Create a launcher with PBS or TORQUE workers.

Create an R6 object to launch and maintain workers as jobs on a PBS or TORQUE cluster.

Usage

crew_launcher_pbs(
  name = NULL,
  seconds_interval = 0.5,
  seconds_timeout = 60,
  seconds_launch = 86400,
  seconds_idle = Inf,
  seconds_wall = Inf,
  tasks_max = Inf,
  tasks_timers = 0L,
  reset_globals = TRUE,
  reset_packages = FALSE,
  reset_options = FALSE,
  garbage_collection = FALSE,
  crashes_error = 5L,
  tls = crew::crew_tls(mode = "automatic"),
  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 launcher.
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().
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.
tls: A TLS configuration object from crew_tls().
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.
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.

Details

WARNING: the crew.cluster PBS plugin is experimental and has not actually been tested on a PBS cluster. Please proceed with caution and report bugs to https://github.com/wlandau/crew.cluster.

To launch a PBS/TORQUE worker, this launcher creates a temporary job script with a call to crew::crew_worker() and submits it as an PBS job with qsub. To see most of the lines of the job script in advance, use the script() method of the launcher. It has all the lines except for the job name and the call to crew::crew_worker(), both of which will be inserted at the last minute when it is time to actually launch a worker.

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.

Usage

Arguments

Details

Attribution

See also