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[Maturing] SGE options.

Source: R/crew_options_sge.R
crew_options_sge.Rd

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

gpu is the 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

Arguments memory_gigabytes_limit, memory_gigabytes_required, cores, and gpu 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 sge: crew_class_launcher_sge, crew_class_monitor_sge, crew_controller_sge(), crew_launcher_sge(), crew_monitor_sge()

Examples

  crew_options_sge()
#> $verbose
#> [1] FALSE
#> 
#> $command_submit
#> [1] ""
#> 
#> $command_terminate
#> [1] ""
#> 
#> $script_directory
#> [1] "/tmp/Rtmp59XTVt"
#> 
#> $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"