An introduction to High Performance Computing

High-performance computing (HPC) enables researchers to analyse large datasets and run complex computations that would be impractical on a standard computer. Many modern research fields, from life sciences to engineering and data science, rely on HPC clusters to process data efficiently and run large-scale analyses. Understanding how these systems work and how to use them effectively is therefore an increasingly valuable skill for researchers.

In this course, you will receive a practical introduction to working with an HPC cluster, including how to access the system, transfer files, and run applications using the Slurm scheduler. The workshop is based on training materials from The Carpentries and the HPC Carpentry project, which teach foundational computing and data skills for researchers. Through hands-on exercises, you will learn the core concepts needed to confidently run jobs and workflows on HPC systems.

Learning outcomes

  • Work with HPC clusters, including transferring and organising files locally and remotely
  • Submit and manage jobs on a cluster using a scheduler and understand parallel execution
  • Build and run reproducible workflows using Snakemake on HPC systems
  • Understand scalable and reliable HPC practices, from chaining workflow steps to handling computational tasks efficiently

Target audience

  • Interested in learning what HPC is
  • Interested in learning how to access and use HPC resources
  • Anyone interested in learning about how to run applications and workflows on HPC resources
  • Don’t worry if you don’t have programming or informatics experience - as long as basic concepts like file systems and the Unix shell are familiar to you, this course will guide you step by step.
    • And even if you don´t meet these prerequisites, just click here to familiarise yourself with the topics from our other courses

Requirements

  • Just a PC/Laptop with an up-to-date browser Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9, may not be)
    • You will need a PC/Laptop with Admin permissions. If you do not have these permissions, please be aware that you will need to contact your IT department
    • Ideally a two-screen setup so you can follow the workshop while trying on your own
  • Access to a terminal application with ssh capabilities
    • And if you are unsure about this, click here for guidance on how to make this available for your operating system
  • The material explains HPC usage but provides no infrastructure. Third-party resources are suggested but to be used at your own discretion

Training material

Video recordings

These recordings from previous workshops allow you to revisit the course content or work through it at your own pace.

Your trainers
  • Benjamin Wolff (ZB MED - Information Centre for Life Sciences)
  • Alan O'Cais (University of Barcelona)
  • Pedro Fernandez (HPCNow!)
Written material

Here you can explore the written material and exercises which are available in several languages.