slappt 0.0.2

generate slurm scripts for apptainer jobs

Slurm scripts for Apptainer jobs

Contents

• Overview
• Requirements
• Installation
• Quickstart
• Documentation
• Disclaimer

Overview

slappt composes Slurm job scripts for Apptainer workflows from config files or CLI args.

Requirements

slappt requires only Python3.8+.

slappt can also submit scripts to remote clusters. To submit a job script, the host machine must be able to connect via key- or password-authenticated SSH to the target cluster.

Installation

slappt is available on the Python Package Index and can be installed with pip:

pip install slappt

Quickstart

Say you have a Slurm cluster with apptainer installed, and you have permission to submit to the batch partition.

Copy the hello.yaml file from the examples directory to your current working directory, then run:

slappt hello.yaml > job.sh

Alternatively, without the configuration file:

slappt --image docker://alpine \
       --shell sh \
       --partition batch \
       --entrypoint "echo 'hello world'" > hello.sh

Note: for most image definitions, specifying the shell is likely not necessary, as the default is bash. However, for images that don't have bash installed (e.g., alphine only has sh) a different shell must be selected.

Your hello.sh script should now contain:

#!/bin/bash
#SBATCH --job-name=0477f4b9-e119-4354-8384-f50d7a96adad
#SBATCH --output=slappt.0477f4b9-e119-4354-8384-f50d7a96adad.%j.out
#SBATCH --error=slappt.0477f4b9-e119-4354-8384-f50d7a96adad.%j.err
#SBATCH --partition=batch
#SBATCH -c 1
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH --time=01:00:00
#SBATCH --mem=1GB
apptainer exec docker://alpine sh -c "echo 'hello world'"

If already on the cluster, just submit it as usual:

sbatch hello.sh

If you're on a different machine, you can use the extra sshlurm command to submit the script over SSH. For instance, assuming you have key authentication set up for the cluster, and your key is ~/.ssh/id_rsa:

sshlurm hello.sh --host <cluster IP or FQDN> --username <username>

Documentation

Documentation is available at slappt.readthedocs.io.

Disclaimer

This project is not affiliated with Slurm, Apptainer or Singularity and cannot guarantee compatibility with all cluster configurations.