Software development

Summer of HPC at EPCC

Author: Nick Brown
Posted: 2 Mar 2015 | 09:33

The PRACE Summer of HPC (SoHPC) offers university students the opportunity to spend two months at a European HPC centre working on a topical summer project.

Having hosted students during the 2013 and 2014 programmes, we at EPCC are excited to be once again involved and will host three students this summer, one per project that we have proposed. 

Worldwide co-design centres & software development for exascale

Author: Nick Brown
Posted: 24 Feb 2015 | 12:05

The European Exascale Software Initiative is a consortium of 29 organisations and around 100 individuals who are working towards providing key recommendations on European policy with a particular focus on how software can be developed and techniques further improved to help meet the challenges that exascale computing might bring.

The first version of this project, EESI-1, highlighted a number of key areas for further investigation and consideration. The EESI-2 project, which has been running since 2013, has built upon this and focused its attention on these areas.

Free pizza, prizes and research software best practice: Collaborations Workshop 2015... Registration open!

Author: Mike Jackson
Posted: 13 Feb 2015 | 12:45

Oxford e-Research CentreThe Software Sustainability Institute’s Collaborations Workshop 2015 (CW15) will be held from 25-27 March 2015 in Oxford, UK.

CW15 focuses on software, best practice and the social side of working past the boundaries of traditional disciplines and roles to accelerate research outcomes. Or, put differently, interdisciplinarity done right!

Them bones, them bones: finite element bone-modelling

Author: Neelofer Banglawala
Posted: 27 Jan 2015 | 22:16

Macaque cranium
with muscle

I have been re-architecting the solver-side of VOX-FE, a voxel-based finite element bone modelling suite developed by Prof. Michael Fagan's Medical & Biological Engineering group at the University of Hull. The suite comprises a GUI (you can read more about it in this blog post) and a linear solver. VOX-FE creates bone models made up of small cuboid elements by directly converting Computed Tomographic data into these elements. This circumvents the problems faced by the more common method of model creation via mesh interpolation (loss of detail, scaling issues). VOX-FE's approach makes modelling an entire skull with surrounding soft tissue a realisable goal. However, it’s not quite there yet.

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.  

The Message-Passing Interface: unlocking the power of software

Author: Mike Jackson
Posted: 8 Jan 2015 | 11:53

Simulation by IES of daylight on a building.






EPCC helped lead the way in creating the standardised Message-Passing Interface (MPI) programming system to enable faster, more powerful, problem solving using parallel computing. It is now the ubiquitous de-facto standard among both hardware and software vendors.

Mike Jackson and Dan Holmes explain how EPCC continues to be involved in its development and use.

Software for the Future

Author: Adrian Jackson
Posted: 7 Jan 2015 | 10:18

Reconstructed neuronal connections in the brain Credit: Thomas Schultz - CC BY-SABig-Data compressive sensing: fast, parallelised and distributed algorithms

EPCC is excited to be part of a new project, funded through EPSRC's Software for the Future programme, to develop and exploit compressive-sensing algorithms for large-scale data problems.

Greenhouse gases and GPUs

Author: Iain Bethune
Posted: 17 Dec 2014 | 16:32

We have just reached the end of a short project collaborating with Atmospheric Geochemists at the universities of Edinburgh and Bristol. After they purchased two machines each, both with dual Intel Xeon Ivy-bridge 12-core CPUs and NVIDIA Tesla K20x GPUs, EPCC was tasked to investigate the feasability of using the GPUs to improve the performance of their software.

Software Carpentry returns to Edinburgh

Author: Mike Jackson
Posted: 11 Dec 2014 | 12:24

Edinburgh Software Carpentry workshop attendeesLast week EPCC's ARCHER training team ran another Software Carpentry workshop here in Edinburgh, on 3rd and 4th of December. The workshop provided attendees with an introduction to version control and Git, building programs with Python, automating tasks with Make, and how (and how much) to test programs. These were set within the context of best practices for scientific computing.

Intel Parallel Computing Centre: progress report

Author: Adrian Jackson
Posted: 21 Nov 2014 | 10:29

EPCC's Grand Challenges Optimisation Centre, an Intel Parallel Computing Centre which we announced earlier in the year, has made significant progress over recent months. 

The collaboration was created to optimise codes for Intel processors, particularly to port and optimise scientific simulation codes for Intel Xeon Phi co-processors. As EPCC also runs the ARCHER supercomputer, which contains a large number of Intel Xeon processors (although no accelerators or co-processors), for EPSRC and other UK research funding councils, we also have a strong focus on ensuring that scientific simulation codes are highly optimised for these processors. Therefore, the IPCC work at EPCC has been concentrating on improving the performance of a range of codes that are heavily used for computational simulation in the UK on both Intel Xeon and Intel Xeon Phi processors.