HPC

Agony and ExTASY

Author: Iain Bethune
Posted: 8 Jun 2015 | 16:41

ExTASY project logo

Over 18 months ago, we kicked off the ExTASY project. Our lofty aim was to tackle one of the 'Grand Challenges' of biochemistry - effective sampling of complex biomolecules using Molecular Dynamics to provide a physical understanding of their function and behaviour.

MPI 3.1 ratified

Author: Daniel Holmes
Posted: 8 Jun 2015 | 13:17

The MPI 3.1 standard, a minor update to the existing MPI 3.0 Standard, was ratified last week at the latest MPI Forum meeting

CP2K-UK: One year on

Author: Iain Bethune
Posted: 5 Mar 2015 | 09:36

CP2K LogoEarlier this month we held the second annual CP2K User Group Meeting at King's College London, in the shadow of London's iconic 'Shard'.  The meeting was even more popular than last year's, with around 60 people coming along to learn about the latest new features available in CP2K, and to hear from a wide range of existing users what they are doing with the code.  

CMCGS2015: Two days of Maths in Singapore

Author: Iain Bethune
Posted: 10 Feb 2015 | 14:33

Last week I was lucky enough to spend a few days in the tropical city of Singapore, attending the Computational Mathematics, Computational Geometry & Statistics (CMCGS) 2015 conference. I was there to present a review paper on the achievements of the PrimeGrid project, which I have blogged and talked about before, but as a more mathematical rather than computationally-themed conference, it was also a good chance to make contact with researchers who might be less au fait with parallel computing than most.

Hotel Fort Canning, Singapore

VOX-FE GUI developments

Author: Iain Bethune
Posted: 25 Jan 2015 | 15:55

For the last few years, I have had the opportunity to collaborate with Prof. Michael Fagan of the Medical and Biological Engineering group at the University of Hull on the development of his VOX-FE voxel finite-element (FE) bone modelling software. Past projects under EPSRC and HECToR dCSE funding allowed us to improve the scaling of the core solver and implementent parallel I/O, but it has become increasingly apparently that this was papering over the cracks, and a complete re-engineering of the code base would be required to make it portable, scalable and flexible enough to be useable.  

Energy efficiency in parallel computing

Author: Michele Weiland
Posted: 14 Jan 2015 | 15:30

The Adept project is addressing the challenge of the energy-efficient use of parallel technologies. It builds on the expertise of software developers from high-performance computing to exploit parallelism for performance, and on the expertise of Embedded systems engineers in managing energy usage. Adept is developing a tool to guide software developers and help them model and predict the power consumption and performance of parallel software and hardware.

The Message-Passing Interface: unlocking the power of software

Author: Mike Jackson
Posted: 8 Jan 2015 | 11:53

Simulation by IES of daylight on a building.

 

 

 

 

 

EPCC helped lead the way in creating the standardised Message-Passing Interface (MPI) programming system to enable faster, more powerful, problem solving using parallel computing. It is now the ubiquitous de-facto standard among both hardware and software vendors.

Mike Jackson and Dan Holmes explain how EPCC continues to be involved in its development and use.

The Auditory Project – an investigation into modelling the human ear using HPC

Author: Fiona Reid
Posted: 14 Nov 2014 | 15:12

The Auditory pilot project investigated the use of HPC to enable faster run times for computational models of the human cochlea. It was a collaboration between EPCC and Dr Michael Newton of the University of Edinburgh’s Acoustics and Audio group.

We began with an existing cochlea model code written in Matlab, which took many hours to run on a single processor. Our initial profiling of the Matlab code showed that almost the entire runtime (see Figure 1) was taken up by this solver and thus any attempts to parallelise the code would require a C/C++ replacement to be found. 

Bang went the Borders

Author: Iain Bethune
Posted: 23 Oct 2014 | 14:42

Last month, EPCC took part in the Bang Goes The Borders science festival at St Mary's Primary School in Melrose.  Lorna Smith, Justs Zarins and I spent the day telling people from pre-schoolers to retirees all about supercomputers, how they work, and what they are used for.  

Volunteer computing & the hunt for prime numbers

Author: Iain Bethune
Posted: 29 Sep 2014 | 15:52

As well as helping out with our drop-in workshop at the British Science Festival in early September, I also had the chance to give a talk as part of the Festival's public lecture programme. Over 75 people turned out early on Sunday morning to hear 'Seventeen or Bust: Solving hard mathematical problems with your help!', where I explained how the PrimeGrid project is working on a solution to Sierpinski's conjecture, a fifty-year-old unsolved problem in Number Theory, as well as finding record-sized prime numbers in the process.

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