Hands-on Introduction to HPC for Life Scientists

Date: Wednesday 29th November – Friday 1st December 2017
Venue: EPCC, James Clerk Maxwell Building (JCMB 3305), University of Edinburgh
Application opens: Sunday June 23 2017
Participation: First come, first served
Contact: Vera Matser
Registration fee: £0

Register here

This course provides an introduction to High-Performance Computing (HPC) for researchers in the life sciences, using ARCHER as a platform for hands-on training exercises.

The course is co-organised and funded by BioExcel and PRACE (http://www.prace-ri.eu/), and delivered in collaboration with ARCHER – the UK national supercomputing service (http://archer.ac.uk).

BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to be considered for a travel bursary email Vera Matser (matser [at] ebi.ac.uk). Eligibility criteria and conditions for the travel grants are available here – BioExcelTravelGrant.


High-performance computing (HPC) is a fundamental technology used to solve a wide range of scientific research problems. Many important challenges in science such as protein folding, the search for the Higgs boson, drug discovery, and the development of nuclear fusion all depend on simulations, models and analyses run on HPC facilities to make progress.

This course introduces HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in future. The course will cover basic concepts in HPC hardware, software, user environments, filesystems, and programming models. It also provides an opportunity to gain hands-on practical experience and assistance using an HPC system (ARCHER, the UK national supercomputing service) through examples drawn from the life sciences, such as biomolecular simulation.

Learning outcomes

On completion of the course, we expect that attendees will understand and be able to explain:

• Why HPC? – What are the drivers and motivation? Who uses it and why?
• The UK & EU HPC landscape – HPC facilities available to researchers
• HPC hardware – Building blocks and architectures
• Parallel computing – Programming models and implementations
• Using HPC systems
• Access
• Batch schedulers & resource allocation
• Running jobs
• Dealing with errors
• Compiling code
• Using libraries
• Performance
• The Future of HPC


This course follows on naturally from the BioExcel Summer School on Foundation skills for HPC in computational biomolecular research (http://bioexcel.eu/events/bioexcel-summer-school/)

Familiarity with basic Linux commands (at the level of being able to navigate a file system) is recommended. You may find a Linux ‘cheat sheet’ such as http://www.archer.ac.uk/documentation/user-guide/linux.php#quickref useful if you are less familiar with Linux.

No programming skills or previous HPC experience is required.

Desktop computers running Windows will be available, however you are encouraged to bring your own laptop (running Windows, Linux, or macOS) as you will find it useful to learn how to set this up to connect to ARCHER (with assistance from course helpers if needed) and perform the hands-on practicals.



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29 Nov, 2017 - 01 Dec, 2017
10:00 - 15:00

EPCC, The University of Edinburgh


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