MRC LMS - Introduction to HPC and cluster computing

MRC LMS Bioinformatics

LMS email address Jesus.Urtasun@lms.mrc.ac.uk

ICL email address jurtasun@ic.ac.uk

Find the content of the course in GitHub:

LMS Introduction to HPC and cluster computing

This course provides an introduction to High Performance Computing (HPC) and basics of cluster programming (...)

Roadmap of the course

Chapter 1. Introduction to HPC.

• Basics of Bash / Shell and Linux OS.
• Scheduler, partitions, connect remotely to an HPC cluster.
• Navigate JEX, launch a SLURM job and check execution.

Chapter 2. Working on an HPC environemnt.

• Check job status and queues (squeue, sinfo).
• Inspect available software with module avail.
• Load and manage modules (module load, module list).
• Understand basic resource usage (CPU, memory, time).

Chapter 3. Managing software and resources.

• Introduction to conda environments (create, activate, install).
• Switching between partitions (e.g. cpu, hmem, gpu).
• Choosing appropriate resources for jobs.
• Basic troubleshooting of jobs and environments.

Remote access to LMS JEX

To access JEX, the LMS HPC cluster, open a terminal and type

ssh user@jex.lms.mrc.ac.uk

where user should be your username as set up with corresponding IT service.

You will be asked to input your passsword to access, also set up with IT.

Remote access to Imperial CX3

To access CX3, the Imperial College HPC cluster, open a terminal and type

username@login.cx3.hpc.imperial.ac.uk

where user should be your username as set up with corresponding IT service.

You will be asked to input your passsword to access, also set up with IT.

Setting up Python and R on your own machine

Setting up Python and R on your own machine

Instructions for Mac and Linux

Instructions for Mac and Linux (...)

Instructions for Windows

Instructions for Windows (...)

Licence

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Licence.