Introduction to HPC

This material is inspired and using extracs from "HCP Training Bio-imaging", by Benjamin Pavie and Tatiana Woller. Use was authorized.

This material in under active development at the moment.

Hello and welcome to our VIB workshop! We are very happy to have you here.

This is the 2nd edition of this workshop.

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

General context

Welcome to our Introduction to HPC workshop! We are very happy to have you here.

This is the 2nd edition of this workshop

The half day session aims to introduce the different options available withing the Flemish system, while enabling studnets to quicl adapt to any HPC system they migh access around the globe. With some best practices and differences and similarities within each system.

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

Proposed Schedule

Half day Schedule:

• 9:00 - 09:30 - Introduction
• 09:30 - 10:30 - Accessing in the terminal and ondemand
• 10:30 - 10:45 - Coffee Break
• 10:45 - 11:30 - Interactive sessions (debug and testing)
• 11:30 - 12:00 - Querying and using modules in the HPC
• 12:00 - 12:30 - Submitting and managing jobs

Lesson overview

License: Creative Commons Attribution share alike 4.0 International License

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

Level: Beginner

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

1. Basic of command line

Description

In this half-day introduction, you will have the opportunity to know a bit more about the structure of the HPC (tiers), what resources you have available, and most importantly, how to use and navigate the HPC.

In this course, you will learn the differences and similarities between

• VSC (Vlaams Supercomputer Centrum) instances in Gent and Leuven

• VIB Data Core

• And a glimpse of what you could find beyond.

It is our aim that you can more easily adjust to any HPC system that you encounter in your professional life.

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

1. Describe differences and similarities among HPC Tiers and usage

2. Access existing HPC infrastructures in Flanders, such as VSC and VIB Data Core

3. Use the different environments in the HPC (storage, analysis, and debug)

4. Querying and using modules and their versions in the HPC

5. Submit jobs to use software and scripts on the cluster

6. Check information about submitted jobs

Time estimation: 4 hours

Requirements: The (technical) installation requirements are described in Chapter 2

Supporting Materials:

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

• How to install Globus for windows: : https://docs.globus.org/globus-connect-personal/install/windows/

• Documentation VSC: https://docs.vscentrum.be

Acknowledgement:

• VIB Data Core
• VIB Bioimaging Core Leuven

Funding:

PURL:

Authors and Contributors

Authors

• [Bruna Piereck](@orcid
• [Janick Mathys](@orcid

Contributors

• Boris Depoortere

Citing this lesson

Please cite as:

1. ...

Chapters List

Material for the HPC training for bioimaging analysis.

Introduction

HPC Infrastructure overview

BAND introduction

Software modules

Data transfer with Globus

Jupyter Notebooks

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