Skip to content

Scheduling Overview

The BIH HPC uses the Slurm scheduling system. This section of the manual attempts to give an overview of what scheduling is and how you can use the Slurm scheduler. For more detailed information, you will have to refer to the Slurm website and the Slurm man pages (e.g., by entering man sbatch or man srun on the HPC terminal's command line).

For a quick introduction and hands-on examples, please see the manual sections

Also, make sure that you are aware of our How-To: Debug Software and How-To: Debug Software on HPC Systems guides in the case that something goes wrong.

Annotated Contents

  • Background on Scheduling -- some background on scheduling and the terminology used
  • Quickstart -- explains the most important Slurm commands, with examples
  • Cheat Sheet -- for quick reference
  • Job Scripts -- how to setup job scripts with Slurm
  • Memory Allocation -- memory allocation (⚠ one of the most important concepts that is most often found confusing)
  • Introduction to Slurm Commands
    • srun -- running parallel jobs now
    • sbatch -- submission of batch jobs
    • scancel -- stop/kill jobs
    • sinfo -- display information about the Slurm cluster
    • squeue -- information about pending and running jbos
    • scontrol -- detailed information (and control)
    • sacct -- access Slurm accounting information (pending, running, and past jobs)
    • Format Strings in Slurm -- format strings allow to display extended information about Slurm scheduler objects
  • Slurm and Snakemake -- how to use Snakemake with Slurm
  • X11 Forwarding -- X11 forwarding in Slurm (simple; short)
  • Rosetta Stone -- lookup table for SGE <-> Slurm
  • Migrating from SGE -- hints for migrating from SGE to Slurm (🕸 deprecated, will be removed)

A Word on "Elsewhere"

Many other facilities run Slurm clusters and make their documentation available on the internet. We list some that we found useful below. However, be aware that Slurm is a highly configurable and extensible system. Other sites may have different configurations and plugins enabled than we have (or might even have written custom plugins that are not available at BIH). In any case, it's always useful to look "über den Tellerrand".

Last update: January 6, 2022