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[Experimental] Create a controller with a PBS/TORQUE launcher.

Source: R/crew_controller_pbs.R
crew_controller_pbs.Rd

Create an R6 object to submit tasks and launch workers on a PBS or TORQUE cluster.

Usage

crew_controller_pbs(
  name = NULL,
  workers = 1L,
  host = NULL,
  port = NULL,
  tls = crew::crew_tls(mode = "automatic"),
  tls_enable = NULL,
  tls_config = NULL,
  seconds_interval = 0.25,
  seconds_timeout = 60,
  seconds_launch = 86400,
  seconds_idle = 300,
  seconds_wall = Inf,
  seconds_exit = NULL,
  retry_tasks = TRUE,
  tasks_max = Inf,
  tasks_timers = 0L,
  reset_globals = TRUE,
  reset_packages = FALSE,
  reset_options = FALSE,
  garbage_collection = FALSE,
  crashes_error = 5L,
  r_arguments = c("--no-save", "--no-restore"),
  options_metrics = crew::crew_options_metrics(),
  options_cluster = crew.cluster::crew_options_pbs(),
  verbose = NULL,
  command_submit = NULL,
  command_terminate = NULL,
  command_delete = NULL,
  script_directory = NULL,
  script_lines = NULL,
  pbs_cwd = NULL,
  pbs_log_output = NULL,
  pbs_log_error = NULL,
  pbs_log_join = NULL,
  pbs_memory_gigabytes_required = NULL,
  pbs_cores = NULL,
  pbs_walltime_hours = NULL
)

Arguments

name

Name of the client object. If NULL, a name is automatically generated.

workers

Integer, maximum number of parallel workers to run.

host

IP address of the mirai client to send and receive tasks. If NULL, the host defaults to the local IP address.

port

TCP port to listen for the workers. If NULL, then an available ephemeral port is automatically chosen.

tls

A TLS configuration object from crew_tls().

tls_enable

Deprecated on 2023-09-15 in version 0.4.1. Use argument tls instead.

tls_config

Deprecated on 2023-09-15 in version 0.4.1. Use argument tls instead.

seconds_interval

Number of seconds between polling intervals waiting for certain internal synchronous operations to complete, such as checking mirai::status()

seconds_timeout

Number of seconds until timing out while waiting for certain synchronous operations to complete, such as checking mirai::status().

seconds_launch

Seconds of startup time to allow. A worker is unconditionally assumed to be alive from the moment of its launch until seconds_launch seconds later. After seconds_launch seconds, the worker is only considered alive if it is actively connected to its assign websocket.

seconds_idle

Maximum number of seconds that a worker can idle since the completion of the last task. If exceeded, the worker exits. But the timer does not launch until tasks_timers tasks have completed. See the idletime argument of mirai::daemon(). crew does not excel with perfectly transient workers because it does not micromanage the assignment of tasks to workers, so please allow enough idle time for a new worker to be delegated a new task.

seconds_wall

Soft wall time in seconds. The timer does not launch until tasks_timers tasks have completed. See the walltime argument of mirai::daemon().

seconds_exit

Deprecated on 2023-09-21 in version 0.1.2.9000. No longer necessary.

retry_tasks

TRUE to automatically retry a task in the event of an unexpected worker exit. FALSE to give up on the first exit and return a mirai error code (code number 19). TRUE (default) is recommended in most situations. Use FALSE for debugging purposes, e.g. to confirm that a task is causing a worker to run out of memory or crash in some other way.

tasks_max

Maximum number of tasks that a worker will do before exiting. See the maxtasks argument of mirai::daemon(). crew does not excel with perfectly transient workers because it does not micromanage the assignment of tasks to workers, it is recommended to set tasks_max to a value greater than 1.

tasks_timers

Number of tasks to do before activating the timers for seconds_idle and seconds_wall. See the timerstart argument of mirai::daemon().

reset_globals

TRUE to reset global environment variables between tasks, FALSE to leave them alone.

reset_packages

TRUE to unload any packages loaded during a task (runs between each task), FALSE to leave packages alone.

reset_options

TRUE to reset global options to their original state between each task, FALSE otherwise. It is recommended to only set reset_options = TRUE if reset_packages is also TRUE because packages sometimes rely on options they set at loading time.

garbage_collection

TRUE to run garbage collection between tasks, FALSE to skip.

crashes_error

Positive integer scalar. If a worker exits crashes_error times in a row without completing all its assigned tasks, then the launcher throws an informative error. The reason for crashes_error is to avoid an infinite loop where a task crashes a worker (through a segfault, maxing out memory, etc) but the worker always relaunches. To monitor the resources of crew workers, please see https://wlandau.github.io/crew/articles/logging.html.

r_arguments

Optional character vector of command line arguments to pass to Rscript (non-Windows) or Rscript.exe (Windows) when starting a worker. Example: r_arguments = c("--vanilla", "--max-connections=32").

options_metrics

Either NULL to opt out of resource metric logging for workers, or an object from crew_options_metrics() to enable and configure resource metric logging for workers. For resource logging to run, the autometric R package version 0.1.0 or higher must be installed.

options_cluster

An options list from crew_options_pbs() with cluster-specific configuration options.

verbose

Deprecated. Use options_cluster instead.

command_submit

Deprecated. Use options_cluster instead.

command_terminate

Deprecated. Use options_cluster instead.

command_delete

Deprecated on 2024-01-08 (version 0.1.4.9001). Use command_terminate instead.

script_directory

Deprecated. Use options_cluster instead.

script_lines

Deprecated. Use options_cluster instead.

pbs_cwd

Deprecated. Use options_cluster instead.

pbs_log_output

Deprecated. Use options_cluster instead.

pbs_log_error

Deprecated. Use options_cluster instead.

pbs_log_join

Deprecated. Use options_cluster instead.

pbs_memory_gigabytes_required

Deprecated. Use options_cluster instead.

pbs_cores

Deprecated. Use options_cluster instead.

pbs_walltime_hours

Deprecated. Use options_cluster instead.

Attribution

The template files at https://github.com/mschubert/clustermq/tree/master/inst informed the development of the crew launcher plugins in crew.cluster, and we would like to thank Michael Schubert for developing clustermq and releasing it under the permissive Apache License 2.0. See the NOTICE and README.md files in the crew.cluster source code for additional attribution.

See also

Other pbs: crew_class_launcher_pbs, crew_launcher_pbs(), crew_options_pbs()

Examples

if (identical(Sys.getenv("CREW_EXAMPLES"), "true")) {
controller <- crew_controller_pbs()
controller$start()
controller$push(name = "task", command = sqrt(4))
controller$wait()
controller$pop()$result
controller$terminate()
}