Perls of wisdom

Posted on 9 November 2015 by Thomas Green

It has been a long summer and it is time again to create a little post for a recent encounter on our supercomputer. Errors in Perl Perl is a common language which is very common within the Genomic communnity. Recently we had an interesting Perl issue where a job would just run for its maximum
Read more


Rating value

Summarising job performance

Posted on 13 August 2015 by Thomas Green

Recently we have implements an automatic job summary which is printed at the end of a user’s job that run on our supercomputer at Cardiff University. These job summaries are to help the user understand what impact the job has had and how to improve future jobs – just like energy efficiency ratings. This post
Read more


United nations assembly.

Research seminar – Accelerating computing

Posted on 2 July 2015 by Thomas Green

Using accelerators such as GPUs and Intel Phi technologies are becoming a popular method to extend the performance of certains codes. ARCCA is holding a research seminar which covers this topic. All are welcome to attend, even if you are not planning to use the technologies its is great to see the cutting-edge research Cardiff
Read more


Iceberg

Floating in numbers

Posted on 26 June 2015 by Thomas Green

Just like an iceberg, floating point numbers can have hidden danger lurking just under the surface. A recent email through a mailing list reminded me about the subtlties of handling floating point numbers. Floating point numbers are represented by mantissa*(base**exponent), see floating point numbers. There are many occassions where programmers may forget that floating point
Read more


Messing with meshes

Posted on 2 April 2015 by Thomas Green

A researcher has recently been trying to get to grips with meshes where they have scanned in some materials and would like to model this within COMSOL (multi-physics modelling package). There are a range of software which can be used to manipulate and display meshes. After some searching we found Gmsh seems to be very
Read more


Making a network work

Posted on 19 March 2015 by Thomas Green

We recently installed new nodes into our supercomputer. As part of the process we have to run tests to assess the new nodes. Since this was an extension to the existing infrastructure there were limits on how many high-speed links (or Infiniband (IB) connections) could be wired in, and the use for the nodes would
Read more


DRMAA

Working with DRMAA

Posted on 2 March 2015 by Thomas Green

Anyone who might have read earlier posts might have come across previous post on Galaxy. This used DRMAA to submit jobs when using a PBS Pro as a job scheduler. However recent issues whilst we upgraded our systems uncovered some unexpected issues with DRMAA. Going native with DRMAA First issue is with a feature of
Read more


Docker logo

Docking to Docker

Posted on 2 February 2015 by Thomas Green

Another month has passed and we have been very busy in ARCCA at Cardiff University with installation of the new hardware and installing new services. These are a few of the reasons why updates in the past few weeks have been infrequent but as I keep saying to myself: Must do better… However recently we
Read more


Firewall

Putting out fires

Posted on 19 January 2015 by Thomas Green

Recently we have reinstalled our operating system on a server to update to the most recent version from the vendor.  One aspect all new systems should have is some form of firewall to stop unintended or even non-hostile probes to cause issues – but why is this important. Laying the ground To stop the obvious
Read more


Terminal to Raven.

The December spring…

Posted on 19 December 2014 by Thomas Green

UPDATE – 20/12/2014 – Work still progressing on Raven and access will be given over the weekend of the 20th/21st with full service restored on Monday 22nd December. Since the last blog post on the datacentre we have a number of items to report to “spring” us back into action. Work in the datacentre The
Read more