Introduction to HPC for Life Scientists

Description:

This course provides an introduction to High-Performance Computing (HPC) for researchers in the life sciences, using ARCHER2 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 ARCHER2 - the UK national supercomputing service (https://www.archer2.ac.uk/).

Overview

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 (ARCHER2, 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

Schedule

Day 1

• 10:00 Welcome
• 10:15 Who we are: Introducing BioExcel, PRACE, and EPCC training
• 11:00 LECTURE: High-Performance Computing (HPC)
• 11:20 PRACTICAL: Connecting to ARCHER2
• 11:40 BREAK
• 12:00 LECTURE: HPC Architectures (pre-recorded)
• 12:20 PRACTICAL: Overview of the ARCHER2 system and modules
• 13:00 LUNCH
• 13:40 LECTURE: Batch systems and parallel application launchers (pre-recorded)
• 14:00 PRACTICAL: Batch Systems and ARCHER2 Slurm Scheduler
• 14:30 BREAK
• 14:50 LECTURE: Parallel Computing
• 15:20 PRACTICAL: HMMER (1 of 2)
• 15:55 LECTURE: Review of Day 1
• 16:00 Finish

Day 2

• 10:00 Welcome
• 10:05 LECTURE: Measuring Parallel Performance
• 10:35 PRACTICAL: HMMER (2 of 2)
• 11:20 BREAK
• 11:40 LECTURE: Computational Building Blocks: Software
• 12:10 LECTURE: Computational Building Blocks: Hardware
• 12:40 LUNCH
• 13:30 PRACTICAL: Benchmarking Molecular Dynamics Performance Using GROMACS
• 14:00 LECTURE: Parallel Models to Exploit Parallelism
• 14:30 BREAK
• 14:50 PRACTICAL: Benchmarking Molecular Dynamics Using GROMACS
• 15:20 LECTURE: Building and compiling software: from algorithm to executable
• 15:45 LECTURE: Review of Day 2
• 16:00 Finish

Day 3

• 10:00 Welcome
• 10:05 PRACTICAL: Benchmarking Molecular Dynamics Using GROMACS
• 10:35 LECTURE: Pipelines and Workflows
• 11:20 BREAK
• 11:40 QM/MM Simulations Using CP2K
• 12:40 LUNCH
• 13:30 LECTURE: The future of HPC
• 14:00 QM/MM Simulations Using CP2K
• 14:30 BREAK Break
• 14:50 LECTURE: The HPC landcsape in the EU and UK
• 15:20 LECTURE: Course review and where next?
• 15:40 Finish

Pre-requisites

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.

This course is part-funded by the PRACE project and is free to all.