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

crew_options_lsf

R Documentation

LSF options.

Description

Set options for LSF job management.

Usage

crew_options_lsf(
  verbose = FALSE,
  command_submit = as.character(Sys.which("bsub")),
  command_terminate = as.character(Sys.which("bkill")),
  script_directory = tempdir(),
  script_lines = character(0L),
  cwd = getwd(),
  log_output = "/dev/null",
  log_error = "/dev/null",
  memory_gigabytes_limit = NULL,
  memory_gigabytes_required = NULL,
  cores = NULL
)

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`	Character of length 1, directory to launch the worker from (as opposed to the system default). `cwd = "/home"` translates to a line of `⁠#BSUB -cwd /home⁠` in the LSF job script. `cwd = getwd()` is the default, which launches workers from the current working directory. Set `cwd = NULL` to omit this line from the job script.
`log_output`	Character of length 1, file pattern to control the locations of the LSF worker log files. By default, both standard output and standard error go to the same file. `log_output = "crew_log_%J.log"` translates to a line of `⁠#BSUB -o crew_log_%J.log⁠` in the LSF job script, where `⁠%J⁠` is replaced by the job ID of the worker. The default is `⁠/dev/null⁠` to omit these logs. Set `log_output = NULL` to omit this line from the job script.
`log_error`	Character of length 1, file pattern for standard error. `log_error = "crew_error_%J.err"` translates to a line of `⁠#BSUB -e crew_error_%J.err⁠` in the LSF job script, where `⁠%J⁠` is replaced by the job ID of the worker. The default is `⁠/dev/null⁠` to omit these logs. Set `log_error = NULL` to omit this line from the job script.
`memory_gigabytes_limit`	Positive numeric scalar, memory limit in gigabytes of the worker. `memory_gigabytes_limit = 4` translates to a line of `⁠#BSUB -M 4G⁠` in the LSF job script. `memory_gigabytes_limit = NULL` omits this line.
`memory_gigabytes_required`	Positive numeric scalar, memory requirement in gigabytes. `memory_gigabytes_required = 4` translates to a line of `⁠#BSUB -R 'rusage[mem=4G]'⁠` in the LSF job script. `memory_gigabytes_required = NULL` omits this line.
`cores`	Optional positive integer scalar, number of CPU cores for the worker. `cores = 4` translates to a line of `⁠#BSUB -n 4⁠` in the LSF job script. `cores = 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.