Modelling & simulation

Optimising OpenMP implementation of Tinker, a molecular dynamics modelling package

Author: Weronika Filinger
Posted: 3 Jul 2014 | 11:42

Do you use scientific codes in your research? Are the things you can do with it limited by the execution time? The code has been parallelised but does not scale well? How should you go about improving the performance? What can you do when you do not have full understanding of the code? There are some general steps that can be taken to improve the performance of parallelised codes. In this article I will describe briefly the process I have undertaken to optimise the parallel performance of a computational chemistry package, TINKER, as part of the EPCC/SSI APES project.

EPCC wins HPC Innovation Excellence Award

Author: Adrian Jackson
Posted: 24 Jun 2014 | 14:10

Electrostatic potential fluctuations in an annular region at mid-radius in the MAST tokamak, from a gyrokinetic simulation of the saturated turbulence using the GS2 code. A wedge of plasma has been removed from the visualisation so as to view the nature of the fluctuations inside the annulus.EPCC is delighted to be part of a team that has won an HPC Innovation Excellence Award. Presented at the International Supercomputing Conference (ISC14) in Leipzig (22-26 June 2014), the awards recognise outstanding application of HPC Computing for Business and Scientific Achievements.

1st Annual CP2K UK users' meeting

Author: Iain Bethune
Posted: 6 Feb 2014 | 09:50

Last week we held the first in a series of annual meetings for the CP2K user community at the University of London Garden Halls.

I blogged about it in the run-up to the meeting, but as with any first until you're there you don't know quite what to expect. I was very pleased to see over 50 attendees on the day, ranging from new PhD students to professors, and expert CP2K users to complete novices.

Goodbye BonFIRE project; hello BonFIRE facility

Author: Kostas Kavoussanakis
Posted: 16 Dec 2013 | 09:57

The BonFIRE project created a multi-cloud facility to foster experimentation and testing of cloud and distributed applications. Just last week BonFIRE had its final, successful review. The project was rated Excellent, a true reflection of the effort contributed by the partners and the results that we achieved.

Software

When we started BonFIRE three and a half years ago, we had nothing tangible, only promising people and some ideas. By Month 2 we had the first set of requirements; by Month 4 the first Architecture, including a definition of the BonFIRE offering and the BonFIRE Principles; and by Month 12, the first facility for our partner-experimenters to use. By that time we were a team.

EPCC explores Soft Condensed Matter

Author: Oliver Henrich
Posted: 11 Nov 2013 | 10:55

Today computer simulation is firmly established as the third pillar of science beside theory and experiment. As part of its research activities on modelling and large-scale simulation of soft condensed matter, EPCC maintains a long-standing collaboration with the Institute for Condensed Matter and Complex Systems (ICMCS) at the University of Edinburgh and the Centre for Computational Science at University College London.

Project ExTASY: solving the sampling problem

Author: Iain Bethune
Posted: 15 Oct 2013 | 12:18

Alongside APES, EPCC plays an important role in another project jointly funded by EPSRC and the US National Science Foundation to overcome one of the "Grand Challenges in the Chemical Sciences".

Free Energy Landscape of Alanine-12

Dinosaur racing, two months later

Author: Guest blogger
Posted: 30 Aug 2013 | 09:43

The PRACE Summer of HPC is a placement programme for undergraduate and postgraduate students. This post was written by Antoine Dewilde, one of the students who spent the summer here at EPCC.

In a previous post, I presented my project on making a dinosaur racing competition. In that post, I gave some background information about virtual palaeontology, and the purpose of my project here in Edinburgh. If you haven’t read it yet, now might be a good time to do so!

So, now that the project (and the summer) is almost finished, let us see what has happened in these past two months – and what you will soon be able to enjoy!

Summer of HPC students @ EPCC: end-of-project videos

Author: Irina Nazarova
Posted: 30 Aug 2013 | 09:04

The first PRACE Summer of HPC (SoHPC) programme has now finished. Each of the 4 students hosted by EPCC has made a short video about their project, which you can watch below. You can also read about the students in my earlier post.

How fast is a dinosaur?

Author: Guest blogger
Posted: 19 Aug 2013 | 10:40

Is a dinosaur faster if it has longer legs? Is it better for it to be bigger, and hence cover more distance, or to be smaller and lighter? Which species is the fastest? Thanks to high-performance computing, you will soon be able to experiment yourself, and try and find answers to all those questions!

Pages