Productivity tips for Apocrita cluster users

Posted on Wed 23 October 2019 in tutorial by Simon Butcher

This article presents a selection of useful tips for running successful and well-performing jobs on the QMUL Apocrita cluster.


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Comparing common compression tools using real-world data

Posted on Thu 10 October 2019 in article by Simon Butcher

Compression tools can significantly reduce the amount of disk space consumed by your data. In this two-part article, we will look at the effectiveness of some compression tools on real-world data sets, make some recommendations, and perhaps persuade you that compression is worth the effort.


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Modules Update August 2019

Posted on Fri 09 August 2019 in news by Tom Bradford

Since the last update in April, we have updated the following module files:

Application Name Application Version Arch Status Set as Default?
abaqus 2019 x86_64 moved from dev to production no
anaconda2 2019.03 ppc64le added to dev N/A
anaconda3 2019.03 ppc64le added to dev N/A
ansys …

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Simplification of parallel queues on Apocrita

Posted on Thu 27 June 2019 in news by Simon Butcher

We are simplifying the way that the multi-node parallel jobs are run on the cluster.

Currently, users wishing to run multi-node MPI jobs on the public queues must choose beforehand whether to run on the nxv parallel nodes or the sdv parallel nodes, and to configure the job accordingly for …


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Cluster Update Summary

Posted on Wed 12 June 2019 in news by Simon Butcher

As part of our commitment to providing stable and manageable systems, here is a round-up of some recent updates we have been working on behind the scenes:

1) Upgrade of all HPC cluster nodes to CentOS 7.6

Over the last couple of weeks, you may have noticed a few …


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Storage Upgrade 19th - 20th June 2019

Posted on Wed 12 June 2019 in news by Peter Childs

Apocrita Research Data Storage: Notice of "at risk" period

Wednesday 19th and Thursday 20th June 2019.

We will be performing essential firmware updates and patching to the storage system on the Apocrita HPC Cluster. This is to finalise the upgrade work we have been caring out over recent months.

We …


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Getting REAL with Fortran

Posted on Wed 12 June 2019 in rse by Iain Barrass

Fortran provides a variety of intrinsic representations of real numbers. In this post we look at what these representations are and how we choose a particular representation for our work.


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GitHub Enterprise Maintenance 02/05/2019

Posted on Fri 26 April 2019 in news by Tom Bradford

On Thursday 02/05/2019 at 10:00 the GitHub Enterprise instance will be taken down for maintenance to increase the disk capacity that contains user data as it is currently over 80% full.

The maintenance should take around 1 hour. During that time you will not be able to …


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Modules Update April 2019

Posted on Fri 26 April 2019 in news by Tom Bradford

Since the last update in March, we have updated the following module files:

Updates to the Production Environment

  • Added anaconda2 2018.12
  • Added anaconda3 2018.12
  • Added cellranger 3.0.2
  • Added nagfor 6.2
  • Moved perl5lib to perl5lib/5.26.0
  • Added relion 3.0 and 3.0-gpu
  • Added …

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Running Machine Learning workloads on Apocrita

Posted on Fri 22 March 2019 in tutorial by Simon Butcher

In this tutorial we'll be showing you how to run a TensorFlow job using the GPU nodes on the Apocrita HPC cluster. We will expand upon the essentials provided on the QMUL HPC docs site, and provide more explanation of the process. We'll start with installation, and run through some …


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