October 30, 2019 to November 1, 2019
Europe/London timezone

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/840/registrations/

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.

Laptop computers 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.


Day 1

10:00 - Welcome, introduction, and course overview
What can BioExcel do for me?
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 using HMMER
13:00 - BREAK - Lunch
14:00 - LECTURE - Parallel Computing Patterns
14:30 - LECTURE - Measuring Parallel Performance
15:00 - PRACTICAL - Sequence Alignment using HMMER
15:30 - BREAK - Coffee & Tea
16:00 - PRACTICAL - Sequence alignment using HMMER
16:15 - LECTURE - Building Blocks - Software (Operating System, Processes and Threads)
16:45 - LECTURE - Building Blocks - Hardware (Processors/CPUs/cores, Memory, Accelerators)
17:15 - Review of the day
17:30 - Finish

Day 2

9:30 - Summary of day 1
9:45 - LECTURE - Parallel Models
10:30 - PRACTICAL - Molecular Dynamics using GROMACS
11:00 - BREAK - Coffee & Tea
11:30 - PRACTICAL - Molecular Dynamics using GROMACS
12:00 - LECTURE - HPC Architectures
12:30 - LECTURE - Batch Systems & Parallel Application Launchers
13:00 - BREAK - Lunch
14:00 - PRACTICAL - Molecular Dynamics using GROMACS
14:30 - LECTURE - Compilers and Building Software
15:00 - BREAK - Coffee & Tea
15:30 - PRACTICAL - QM/MM simulation using CP2K
16:30 - LECTURE - Parallel libraries
17:00 - Review of the day
17:15 - Finish of session

Day 3

9:30 - Summary of day 2
9:45 - LECTURE - Pipelines and workflows
10:15 - PRACTICAL - QM/MM simulation using CP2K
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 survey
15:00 - Finish

Course Materials


Course Dinner

The course dinner (paid for by BioExcel) will be at 7pm on Thursday 31st October at Pizza Express Birmingham Mailbox

Travel Grant

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, application instructions as well as eligibility criteria and conditions for the travel grants are available through the link below.


Deadline for Travel Grant applications is 30th September 2019.

Any questions about the travel grants please email Michelle Mendonca (info@bioexcel.eu).


Participants are responsible for booking their own accommodation and travel.

On-campus accommodation can be found at https://conferences.bham.ac.uk/accommodation/hotels-on-campus/. Hotels in the centre of Birmingham are also an option as the University's Edgbaston campus (closest train station "University") is only a short (~10 minute) train ride from Birmingham New Street station.

Large Meeting & Teaching Room
Centre for Computational Biology Haworth Building University of Birmingham (Edgbaston Campus) B15 2FG
This course is part-funded by the PRACE project and is free to all. Please register using the online form. If you have any questions, please consult the course forum page or contact support@archer.ac.uk.