Software

R users can calculate Hamming distance faster

Author: Terry Sloan
Posted: 10 Jan 2014 | 14:09
 
EPCC and the Division of Pathway Medicine at the University of Edinburgh have released version 1.0.5 of the SPRINT R software package. This includes a new faster parallel implementation of the Hamming distance function.

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

"What Makes Good Code Good?" at INTECOL13

Author: Mike Jackson
Posted: 26 Aug 2013 | 10:21

London Docklands

I ran the latest instalment of The Software Sustainability Institute's "What Makes Good Code Good" discussions at INTECOL13 in London's Docklands on 21st August.

I attended at the invitation of Matthew Smith from the BES Computational Ecology Specialist Interest Group and Microsoft Research, and Greg Wilson from Software Carpentry. I'd expected about 20 attendees and was pleasantly surprised (nay, stunned) when about 100 turned up. 

EPCC joins the OpenACC consortium

Author: Adrian Jackson
Posted: 18 Jul 2013 | 14:00

EPCC has recently joined the OpenACC consortium. OpenACC, a directives-based parallel programming standard, is designed to simplify the programming and utilisation of heterogenous computer systems, where standard CPUs and accelerators (such as GPUs) are combined.   Using OpenACC, developers can specify loops and regions of code in standard C, C++ and Fortran to be offloaded from a CPU to an attached accelerator, and also target parallelism on a range of different CPUs and accelerators without having to modify source code.

The Software Sustainability Institute at INTECOL13

Author: Mike Jackson
Posted: 8 Jul 2013 | 07:55

On 21st August 2013, The Software Sustainability Institute will be attending INTECOL13 in London's Docklands. The 11th International Congress of Ecology, hosted by the British Ecological Society and INTECOL, is one of the world's premier conferences for ecologists. At the invitation of Matthew Smith of the BES Computational Ecology Specialist Interest Group and Microsoft Research, and Greg Wilson of Software Carpentry, we've both a talk and a session. INTECOL13 logo

MPI: sending and receiving in multi-threaded MPI implementations

Author: Daniel Holmes
Posted: 5 Jul 2013 | 16:06

Have you ever wanted to send a message using MPI to a specific thread in a multi-threaded MPI process? With the current MPI Standard, there is no way to identify one thread from another. The whole MPI process has a single rank in each communicator.

Are we underestimating the real challenge of Exascale?

Author: Mark Parsons
Posted: 28 Jun 2013 | 10:13

Reaching the Exascale is rightly posed as a combination of challenges related to (i) energy efficiency, (ii) heterogeneity and resiliency of computation, storage and communication, and (iii) the scale of the parallelism involved. Many discussions about Exascale focus on the first two challenges. This is understandable – building an Exascale system with today’s most energy efficient technology would still require around 480 MWatts.

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

Making waves: TPLS code released as Open Source

Author: Iain Bethune
Posted: 10 Jun 2013 | 12:26

TPLS (Two-Phase Level Set) is a Computational Fluid Dynamics code developed by Dr Prash Valluri of the University of Edinburgh's School of Engineering and Dr Lennon Ó Náraigh of University College Dublin. It simulates the interface between two fluid phases, a phenomenon with a number of industrial applications including oil and gas hydrate transport, cleaning processes, distillation/absorption, and evaporative cooling of microelectronics.

Pages