Software

Dedicated to software topics.

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
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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
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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
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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
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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
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Bashing those script bugs

Posted on 20 November 2014 by Thomas Green

Recently we had a user report a problem where they had managed to start copying the complete filesystem of a compute node into their home directory. Fortunately for us we had setup quotas on our users home space so it stopped when it filled up their quota but it seemed it was all due to
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Portal to a new Galaxy

Posted on 24 October 2014 by Thomas Green

Within the ARCCA team we are investigating ways we can open up high-performance computing (HPC) to a wider audience. I should add this is not just an issue within ARCCA but a more general trend across HPC organisations. The name for website which provide easier access to HPC are called Portals or Gateways. The Extreme
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Performant Python with Intel MKL

Posted on 15 October 2014 by Thomas Green

ARCCA have recently been helping a research group at Cardiff University to benchmark their code. The code was based on Python and had many options to perform FFT analysis. One particular option was to use the Intel MKL directly within the Python code. This was particularly useful since the MKL would have had optimisations for
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Postive performance with C++

Posted on 1 October 2014 by Thomas Green

Recently a researcher has come to us with a performance issue in their code.  The code was written in C++ and was taking a very long time to run – reaching a limit on the time a job can run within our scheduler. Profile of the culprit First thing to do when given a task
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Excelling in R

Posted on 1 September 2014 by Thomas Green

Recently we have helped researchers wanting to perform a large analysis of data that was in an Excel spreadsheet. We had over 70,000 rows and around 20 columns which required lots of conditional summing and checks to be performed. After trying to use Excel to perform the analysis on my Mac it seemed the conditional
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