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[Experimental] PBS options.

Source: R/crew_options_pbs.R
crew_options_pbs.Rd

Set options for PBS job management.

Usage

crew_options_pbs(
  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,
  log_output = "/dev/null",
  log_error = NULL,
  log_join = TRUE,
  memory_gigabytes_required = NULL,
  cores = NULL,
  walltime_hours = 12
)

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 set the working directory of the worker to the working directory it was launched from. cwd = TRUE is translates to a line of cd "$O_WORKDIR" in the job script. This line is inserted after the content of script_lines to make sure the #PBS directives are above system commands. cwd = FALSE omits this line.

log_output

Character of length 1, file or directory path to PBS worker log files for standard output. log_output = "VALUE" translates to a line of #PBS -o VALUE in the PBS 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 PBS worker log files for standard error. log_error = "VALUE" translates to a line of #PBS -e VALUE in the PBS 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 #PBS -j oe in the PBS job script, while log_join = FALSE is equivalent to #PBS -j n. If log_join = TRUE, then log_error should be NULL.

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 #PBS -l mem=2.4gb in the PBS 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 for the worker ("slots" in PBS lingo). cores = 4 translates to a line of #PBS -l ppn=4 in the PBS job script. cores = NULL omits this line.

walltime_hours

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

walltime_hours is the hours of wall time to request for the worker. walltime_hours = 23 translates to a line of #PBS -l walltime=23:00:00 in the job script. walltime_hours = NULL omits this line.

Value

A classed list of options.

Retryable options

Arguments memory_gigabytes_required, cores, and walltime_hours 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 pbs: crew_class_launcher_pbs, crew_controller_pbs(), crew_launcher_pbs()

Examples

  crew_options_pbs()
#> $verbose
#> [1] FALSE
#> 
#> $command_submit
#> [1] ""
#> 
#> $command_terminate
#> [1] ""
#> 
#> $script_directory
#> [1] "/tmp/Rtmp59XTVt"
#> 
#> $script_lines
#> character(0)
#> 
#> $cwd
#> [1] TRUE
#> 
#> $log_output
#> [1] "/dev/null"
#> 
#> $log_error
#> NULL
#> 
#> $log_join
#> [1] TRUE
#> 
#> $memory_gigabytes_required
#> NULL
#> 
#> $cores
#> NULL
#> 
#> $walltime_hours
#> [1] 12
#> 
#> attr(,"class")
#> [1] "crew_options_pbs"     "crew_options_cluster" "crew_options"