Welcome to the QMUL HPC documentation site

Rocky 9 documentation site

This site provides information for using Apocrita with the new Rocky 9 operating system. Pages published on this site have been reviewed by the ITS Research team and are accurate for the Rocky 9 operating system only. The old CentOS 7 documentation is available on our legacy docs site.

All jobs now require an extra parameter!

During the cluster migration phase, all jobs submitted with qlogin and qsub now require an extra parameter to route your job to nodes running the desired Operating System.

Rocky 9 jobs must add -l rocky to run on a Rocky 9 node. For the legacy CentOS 7 cluster currently draining for upgrade, add -l centos. Our job verification script will now reject jobs that lack one of these options, or incorrectly request both.

Other documentation pages on this site have not been updated to reflect this change.

This site supports the research computing services, including QMUL's High Performance Compute cluster, provided by the ITS Research group at Queen Mary University of London. It provides information on use, policy and best practices, alongside documentation for computing applications available on the cluster, to maximise cluster efficiency and total research output.

Apocrita

Apocrita is a heterogeneous HPC cluster comprising around 300 nodes and 13,500 cores, managed by ITS Research at Queen Mary University of London for the primary purpose of supporting research performed by QMUL researchers. It is owned by QMUL and located in the Virtus shared data centre in Slough.

Why use Apocrita?

Using an HPC cluster can substantially reduce the time taken to compute problems by running analyses in parallel or breaking them up into pieces. Both strategies allow for the problem to be worked on by many separate compute cores (CPUs) at the same time.

The Apocrita system has been specifically designed to meet the needs of a wide variety of research in the areas of our three faculties: Humanities and Social Sciences, Science and Engineering, and Medicine and Dentistry.

Citing Apocrita in your research

Published research which has used the Apocrita HPC system should reference this facility using the following text:

This research utilised Queen Mary's Apocrita HPC facility, supported by QMUL Research-IT. http://doi.org/10.5281/zenodo.438045

We also ask that you acknowledge assistance from ITS Research where applicable. Please see the citing page for examples.

Getting started

New cluster accounts for eligible users can be requested here. There are also sections on how to log in, change your password, submit a job, and a description of the various nodes available on the cluster.

There is also a current list of installed applications and how to use some of the more popular ones.

We host two instances of GitHub Enterprise, one using centralised QMUL login credentials and the other with ITS Research (HPC) credentials. If you are interested in using this GitHub Enterprise service, please compare each version and select the most appropriate instance for your research needs.

ITS Research also provide support to some eligible users on Tier 2 HPC systems.

Getting help

For assistance, please see the Getting Help page for what information to supply when contacting us.