Software

Dual-resolution simulations with LAMMPS

Author: Iain Bethune
Posted: 8 Oct 2016 | 11:46

Hierarchy of multiscale modeling

Over the last year I've been working with Prof. Jon Essex of Southampton University on an ARCHER eCSE project with the pithy title of "Implementation of Dual Resolution Simulation Methodology in LAMMPS".  

So what do I mean by dual-resolution simulations?

​A not-so-brief history of research software engineers

Author: Guest blogger
Posted: 22 Aug 2016 | 11:28

This guest post by Simon Hettrick, Deputy Director of the Software Sustainability Institute, explains how the role of research software engineer has gained greater definition and recognition.

On a beautifully sunny day in March 2012, a small group met at Queen’s College Oxford and challenged a long-standing problem: why is there no career for software developers in academia? They didn’t know it at the time, but this meeting led to a nationwide campaign that created a vibrant and rapidly growing community, and established a new role in research: the Research Software Engineer.

ExTASY: a flexible and scalable approach to biomolecular simulation

Author: Iain Bethune
Posted: 18 Jul 2016 | 12:20

Over the last 10 years, the growth in performance of HPC systems has come largely from increasing core counts, which poses a question of application developers and users – how to best make use of the parallelism on offer?

If you're only going to learn one programming language, you should learn...

Author: Adrian Jackson
Posted: 21 Jun 2016 | 07:59

Choice, choice, choice A Piper

I'm often asked "What programming language should I learn for scientific computing?".  Or I get involved in religious-like discussions about the best programming language for a particular task, or of all time (think Python vs Fortran, Go vs C, etc...). What's my answer?

Just recently I realised that, to me, programming languages are like musical instruments.

Better programming languages for HPC

Author: Stephen Booth
Posted: 5 May 2016 | 16:43

Recently I seem to have had many conversations about programming languages for HPC. In some ways this is not a new subject - I have been having similar conversations for the last 20 years. However as HPC hardware evolves, machines become more complex and the issues that need to be addressed by programmers also become more complex. So it is not surprising that we are wondering if there is more the compiler could be doing to help us.

Code for failure

Author: Adrian Jackson
Posted: 14 Apr 2016 | 21:02

Writing programs assuming that they will be incorrect

I was thinking about development methodologies and software design principles recently and have decided that one of the things I've learned is that it is essential to write programs with the assumption they are going to fail.

I don't think that any of us like to think that the programs we write or maintain will go wrong, or have mistakes/problems in them. However, as I've discussed previously, it is very hard to develop code without making mistakes: coding mistakes, algorithmic errors, mistaken assumptions, etc...

Get into SHAPE! Removing barriers to HPC adoption for SMEs

Author: Paul Graham
Posted: 13 Apr 2016 | 14:47

SHAPE (SME HPC Adoption Programme in Europe) is a pan-European initiative supported by PRACE (Partnership for Advanced Computing in Europe). The Programme aims to raise awareness and provide European SMEs with the expertise necessary to take advantage of the innovation possibilities created by high-performance computing (HPC), thus increasing their competitiveness. SHAPE allows SMEs to benefit from the expertise and knowledge developed within the top-class PRACE Research Infrastructure.

Making the most of ARCHER for Materials Chemistry

Author: Iain Bethune
Posted: 15 Feb 2016 | 15:38

Ab initio modelling of oil formation in clay mineralsIn early December we added a visualisation of the most heavily used application codes to the ARCHER website.  At the moment it only shows data for the current month, but we've been recording the data since the ARCHER service began back in 2013 (table below).

Getting hands-on with ExTASY

Author: Iain Bethune
Posted: 19 Nov 2015 | 11:11

One of the projects I'm currently leading at EPCC is ExTASY, which is building an 'Extensible Toolkit for Advanced Sampling and analYsis'.  I've blogged in the past about the goals of the project, and the painful process leading up to our first public release. As the project is now well into its final year, we are turning our attention to community outreach - showing off what we have built to the biomolecular simulation community and getting their feedback.

The Mozilla Lab Global Science Sprint 2015

Author: Mario Antonioletti
Posted: 8 Jun 2015 | 10:03

I had not intended to go to the Mozilla Global Science Sprint 2015. However, EPCC acted as a hub for local developers who wanted to participate and Neil Chue Hong (Director of the Software Sustainability Institute, and based here at EPCC) asked me to set up the room and make the initial connection in case he was unavailable. I managed to set up the servers and then stayed.

So what is the Mozilla Global Science Sprint?

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