Skip to contents

[Experimental] LSF options.

Source: R/crew_options_lsf.R
crew_options_lsf.Rd

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 vector, usually with a single element. Supply a vector to make memory_gigabytes_limit a retryable option (see the "Retryable options" section for details).

memory_gigabytes_limit is the 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 vector, usually with a single element. Supply a vector to make memory_gigabytes_required a retryable option (see the "Retryable options" section for details).

memory_gigabytes_required is the 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 vector, usually with a single element. Supply a vector to make cores a retryable option (see the "Retryable options" section for details).

cores is the 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

Arguments memory_gigabytes_limit, memory_gigabytes_required, and cores are retryable options. Each of these arguments be a vector where each successive element is used during a retry if the worker previously exited without completing all its assigned tasks. The last element of the vector is used if there are more retries than the length of the vector. Control the number of allowable retries with crashes_error argument of the controller.

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.

See also

Other lsf: crew_class_launcher_lsf, crew_controller_lsf(), crew_launcher_lsf()

Examples

  crew_options_lsf()
#> $verbose
#> [1] FALSE
#> 
#> $command_submit
#> [1] ""
#> 
#> $command_terminate
#> [1] ""
#> 
#> $script_directory
#> [1] "/tmp/Rtmp59XTVt"
#> 
#> $script_lines
#> character(0)
#> 
#> $cwd
#> [1] "/home/runner/work/crew.cluster/crew.cluster/docs/reference"
#> 
#> $log_output
#> [1] "/dev/null"
#> 
#> $log_error
#> [1] "/dev/null"
#> 
#> $memory_gigabytes_limit
#> NULL
#> 
#> $memory_gigabytes_required
#> NULL
#> 
#> $cores
#> NULL
#> 
#> attr(,"class")
#> [1] "crew_options_lsf"     "crew_options_cluster" "crew_options"