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slurmtools

Adding notifications for slurm job status

This guide will expand upon how to write a template file to incorporate ntfy.sh . notifications!

ntfy (pronounced notify) is a simple HTTP-based pub-sub notification service. It allows you to send notifications to your phone or desktop via scripts from any computer, and/or using a REST API. It’s infinitely flexible, and 100% free software.

Prerequisites

  1. Familiarity with submit_slurm_job
  2. Familiarity with simple template files

ntfy.sh alerts

We can start by adding a notification when the job starts and when it ends. Looking at the ntfy.sh website we can see:

Publishing messages can be done via PUT or POST. Topics are created on the fly by subscribing or publishing to them. If you use ntfy without sign-up, the topic is essentially a password, so pick something that’s not easily guessable. If you purchase ntfy Pro, you can reserve topic names instead.

With the command to do this is:

curl -d "Backup successful 😀" ntfy.sh/mytopic

Updating template file

We can add this command to our template file to fire off before the nonmem job starts and immediately after it finishes.

slurm-job.tmpl
#!/bin/bash
#SBATCH --job-name="{{job_name}}"
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task={{ncpu}}
#SBATCH --partition={{partition}}
#SBATCH --account={{project_name}}


#{{project_path}}
# submit_slurm_job uses the whisker package to populate template files
# https://github.com/edwindj/whisker


{{#ntfy}}
curl -d "NONMEM job {{job_name}} is starting" ntfy.sh/{{mytopic}}
{{/ntfy}}


{{#parallel}}
{{bbi_exe_path}} nonmem run local {{model_path}}.mod --parallel --threads={{ncpu}} --config {{bbi_config_path}}
{{/parallel}}




{{^parallel}}
{{bbi_exe_path}} nonmem run local {{model_path}}.mod --config {{bbi_config_path}}
{{/parallel}}


{{#ntfy}}
curl -d "NONMEM job {{job_name}} has finished" ntfy.sh/{{mytopic}}
{{/ntfy}}

We can provide the needed arguments (mytopic and ntfy) through the slurm_template_opts argument using the following call to submit_slurm_job

ntfy-submit.R
library(slurmtools)
library(bbr)


nonmem_path <- file.path("path", "to", "nonmem", "models")


mod <- bbr::read_model(file.path(nonmem_path "1001"))
submit_slurm_job(
    mod,
    bbi_config_path = file.path(nonmem_path, "new-bbi.yml"),
    slurm_template_opts = list(
        ntfy = TRUE,
        mytopic = 'slurmtools_example_ntfy'
    )
)

Job status alerts

This sends off two messages to ntfy.sh :