Week 5: Software usage and batch jobs at OSC


2 Content overview

This week, we’ll start with an introduction to OSC and supercomputers. Then, we’ll see how we can submit shell scripts to OSC’s queue for compute jobs with the widely-used Slurm resource manager. Finally, we will learn about installing and managing software with Conda, and loading pre-installed software with the “module” system.

Some of the things you will learn this week:

  • When and why we need to run our analyses on supercomputers.
  • Key terminology around supercomputers.
  • Different ways to access and transfer data to and from OSC.
  • Different ways to start “compute jobs”: via OnDemand, with interactive jobs, and with scripts.
  • Some strategies around requesting appropriate resources for your compute jobs.
  • The Slurm/sbatch syntax to request specific resources for your compute jobs.
  • How to monitor Slurm jobs.
  • How to load pre-installed software at OSC with the “module” system.
  • How to install and manage software with Conda.

2.1 Optional readings

  • Buffalo Chapter 4: “Working with Remote Machines”
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