Submit R program as a SLURM job

Usage

abba_slurm_submit_job(
  program_path,
  log_path = NULL,
  r_version = NULL,
  user_tag = NULL,
  cpu_cores = getOption("abba.slurm.cpu.cores"),
  memory = getOption("abba.slurm.memory"),
  username = NULL,
  working_dir = NULL,
  job_timeout = 3600,
  ...
)

Arguments

program_path: Full path to the R program file. Must be accessible from the SLURM node
log_path: desirable parent folder for program's log file. Defaults to parent folder of R program.
r_version: Version of R that will be used to run the program. Can be specified as a full path to Rscript executable, or as a label of R version that is displayed in the Workbench GUI.
user_tag: custom string that will be added to the job name.
cpu_cores: Amount of CPU cores that will be requested for the job.
memory: Amount of RAM in megabytes that will be requested for the job.
username: user whose permission level is used to execute the script. Defaults to user submitting the job.
working_dir: working directory for the SLURM job. Defaults to parent directory of program_path.
job_timeout: time limit for a job. Must be specified in a format of "days-hours:minutes:seconds" If exceeded, job will be cancelled.
...: additional arguments (currently unused)

Value

job ID

Examples

if (FALSE) { # \dontrun{
job_id <- abba_slurm_submit_job("/home/user/tfl/t1_dm.sas")
 } # }