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This function pauses execution of an R script while a scheduled qsub job is not yet complete.

Source: R/hpc_functions.R
wait_for_job.Rd

It is intended to give you control over job dependencies within R when the formal PBS depend approach is insufficient, especially in the case of a script that spawns child jobs that need to be scheduled or complete before the parent script should continue.

Usage

wait_for_job(
  job_ids,
  repolling_interval = 60,
  max_wait = 60 * 60 * 24,
  scheduler = "local",
  quiet = TRUE,
  stop_on_timeout = TRUE
)

Arguments

job_ids

One or more job ids of existing PBS or slurm jobs, or process ids of a local process for scheduler="sh".

repolling_interval

How often to recheck the job status, in seconds. Default: 30

max_wait

How long to wait on the job before giving up, in seconds. Default: 24 hours (86,400 seconds)

scheduler

What scheduler is used for job execution. Options: c("torque", "qsub", "slurm", "sbatch", "sh", "local")

quiet

If TRUE, wait_for_job will not print out any status updates on jobs. If FALSE, the function prints out status updates for each tracked job so that the user knows what's holding up progress.

stop_on_timeout

Logical. If TRUE, the function throws an error if the max_wait is exceeded. If FALSE, it returns FALSE instead of stopping. Default is TRUE.

Value

Returns (invisibly) TRUE if all jobs completed successfully, FALSE if any job failed or timeout occurred and stop_on_timeout = FALSE. Otherwise, stops execution with an error if the timeout is exceeded.

Details

Note that for the scheduler argument, "torque" and "qsub" are the same; "slurm" and "sbatch" are the same, and "sh" and "local" are the same.

Author

Michael Hallquist

Examples

if (FALSE) { # \dontrun{
# example on qsub/torque cluster
wait_for_job("7968857.torque01.util.production.int.aci.ics.psu.edu", scheduler = "torque")

# example of waiting for two jobs on slurm cluster
wait_for_job(c("24147864", "24147876"), scheduler = "slurm")

# example of waiting for two jobs on local machine
wait_for_job(c("9843", "9844"), scheduler = "local")
} # }