Introduction to High Performance Computing for Life Scientists

Description

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.

This course is presented by:

General Information

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by the ARCHER2 Training Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. Where the course is being run in person and face-to-face, the workshop organizers have checked that:

• The room is wheelchair / scooter accessible.
• Accessible restrooms are available.

All course materials will be provided in advance of the lesson online. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email J.Sindt@ed.ac.uk for more information.

Prerequisites

You should be happy with connecting using basic bash commands, such as cd, mv, cp, and ssh. Familiarity with using the Linux command line will be useful, but you do not need to be an epexrt in shell scripting. You should also be happy editing plain text files in a remote terminal (or, alternatively, editing them on your local system and copying them to the remote HPC system using scp).