SGE options.

Set options for SGE job management.

Usage

crew_options_sge(
  verbose = FALSE,
  command_submit = as.character(Sys.which("qsub")),
  command_terminate = NULL,
  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: Deprecated on 2025-08-26 in crew.cluster version 0.3.8.9001. No longer needed.
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.

Examples

  crew_options_sge()
#> $verbose
#> [1] FALSE
#> 
#> $command_submit
#> [1] ""
#> 
#> $script_directory
#> [1] "/tmp/Rtmp6NuWnl"
#> 
#> $script_lines
#> character(0)
#> 
#> $cwd
#> [1] TRUE
#> 
#> $envvars
#> [1] FALSE
#> 
#> $log_output
#> [1] "/dev/null"
#> 
#> $log_error
#> NULL
#> 
#> $log_join
#> [1] TRUE
#> 
#> $memory_gigabytes_limit
#> NULL
#> 
#> $memory_gigabytes_required
#> NULL
#> 
#> $cores
#> NULL
#> 
#> $gpu
#> NULL
#> 
#> attr(,"class")
#> [1] "crew_options_sge"     "crew_options_cluster" "crew_options"