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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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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New high performance storage for scratch data

Posted on Wed 20 March 2019 in news by Peter Childs

We are pleased to announce a new scratch storage array that is based on fast NvME based hardware. This will hopefully make I/O related tasks much faster.

Scratch space is the recommended location for temporarily storing data produced by cluster jobs. We often see jobs failing on the cluster …


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NAG Fortran compiler available on Apocrita for SEF

Posted on Mon 18 March 2019 in news by Iain Barrass

The School of Economics and Finance has a departmental licence for the Fortran compiler from NAG. The compiler, release 6.2, is now available on Apocrita.

Using the compiler

The compiler is available through a module on the cluster:

$ module load nagfor/6.2-6227
$ nagfor -V
NAG Fortran Compiler Release …

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Modules Update March 2019

Posted on Mon 11 March 2019 in news by Tom Bradford

Since the last update (on 29/11/2018), we have updated the following module files:

Updates to the Production Environment

  • Added bartender 1.1 (now the default)
  • Added boost 1.68.0 (now the default)
  • Added castep 18.1-intel* (now the default)
  • Added cuda 9.0.176
  • Added cudnn 7 …

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GitHub Enterprise Upgrade 2.16

Posted on Thu 14 February 2019 in news by Tom Bradford

On Wednesday 2019-02-20 at 14:00 we will be applying an upgrade to our GitHub Enterprise instance to version 2.16.2, which includes bug fixes and the latest security updates.

The update should take around 1 hour. During that time you will not be able to perform any git …


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Retirement of legacy scratch filesystem on /data/scratch

Posted on Fri 25 January 2019 in news by Dan Whitehouse

Our infrastructure team have been busy at work preparing Apocrita for new high performance scratch storage. As part of this work we need to decommission our legacy scratch (mounted on '/data/scratch').

To check if you have files on the old scratch storage please use:

ls /data/scratch/$USER

If …


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