ARCHER

Spark-based genome analysis on Cray-Urika and Cirrus clusters

Author: Rosa Filgueira
Posted: 16 Jan 2019 | 11:06

Analysing genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation.

Typically in a cancer genomics analysis, both a tumour sample and a “normal” sample from the same individual are first sequenced using NGS systems and compared using a series of quality control stages. The first control stage, ‘Sequence Quality Control’ (which is optional), checks sequence quality and performs some trimming. While the second one, ‘Alignment’, involves a number of steps, such as alignment, indexing, and recalibration, to ensure that the alignment files produced are of the highest quality as well as several more to guarantee the variants are called correctly. Both stages compromise a series of intermediately computing and data-intensive steps that very often are handcrafted by researchers and/or analysts.

On the frontline of energy-efficient computing

Author: Paul Clark
Posted: 7 Jan 2019 | 15:14

The Advanced Computing Facility (ACF) on the outskirts of Edinburgh is the high performance computing data centre of EPCC.

Built in the 1970s and operated by EPCC since the turn of the millennium, the ACF site has had significant investment over the years. At present, there are three Computer Rooms, imaginatively called: Computer Room 1 (CR1), Computer Room 2 (CR2), and Computer Room 3 (CR3).

My HPC-Europa visit to EPCC

Author: Guest blogger
Posted: 20 Nov 2018 | 09:08

 

Pablo C. Cañizares came on an HPC-Europa3 visit to EPCC from 23 July–24 October 2018. In this blog article he summarises his visit.

Hi there! I'm Pablo C. Cañizares, a PhD student in Computer Science from the Complutense University of Madrid (UCM), Spain. I work in the Design and Testing of Reliable Systems group in the Computer Science Faculty of the UCM. I visited EPCC for three months under the HPC-Europa3 transnational access programme and was hosted by EPCC's Dr David Henty.

VESTEC: saving the world one byte at a time

Author: Nick Brown
Posted: 15 Nov 2018 | 16:21

With jobs submitted to a batch system, supercomputing has traditionally been centred around an offline, non-interactive approach to running codes such as simulations. However, it is our belief that there is great potential in fusing HPC with real-time data for use as part of urgent decision-making processes in response to natural disasters and crises.

New Prosperity Partnership to develop world first in high-fidelity engineering simulations

Author: Michele Weiland
Posted: 5 Nov 2018 | 14:44

A consortium led by Rolls-Royce and EPCC was recently awarded an EPSRC Prosperity Partnership worth £14.7m to develop the next generation of engineering simulation and modelling techniques, with the aim of developing the world’s first high-fidelity simulation of a complete gas-turbine engine during operation.

eCSE programme: funding software development for UK computational science

Author: Lorna Smith
Posted: 2 Nov 2018 | 23:00

The embedded Computational Science and Engineering (eCSE) programme has allocated funding to the UK computational science community over a period of six years. Integral to ARCHER, the National HPC Service, there has been a series of regular eCSE Calls to fund software development activities.

The last of the Calls has now closed and all funding has been allocated. Although a number of projects are still on-going, this seems a good time to review the benefits of the programme and to see whether its aims have been met.

Making complex machines easier to use efficiently

Author: Daniel Holmes
Posted: 24 Oct 2018 | 16:48

Supercomputers are getting more complex. Faster components would be impossible to cool but, by doing more with less, we can still solve bigger problems faster than ever before.

HPC-Europa Transnational Access Meeting (TAM 2018)

Author: Catherine Inglis
Posted: 23 Oct 2018 | 09:49

EPCC has now been welcoming visitors from the HPC-Europa3 programme for a year. To mark this we hosted the first user group meeting in Edinburgh in October.

ARCHER Image & Video Competition 2018: results!

Author: Clair Barrass
Posted: 18 Oct 2018 | 10:53

Thank you to everyone who submitted images and videos to this year's competition. The outstanding range of entries made judging a most enjoyable experience with so many great demonstrations of the important work being done using ARCHER.

Bang Goes the Borders 2018

Author: Mario Antonioletti
Posted: 28 Sep 2018 | 09:29

While a team of EPCCers were doing outreach in London at New Scientist Live (NSLive) for a second year running, another group of us attended Bang Goes the Borders (BGTB) at St Mary's Primary School in Melrose, which is mostly attended by children aged from 5-12 with their parents. For us this is a relatively local event and this is the eighth year that we been there. It is only a day event but a pretty busy one.

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