Modelling & simulation

Collaborating with EPCC

Author: Guest blogger
Posted: 3 Jul 2013 | 08:38
 
This post was written by Jon Hill from Imperial College, who used to work at EPCC and has been collaborating with us recently. 
A snapshot of a tsunami simulation of the 1755 Lisbon seismogenic tsunami.

I always jump at the chance to work with EPCC. Not just because they are my former employers (ah, the joys of Friday buns). Nor is it due to Edinburgh  being one of my favourite cities and collaborating with EPCC is a good excuse to visit. The main reason for collaborating with EPCC is to use the wealth of experience the people working there have on making scientific code go even faster. Whilst this is extremely important to our research, we don't have the time to do both science and improve code performance.

Beatbox Workshop - Day 2

Author: Mario Antonioletti
Posted: 25 Jun 2013 | 12:33

The second and final day of the Beatbox workshop that Adrian Jackson described yesterday consisted of a tutorial where some of the participants were walked through running Beatbox scripts and using Beatbox in general. 

The whole set-up was done using a bootable 8Gb Linux USB key which contained the key components, including part of the Beatbox distribution. That worked quite well and would be worth considering for this kind of course. The attendees got to take the USB keys away so they could continue evaluating Beatbox after the event, which is kind of neat.

Workshop talk on Beatbox: Biophysically and Anatomically Realistic Cardiac Simulations

Author: Adrian Jackson
Posted: 24 Jun 2013 | 10:22

I'm just preparing to give a talk, along with my colleague Mario, at the Beatbox workshop being held at Manchester University this week. Beatbox is an HPC environment for Biophysically and Anatomically Realistic

ScotCHEM Computational Chemistry Symposium 2013 – or why I need to learn more Chemistry

Author: Toni Collis
Posted: 21 Jun 2013 | 17:05

Last week I attended ScotChem 2013 at the School of Chemistry, University of St Andrews. This two-day event  was founded by Carole Morrison (Chemistry, University of Edinburgh) and Tanja van Mourik (Chemistry, University of St Andrews) to bring together computational chemists in Scotland, and I went along to find out how the HPC community is involved in computational chemistry. This was also the first year that the ScotCHEM meeting was held over two days - the first day was focused on a CCP5 workshop on modelling the chemistry and biochemistry of condensed phases. This workshop also aimed to address the underrepresentation of women in Chemistry by showcasing an all-female cast! It certainly is impressive to see so many female computational chemists, as normally I feel surrounded by men!

GULP: HPC simulations of complex solids and clusters using static lattice techniques

Author: Iain Bethune
Posted: 29 Apr 2013 | 07:09

Inter-crystalline boundaries in ZSM-5

Materials science - understanding how the microscopic structure of matter gives rise to macroscopic properties of materials - is one of EPSRC's key research areas, with applications in fields as diverse as energy storage, electronics, fabrics and nanotechnology.  EPCC helps develop a number of important simulation codes in this area such as CP2K, GROMACS, and in this project GULP, the General Utility Lattice Program.

Scaling to thousands of GPUs on Titan

Author: Alan Gray
Posted: 26 Apr 2013 | 10:45

We have been among the first researchers to take advantage of the massive amounts of computing power available on the world's fastest "Titan" supercomputer (based at Oak Ridge National Laboratory). The full machine will boast 18 thousand GPUs, and just under half of these have been made available recently. We have shown that our highly scalable "Ludwig" soft matter physics application can efficiently take advantage of at least 8192 GPUs in parallel.

The APES Project

Author: Arno Proeme
Posted: 23 Apr 2013 | 10:23

The picture of a great ape cousin hoarding food at Edinburgh Zoo is deliberately misleading!  The "APES" acronym (pronounced "A-PES") actually stands for Advanced Potential Energy Surfaces, and refers to a new project that EPCC is involved in. The project in question is an NSF-EPSRC funded US-UK collaboration that aims to incorporate APES into a range of computational chemistry packages. EPCC's main contribution will be to parallelise software to take advantage of the large-scale compute resources offered by supercomputing clusters such as HECToR and its upcoming successor, ARCHER, as well as NFS-provided resources in the US. This should equip researchers with better tools to advance their understanding of the structure and function of molecules such as, hypothetically, the smell molecule isoamyl acetate (shown), which interacts with simian olfactory receptors to give bananas their irresistible allure. Isoamyl acetate  

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