R: *[Experimental]* Create a launcher with PBS or TORQUE...

crew_launcher_pbs {crew.cluster}

R Documentation

Create a launcher with PBS or TORQUE workers.

Description

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,
  launch_max = 5L,
  tls = crew::crew_tls(mode = "automatic"),
  verbose = FALSE,
  command_submit = as.character(Sys.which("qsub")),
  command_terminate = as.character(Sys.which("qdel")),
  command_delete = NULL,
  script_directory = tempdir(),
  script_lines = character(0L),
  pbs_cwd = TRUE,
  pbs_log_output = "/dev/null",
  pbs_log_error = NULL,
  pbs_log_join = TRUE,
  pbs_memory_gigabytes_required = NULL,
  pbs_cores = NULL,
  pbs_walltime_hours = 12
)

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.
`launch_max`	Positive integer of length 1, maximum allowed consecutive launch attempts which do not complete any tasks. Enforced on a worker-by-worker basis. The futile launch count resets to back 0 for each worker that completes a task. It is recommended to set `launch_max` above 0 because sometimes workers are unproductive under perfectly ordinary circumstances. But `launch_max` should still be small enough to detect errors in the underlying platform.
`tls`	A TLS configuration object from `crew_tls()`.
`verbose`	Logical, whether to see console output and error messages when submitting worker.
`command_submit`	Character of length 1, file path to the executable to submit a worker job.
`command_terminate`	Character of length 1, file path to the executable to terminate a worker job. Set to `""` to skip manually terminating the worker. Unless there is an issue with the platform, the job should still exit thanks to the NNG-powered network programming capabilities of `mirai`. Still, if you set `command_terminate = ""`, you are assuming extra responsibility for manually monitoring your jobs on the cluster and manually terminating jobs as appropriate.
`command_delete`	Deprecated on 2024-01-08 (version 0.1.4.9001). Use `command_terminate` instead.
`script_directory`	Character of length 1, directory path to the job scripts. Just before each job submission, a job script is created in this folder. Script base names are unique to each launcher and worker, and the launcher deletes the script when the worker is manually terminated. `tempdir()` is the default, but it might not work for some systems. `tools::R_user_dir("crew.cluster", which = "cache")` is another reasonable choice.
`script_lines`	Optional character vector of additional lines to be added to the job script just after the more common flags. An example would be `script_lines = "module load R"` if your cluster supports R through an environment module.
`pbs_cwd`	Logical of length 1, whether to set the working directory of the worker to the working directory it was launched from. `pbs_cwd = TRUE` is translates to a line of `⁠cd "$PBS_O_WORKDIR"⁠` in the job script. This line is inserted after the content of `script_lines` to make sure the `⁠#PBS⁠` directives are above system commands. `pbs_cwd = FALSE` omits this line.
`pbs_log_output`	Character of length 1, file or directory path to PBS worker log files for standard output. `pbs_log_output = "VALUE"` translates to a line of `⁠#PBS -o VALUE⁠` in the PBS job script. The default is `⁠/dev/null⁠` to omit the logs. If you do supply a non-`⁠/dev/null⁠` value, it is recommended to supply a directory path with a trailing slash so that each worker gets its own set of log files.
`pbs_log_error`	Character of length 1, file or directory path to PBS worker log files for standard error. `pbs_log_error = "VALUE"` translates to a line of `⁠#PBS -e VALUE⁠` in the PBS job script. The default of `NULL` omits this line. If you do supply a non-`⁠/dev/null⁠` value, it is recommended to supply a directory path with a trailing slash so that each worker gets its own set of log files.
`pbs_log_join`	Logical, whether to join the stdout and stderr log files together into one file. `pbs_log_join = TRUE` translates to a line of `⁠#PBS -j oe⁠` in the PBS job script, while `pbs_log_join = FALSE` is equivalent to `⁠#PBS -j n⁠`. If `pbs_log_join = TRUE`, then `pbs_log_error` should be `NULL`.
`pbs_memory_gigabytes_required`	Optional positive numeric of length 1 with the gigabytes of memory required to run the worker. `pbs_memory_gigabytes_required = 2.4` translates to a line of `⁠#PBS -l mem=2.4gb⁠` in the PBS job script. `pbs_memory_gigabytes_required = NULL` omits this line.
`pbs_cores`	Optional positive integer of length 1, number of cores per worker ("slots" in PBS lingo). `pbs_cores = 4` translates to a line of `⁠#PBS -l ppn=4⁠` in the PBS job script. `pbs_cores = NULL` omits this line.
`pbs_walltime_hours`	Numeric of length 1 with the hours of wall time to request for the job. `pbs_walltime_hours = 23` translates to a line of `⁠#PBS -l walltime=23:00:00⁠` in the job script. `pbs_walltime_hours = NULL` omits this line.

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