Hands-on Introduction to HPC for Life Scientists @ EPCC

JCMB 3305 (EPCC)

JCMB 3305


The University of Edinburgh James Clerk Maxwell Building Mayfield Road Edinburgh EH9 3FD

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 organised and funded by BioExcel - the Centre of Excellence for Computational Biomolecular Research (http://bioexcel.eu) and PRACE, and delivered in collaboration with ARCHER - the UK national supercomputing service (http://archer.ac.uk).


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.


Registration is on a first-come, first-served basis via https://events.prace-ri.eu/event/626/registration/

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.


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 at http://bioexcel.eu/wp-content/uploads/2017/01/BioExcelTravelGrant.pdf


Wednesday November 29th

10:00 - Welcome, introduction, and course overview
Review of HPC skills and competencies framework
Familiarisation with fellow attendees

11:00 - LECTURE - What is HPC?
11:25 - PRACTICAL - Connecting to ARCHER
11:30 - BREAK - Coffee & Tea
12:00 - PRACTICAL - Sequence Alignment
13:00 - BREAK - Lunch
14:00 - LECTURE - Parallel Computing Patterns
14:30 - LECTURE - Measuring Parallel Performance
15:00 - PRACTICAL - Sequence Alignment (continued)
15:30 - BREAK - Coffee & Tea
16:00 - PRACTICAL - Sequence Alignment (continued)
16:15 - LECTURE - Building Blocks - Software (Operating System, Processes and Threads)
16:45 - LECTURE - Building Blocks - Hardware (Processors & cores, Memory, Accelerators)
17:15 - Review of the day
17:30 - Finish

Thursday November 30th

9:30 - Summary of day 1
9:45 - LECTURE - Parallel Models
10:30 - PRACTICAL - Fractal
11:00 - BREAK - Coffee & Tea
11:30 - PRACTICAL - Fractal (continued)
12:00 - LECTURE - HPC Architectures
12:30 - LECTURE - Batch Systems & Parallel Application Launchers
13:00 - BREAK - Lunch
14:00 - PRACTICAL - Molecular Dynamics
15:00 - LECTURE - Compilers and Building Software
15:30 - BREAK - Coffee & Tea
16:00 - PRACTICAL - Molecular Dynamics (continued)
16:30 - LECTURE - Parallel libraries
17:00 - Review of the day
17:15 - Finish

19:00 - Dinner at Amber restaurant

Friday December 1st

9:30 - Summary of day 2
9:45 - LECTURE - Pipelines and workflows
10:15 - PRACTICAL - Molecular Dynamics (continued)
11:00 - LECTURE - The UK & EU HPC Landscape
11:30 - BREAK - Coffee & Tea
12:00 - LECTURE - The Future of HPC
12:30 - LECTURE - "Where next?" and things to remember
13:00 - Lunch
14:00 - Individual consultations, course review and feedback / competency survey
15:00 - Finish

Course Materials




The course dinner will be held at the Amber restaurant, located at the Scotch Whisky Experience near Edinburgh Castle, on Thursday 30th November at 19:00.
For location and travel information see https://www.scotchwhiskyexperience.co.uk/plan-your-visit




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