobs() (vivarium_cluster_tools.psimulate.redis_dbs.registry.RegistryManager method) already_complete() (in module vivarium_cluster_tools.psimulate.jobs) artifact (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) artifact_name (vivarium_cluster_tools.psimulate.paths.OutputPaths property)

B

backoff (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager attribute) backoff_and_retry() (in module vivarium_cluster_tools.utilities) Branch Configuration BRANCH_CONFIGURATION psimulate-run command line option

branch_configuration (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) branches (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) build_job_list() (in module vivarium_cluster_tools.psimulate.jobs) build_launch_script() (in module vivarium_cluster_tools.psimulate.worker.core)

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) cluster_logging_root (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute)

coerce_to_full_path() (in module vivarium_cluster_tools.cli_tools) completed (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager property) 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) CounterSnapshot (class in vivarium_cluster_tools.vipin.perf_counters)

D

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

E

enqueue() (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager method) (vivarium_cluster_tools.psimulate.redis_dbs.registry.RegistryManager method) environment_file (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute)

EnvVariable (class in vivarium_cluster_tools.psimulate.environment) expand_branch_templates() (in module vivarium_cluster_tools.psimulate.branches) extras (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute)

F

failed (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager property) 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

get_cluster_name() (in module vivarium_cluster_tools.utilities) get_drmaa() (in module vivarium_cluster_tools.utilities)

get_results() (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager method) (vivarium_cluster_tools.psimulate.redis_dbs.registry.RegistryManager method) get_summaries() (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary method)

H

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

I

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) jobs_to_finish (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager property) (vivarium_cluster_tools.psimulate.redis_dbs.registry.RegistryManager property)

K

Keyspace (class in vivarium_cluster_tools.psimulate.branches)

keyspace (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute)

L

launch_redis_processes() (in module vivarium_cluster_tools.psimulate.redis_dbs.launcher) load_branch_configuration() (in module vivarium_cluster_tools.psimulate.branches) load_existing_outputs() (in module vivarium_cluster_tools.psimulate.runner) 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) max_runtime (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification attribute) mkdir() (in module vivarium_cluster_tools.utilities) Model Specification MODEL_SPECIFICATION psimulate-run command line option model_specification (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) 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.pip_env vivarium_cluster_tools.psimulate.redis_dbs vivarium_cluster_tools.psimulate.redis_dbs.cli_options vivarium_cluster_tools.psimulate.redis_dbs.launcher vivarium_cluster_tools.psimulate.redis_dbs.registry vivarium_cluster_tools.psimulate.results vivarium_cluster_tools.psimulate.results.cli_options vivarium_cluster_tools.psimulate.results.processing vivarium_cluster_tools.psimulate.runner vivarium_cluster_tools.psimulate.worker vivarium_cluster_tools.psimulate.worker.core 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.psimulate.environment.EnvVariable property) (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager 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

Parameter Uncertainty parameter_update_format() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse) parse() (in module vivarium_cluster_tools.psimulate.model_specification) 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) process_job_results() (in module vivarium_cluster_tools.psimulate.runner) 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 --hardware --max-runtime --max-workers --no-batch --pdb --peak-memory --project --queue --redis -h -m -P -q -r -v -w RESULTS_ROOT psimulate-restart command line option --hardware --max-runtime --max-workers --no-batch --pdb --peak-memory --project --queue --redis -h -m -P -q -r -v -w RESULTS_ROOT

psimulate-run command line option --artifact_path --hardware --max-runtime --max-workers --no-batch --pdb --peak-memory --project --queue --redis --result-directory -h -i -m -o -P -q -r -v -w BRANCH_CONFIGURATION MODEL_SPECIFICATION psimulate-test command line option --hardware --max-runtime --max-workers --no-batch --num-workers --pdb --peak-memory --project --queue --redis --result-directory -h -m -n -o -P -q -r -v -w TEST_TYPE

Q

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

QueueManager (class in vivarium_cluster_tools.psimulate.redis_dbs.registry)

R

Random Seed random_seed (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute) RegistryManager (class in vivarium_cluster_tools.psimulate.redis_dbs.registry) report_initial_status() (in module vivarium_cluster_tools.psimulate.runner) report_performance() (in module vivarium_cluster_tools.vipin.perf_report) result_directory (vivarium_cluster_tools.psimulate.paths.InputPaths attribute) results (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) results_path (vivarium_cluster_tools.psimulate.jobs.JobParameters attribute)

RESULTS_ROOT psimulate-expand command line option psimulate-restart command line option retries_before_fail (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager attribute) 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_type (vivarium_cluster_tools.psimulate.paths.OutputPaths property)

S

set_index_scenario_cols() (in module vivarium_cluster_tools.vipin.perf_report) setup_sim() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse)

shared (vivarium_cluster_tools.psimulate.jobs.JobParameters property) Stochastic Uncertainty submit_worker_jobs() (in module vivarium_cluster_tools.psimulate.cluster.interface)

T

TELEMETRY_PATTERN (vivarium_cluster_tools.vipin.perf_report.PerformanceSummary attribute) TEST_TYPE psimulate-test command line option to_cli_args() (vivarium_cluster_tools.psimulate.cluster.interface.NativeSpecification method)

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) touch() (vivarium_cluster_tools.psimulate.paths.OutputPaths method) try_run_vipin() (in module vivarium_cluster_tools.psimulate.runner)

U

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

update_and_report() (vivarium_cluster_tools.psimulate.redis_dbs.registry.QueueManager method) (vivarium_cluster_tools.psimulate.redis_dbs.registry.RegistryManager 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.pip_env module vivarium_cluster_tools.psimulate.redis_dbs module vivarium_cluster_tools.psimulate.redis_dbs.cli_options module vivarium_cluster_tools.psimulate.redis_dbs.launcher module vivarium_cluster_tools.psimulate.redis_dbs.registry module vivarium_cluster_tools.psimulate.results module vivarium_cluster_tools.psimulate.results.cli_options module vivarium_cluster_tools.psimulate.results.processing module vivarium_cluster_tools.psimulate.runner module vivarium_cluster_tools.psimulate.worker module vivarium_cluster_tools.psimulate.worker.core 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_verbose_and_pdb() (in module vivarium_cluster_tools.cli_tools) work_horse() (in module vivarium_cluster_tools.psimulate.worker.vivarium_work_horse)

worker_logging_root (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) worker_settings (vivarium_cluster_tools.psimulate.paths.OutputPaths attribute) write_results_batch() (in module vivarium_cluster_tools.psimulate.results.processing)