High Performance Computing: structure and practice

August 13, 2026 · View on GitHub

Lesson overview

License: Creative Commons Attribution share alike 4.0 International License

Target Audience: Researchers, Technicians, trainers, anyone with interest in using HPC

Level: Beginner

Prerequisites
To be able to follow this course, learners should:

Have basic command-line skills.

If you lack command-line experience, you can prepare by following this e-learning or Linux introduction.

Description

Large-scale data analysis and complex computations often exceed the limits of standard computing resources. This half-day course provides researchers and professionals with essential knowledge to confidently work with High Performance Computing (HPC) environments.

During the session, you will explore the structure of HPC systems, understand available resources, and learn practical techniques for navigating and using these environments effectively. The course highlights the differences and similarities among the VSC instances in Ghent and Leuven and the VIB Data Core.

The presentation which goes alongside this material can be found here.

Learning Outcomes:
By the end of the course, learners will be able to:

Identify differences and similarities among different HPC instances

Access existing HPC infrastructures in Flanders, including VSC and VIB Data Core

Navigate and use different HPC environments (storage, analysis, and debug)

Query and manage specific modules on the HPC

Submit jobs to run software and scripts on the compute cluster

Monitor and check information about submitted jobs

Time estimation: 4.5 hours (1/2 day)

Requirements: The (technical) installation requirements are described in the chapter Get ready

Supporting Materials:

Presentation

Extra info about HPC in Flanders and data transfer

How to connect to the Open On Demand interface of Tier2 UGent: https://tier.hpc.ugent.be

How to install Globus for Data transfer on Windows: https://docs.globus.org/globus-connect-personal/install/windows/

Documentation VSC (Vlaams Supercomputer Centrum): https://docs.vscentrum.be

Proposed Schedule

13:00 - 13:30 - Introduction

13:30 - 15:00 -Access through terminal and browser

15:00 - 15:15 - Coffee Break

15:15 - 16:00 - Interactive sessions (debug and testing)

16:00 - 16:30 - Querying and using modules in the HPC

16:30 - 17:00 - Submitting and managing jobs

Acknowledgement:

VIB Data Core

VIB Bioimaging Core Leuven

Funding: This project has received funding from VIB.

PURL:

Authors and Contributors

Authors

Bruna Piereck

Janick Mathys

Contributors

Boris Depoortere

We welcome contributors for these materials

Citing this lesson

Please cite as:

Piereck Moura, B., Mathys, J.& Depoortere, B. (2026). High Performance Computing: structure and practice essentials (Version V2026.05.07) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.21919181

Chapters List

Chapter Title
1 Get ready for the course, instalation and accounts
2 HPC Infrastructure
3 Connecting to HPCs
4 VIB Data Core Compute
5 Transferring Data
6 Software on HPCs
7 Jupyter Notebooks

Chapter	Title
1	Get ready for the course, instalation and accounts
2	HPC Infrastructure
3	Connecting to HPCs
4	VIB Data Core Compute
5	Transferring Data
6	Software on HPCs
7	Jupyter Notebooks

Workshop and Material organization

We are using the interactive Open Educational Resource online/offline course infrastructure called LiaScript. It is a distributed way of creating and sharing educational content hosted on github. To see this document as an interactive LiaScript rendered version, click on the following link/badge: LiaScript

References

This material is inspired and uses excerpts from "HCP Training Bio-imaging", by Benjamin Pavie and Tatiana Woller. Use was authorized.
We use information available in the VSC (Vlaams Supercomputer Centrum) Documentation
We also use information availabl only for VIB personel in the VIB Data Core documentation

About us

About ELIXIR Training Platform

The ELIXIR Training Platform was established to develop a training community that spans all ELIXIR member states (see the list of Training Coordinators). It aims to strengthen national training programmes, grow bioinformatics training capacity and competence across Europe, and empower researchers to use ELIXIR's services and tools.

One service offered by the Training Platform is TeSS, the training registry for the ELIXIR community. Together with ELIXIR France and ELIXIR Slovenia, VIB as lead node for ELIXIR Belgium is engaged in consolidating quality and impact of the TeSS training resources (2022-23) (https://elixir-europe.org/internal-projects/commissioned-services/2022-trp3).

The Training eSupport System was developed to help trainees, trainers and their institutions to have a one-stop shop where they can share and find information about training and events, including training material. This way we can create a catalogue that can be shared within the community. How it works is what we are going to find out in this course.

About VIB and VIB Technologies

VIB is an entrepreneurial non-profit research institute, with a clear focus on groundbreaking strategic basic research in life sciences and operates in close partnership with the five universities in Flanders – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel and Hasselt University.

As part of the VIB Technologies, the 12 VIB Core Facilities, provide support in a wide array of research fields and housing specialized scientific equipment for each discipline. Science and technology go hand in hand. New technologies advance science and often accelerate breakthroughs in scientific research. VIB has a visionary approach to science and technology, founded on its ability to identify and foster new innovations in life sciences.

The goal of VIB Technology Training is to up-skill life scientists to excel in the domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management.

Editorial team for this course

Authors: @orcid(Alexander Botzki), @orcid(Bruna Piereck)

Technical Editors: Alexander Botzki

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