How to submit a NONMEM job to slurm with submit_slurm_job

This guide describes how to submit a NONMEM job to slurm using the submit_slurm_job function. First, make sure you have loaded slurmtools and are familiar with the needed options to use slurmtools.

Prerequisites

To use submit_slurm_job you need a few things set before hand

1. A template file ready to be populated
2. All files needed to run NONMEM - control stream and data
3. bbr installed in your R environment
4. A way of running NONMEM such as bbi or nmm

Note

Depending on the complexity of your template file you might need additional information as well!

Once these are set, you’re ready to roll with your Slurm submission!

Submitting a NONMEM job

Here’s the code you’ll use to submit a job with submit_slurm_job, this uses default values for all arguments, many of which are determined via the slurmtools options discussed here.

submit_job.R

library(slurmtools)
library(bbr)

mod <- bbr::read_model(file.path("path", "to", "nonmem", "models", "1001"))
submit_slurm_job(mod)

With all prerequisites in place, running this code sends your NONMEM model to Slurm. Let’s look at what you can expect from the output.

Note

If you’ve already submitted the model, submit_slurm_job by default will not overwrite and existing model. Check out submit_slurm_job Reference Guide for more details on the overwrite argument.

Understanding the output

$status
[1] 0

$stdout
[1] "Submitted batch job 436"

$stderr
[1] ""

$timeout
[1] FALSE

• $status: This shows an exit code of 0, which means everything went smoothly.
• $stdout: Here, you’ll see a message confirming your job submission, along with the job ID (e.g., 436).
• $stderr: If all goes well, this should be empty.
• $timeout: A FALSE value here means there was no timeout during the submission.

Tip

A status code of 0 is what you want! It indicates there were no issues.

Next Steps

For more advanced usage: If you’re interested in learning how to use non-default arguments with submit_slurm_job for more customized job submissions, please check out our submit_slurm_job Reference Guide