An Introduction to High Performance Computing (BioNT)

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. 

This course is part of the BioNT project, funded via the Digital Europe Programme of the European Union. BioNT brings together an international consortium of academic entities and SMEs with the aim to provide a high-quality training program and community for digital skills relevant to the biotechnology industry and biomedical sector.

About this course 

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.

Target audience

This course is perfect for those interested in learning what HPC is, and those looking to understand how to access and use HPC resources. It is also suitable for those interested in knowing how to run applications and workflows on HPC resources. 

No programming or informatics experience? Not to worry. As long as basic concepts like file systems and the Unix shell are familiar to you, this course will guide you step by step.

Entry 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.

The material explains HPC usage but provides no infrastructure. Third-party resources are suggested but to be used at your own discretion.

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.