HPC

Big Data: What's wrong with HPC?

Author: Adrian Jackson
Posted: 3 Sep 2015 | 17:55

Big Data vs HPC

Whilst I was writing my talk for last week's How to Make Big Data work for your business seminar at Edinburgh BioQuarter, it occurred to me that the way computational simulation codes have evolved over the last 40 years has really been a response to big data issues. 

HPCG: benchmarking supercomputers

Author: Adrian Jackson
Posted: 30 Jul 2015 | 14:40

HPCG

The LINPACK library (often known as HPL) has been used to benchmark large-scale computers for over 20 years, with the results being published in the Top500 list. But does it accurately reflect the performance of real applications?

ParCo Symposium on Xeon Phi experiences

Author: Adrian Jackson
Posted: 20 Jul 2015 | 17:12

ParCo Symposium

Experiences of porting and optimising code for Xeon Phi processors

EPCC is jointly organising a symposium at the ParCo conference on experiences from those working on porting and optimising codes for this architecture about the challenges and successes they have experienced when working with the Xeon Phi, and how these also apply to standard parallel computing hardware.

Day 3 of optimising for the Xeon Phi, moving on to vectorisation

Author: Adrian Jackson
Posted: 11 Jun 2015 | 16:01

Moving from OpenMP to vectorisation and MPI

Reality hit home a bit on the third day of our intensive week working with Colfax to optimise codes for the Xeon Phi.

After further implementation and analysis work it appears that the removal of the allocation and deallocation calls from some of the low level routines in CP2K will improve the OpenMP performance on Xeon and Xeon Phi, but only because there is an issue with the Intel compiler that is causing poor performance. The optimisation can see a reduction in runtime of around 20-30% for the OpenMP code, but only with versions 15 and 16 of the Intel compiler, on v14 there is a much smaller performance improvement.

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.

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