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

crew_options_slurm

R Documentation

SLURM options.

Description

Set options for SLURM job management.

Usage

crew_options_slurm(
  verbose = FALSE,
  command_submit = as.character(Sys.which("sbatch")),
  command_terminate = as.character(Sys.which("scancel")),
  script_directory = tempdir(),
  script_lines = character(0L),
  log_output = "/dev/null",
  log_error = "/dev/null",
  memory_gigabytes_required = NULL,
  memory_gigabytes_per_cpu = NULL,
  cpus_per_task = NULL,
  time_minutes = NULL,
  partition = NULL,
  n_tasks = 1
)

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.
`log_output`	Character of length 1, file pattern to control the locations of the SLURM worker log files. By default, both standard output and standard error go to the same file. `log_output = "crew_log_%A.txt"` translates to a line of `⁠#SBATCH --output=crew_log_%A.txt⁠` in the SLURM job script, where `⁠%A⁠` 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_log_%A.txt"` translates to a line of `⁠#SBATCH --error=crew_log_%A.txt⁠` in the SLURM job script, where `⁠%A⁠` 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_required`	Positive numeric scalar, total number of gigabytes of memory required per node. `memory_gigabytes_required = 2.40123` translates to a line of `⁠#SBATCH --mem=2041M⁠` in the SLURM job script. `memory_gigabytes_required = NULL` omits this line.
`memory_gigabytes_per_cpu`	Positive numeric scalar, gigabytes of memory required per CPU. `memory_gigabytes_per_cpu = 2.40123` translates to a line of `⁠#SBATCH --mem-per-cpu=2041M⁠` in the SLURM job script. `memory_gigabytes_per_cpu = NULL` omits this line.
`cpus_per_task`	Optional positive integer scalar, number of CPUs for the worker. `cpus_per_task = 4` translates to a line of `⁠#SBATCH --cpus-per-task=4⁠` in the SLURM job script. `cpus_per_task = NULL` omits this line.
`time_minutes`	Numeric scalar, number of minutes to designate as the wall time of `crew` each worker instance on the SLURM cluster. `time_minutes = 60` translates to a line of `⁠#SBATCH --time=60⁠` in the SLURM job script. `time_minutes = NULL` omits this line.
`partition`	Character string, name of the SLURM partition to create workers on. `partition = "partition1,partition2"` translates to a line of `⁠#SBATCH --partition=partition1,partition2⁠` in the SLURM job script. `partition = NULL` omits this line.
`n_tasks`	Numeric scalar, number of SLURM tasks to run within the job. `n_tasks = 1` translates to a line of `⁠#SBATCH --ntasks=1⁠` in the SLURM job script. `n_tasks = 0` 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.