crew_options_sge: [Maturing] SGE options.
In crew.cluster: Crew Launcher Plugins for Traditional High-Performance Computing Clusters

crew_options_sge

R Documentation

SGE options.

Description

Set options for SGE job management.

Usage

crew_options_sge(
  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,
  envvars = FALSE,
  log_output = "/dev/null",
  log_error = NULL,
  log_join = TRUE,
  memory_gigabytes_limit = NULL,
  memory_gigabytes_required = NULL,
  cores = NULL,
  gpu = 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`	Logical of length 1, whether to launch the worker from the current working directory (as opposed to the user home directory). `cwd = TRUE` translates to a line of `⁠#$ -cwd⁠` in the SGE job script. `cwd = FALSE` omits this line.
`envvars`	Logical of length 1, whether to forward the environment variables of the current session to the SGE worker. `envvars = TRUE` translates to a line of `⁠#$ -V⁠` in the SGE job script. `envvars = FALSE` omits this line.
`log_output`	Character of length 1, file or directory path to SGE worker log files for standard output. `log_output = "VALUE"` translates to a line of `⁠#$ -o VALUE⁠` in the SGE 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 SGE worker log files for standard error. `log_error = "VALUE"` translates to a line of `⁠#$ -e VALUE⁠` in the SGE 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 `⁠#$ -j y⁠` in the SGE job script, while `log_join = FALSE` is equivalent to `⁠#$ -j n⁠`. If `log_join = TRUE`, then `log_error` should be `NULL`.
`memory_gigabytes_limit`	Optional numeric scalar, maximum number of gigabytes of memory a worker is allowed to consume. If the worker consumes more than this level of memory, then SGE will terminate it. `⁠memory_gigabytes_limit = 5.7"⁠` translates to a line of `"#$ -l h_rss=5.7G"` in the SGE job script. `memory_gigabytes_limit = NULL` omits this line.
`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 `⁠#$ -l m_mem_free=2.4G⁠` in the SGE job script. `memory_gigabytes_required = NULL` omits this line.
`cores`	Optional positive integer scalar, number of cores per worker ("slots" in SGE lingo). `cores = 4` translates to a line of `⁠#$ -pe smp 4⁠` in the SGE job script. `cores = NULL` omits this line.
`gpu`	Optional integer scalar, number of GPUs to request for the worker. `gpu = 1` translates to a line of `"#$ -l gpu=1"` in the SGE job script. `gpu = 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.