This training session covers the core skills needed to use the BMRC cluster for scientific computing. The training session is open to all current and prospective users of the BMRC cluster, however complete beginners to Linux and the command line should see the Course Prerequisites below and watch the online training video in advance in order to participate in the hands-on activities.

This Core Skills for the BMRC Cluster training session will cover:

What’s a cluster and why use one?

Running your first job, monitoring and debugging strategies

Using pre-installed software for simplicity and reproducibility

Running jobs with more CPUs or more RAM

Using R and Python

Array jobs and simple pipelining

A BMRC cluster account will be required. If you do not already have an account please request one well in advance by emailing bmrc-help@medsci.ox.ac.uk , stating your University card barcode number and cc’ing your PI where appropriate or stating your group affiliation.

Course Prerequisites

The training session is open to all, including those who are just beginning to using Linux and the command line and/or beginners to using a cluster.

To get the most out of the cluster training and participate in the hands-on activities, those who are beginners to Linux and the command line are encouraged to complete in advance the online Learning Linux Command Line course that is freely available to University members. The important sections are:

Section 2: Command Line Basics

Section 3: Files, Folders, Permissions

Section 4: Common Command-Line Tasks and Tools. This section is optional for this training but recommended and what you learn here will soon become essential as you continue your journey into Linux computing.

Watching sections 2-4 should take around 2 hours in total and you can of course watch in stages.

If you have difficulty accessing the online course directly, please login via skills.it.ox.ac.uk/linkedin-learning (click the red LinkedIn Learning button top right) and then click the link above.