crew_options_pbs: [Experimental] PBS options.
In crew.cluster: Crew Launcher Plugins for Traditional High-Performance Computing Clusters

crew_options_pbs

R Documentation

PBS options.

Description

Set options for PBS job management.

Usage

crew_options_pbs(
  verbose = FALSE,
  command_submit = as.character(Sys.which("qsub")),
  command_terminate = as.character(Sys.which("qdel")),
  script_directory = tempdir(),
  script_lines = character(0L),
  cwd = TRUE,
  log_output = "/dev/null",
  log_error = NULL,
  log_join = TRUE,
  memory_gigabytes_required = NULL,
  cores = NULL,
  walltime_hours = 12
)

Arguments

`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.
`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.
`cwd`	Logical of length 1, whether to set the working directory of the worker to the working directory it was launched from. `cwd = TRUE` is translates to a line of `⁠cd "$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. `cwd = FALSE` omits this line.
`log_output`	Character of length 1, file or directory path to PBS worker log files for standard output. `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.
`log_error`	Character of length 1, file or directory path to PBS worker log files for standard error. `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.
`log_join`	Logical, whether to join the stdout and stderr log files together into one file. `log_join = TRUE` translates to a line of `⁠#PBS -j oe⁠` in the PBS job script, while `log_join = FALSE` is equivalent to `⁠#PBS -j n⁠`. If `log_join = TRUE`, then `log_error` should be `NULL`.
`memory_gigabytes_required`	Optional positive numeric scalar, gigabytes of memory required to run the worker. `memory_gigabytes_required = 2.4` translates to a line of `⁠#PBS -l mem=2.4gb⁠` in the PBS job script. `memory_gigabytes_required = NULL` omits this line.
`cores`	Optional positive integer scalar, number of cores for the worker ("slots" in PBS lingo). `cores = 4` translates to a line of `⁠#PBS -l ppn=4⁠` in the PBS job script. `cores = NULL` omits this line.
`walltime_hours`	Numeric scalar, hours of wall time to request for the worker. `walltime_hours = 23` translates to a line of `⁠#PBS -l walltime=23:00:00⁠` in the job script. `walltime_hours = NULL` omits this line.

Value

A classed list of options.

Retryable options

Retryable options are deprecated in crew.cluster as of 2025-01-27 (version ⁠0.3.4⁠).

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.