An introduction to High Performance Computing
Date: 6 - 8 February 2024
Timezone: Brussels
Duration: 15 hours
This practical introduction to high-performance computing (HPC) will cover all basic concepts needed to access an HPC cluster and to run applications and workflows there.
The course is built upon the Carpentries and HPC Carpentry online learning materials, with HPC Carpentry being a lesson program in incubation for the Carpentries. The Carpentries is a nonprofit organisation that teaches software engineering and data science skills to researchers in order to conduct efficient, open, and reproducible research. Their volunteer instructors (4287) have run 4000+ Workshops in 65 countries since 2012, with 450+ alone in 2022 [3]. All of their lesson materials are freely reusable under the Creative Commons - Attribution licence [4].
Here, we are offering a 3-day workshop, composed of a half-day and 2 full-day sessions, with the primary goal of introducing High-Performance Computing (HPC) to individuals who have limited or no prior experience with such computing resources. The first day is dedicated to guiding participants through the basics of file systems and the Unix shell. This foundation is a prerequisite for the other days which introduces HPC resources, the cluster management tool Slurm, and how to run applications and workflows on such resources.
Contact: BioNT's contact email: [email protected]
Keywords: HPC, High Performance Computing, High performance computing, high-performance computing
Prerequisites:
Requirements:
- There is no need for programming or informatics skills but a basic understanding of what files and directories are is required
- PC/Laptop with an up-to-date browser. Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, may not be)
- The lessons require you to have access to a terminal application with ssh capabilities. If it is unclear what this requirement means, please click here for guidance on how to make this available for your operating system
Learning objectives:
By the end of this workshop, you will be able to:
- Use the UNIX shell (also known as terminal or command line) to connect to a cluster
- Identify problems a cluster can help solve
- Transfer files onto a cluster
- Comfortably manipulate files and directories, locally and on a remote resource
- Submit and manage jobs on a cluster using a scheduler
- Observe the benefits and limitations of parallel execution
- Understand how to construct a reliable, scalable and reproducible scientific workflow as a series of chained rules
- Use a subset of features of the Snakemake workflow tool
- Run a Snakemake workflow on an HPC resource
Organizer: BioNT (BIO Network for Training)
Target audience: Job seeker, Early Career Researchers (ECRs), Small and Medium-sized Enterprises (SMEs)
Event types:
- Workshops and courses
Tech requirements:
Recommendations for your setup and interacting during the workshop:
- To follow the workshop more efficiently, we recommend having a two-screen setup: for example, one to display the instructor’s shared screen and the collaborative pad, and another one for your own coding.
- To actively communicate during the workshop, please familiarise yourself with Markdown formatting by reviewing the HedgeDoc features document.
Credit / Recognition: Certificate upon completion and once the attendance has been confirmed
Cost basis: Free to all
Sponsors: Co-funded by the European Commission, 101100604 - DIGITAL-2022-TRAINING-02
Activity log
