Modelling & simulation
Posted: 21 Jun 2015 | 20:02
The final analysis and future plans
A week ago we finished our 5 days of intensive work optimising CP2K (and to a lesser extent GS2) for Xeon Phi processors. As discussed in previous blog posts (Day4, Day3, Day2, Day1), this was done in conjunction with research engineers from Colfax, and built on the previous year's work on these codes by EPCC staff through the Intel-funded IPCC project.
Posted: 8 Jun 2015 | 16:41
Over 18 months ago, we kicked off the ExTASY project. Our lofty aim was to tackle one of the 'Grand Challenges' of biochemistry - effective sampling of complex biomolecules using Molecular Dynamics to provide a physical understanding of their function and behaviour.
Posted: 8 Jun 2015 | 13:17
Posted: 25 May 2015 | 11:52
Posted: 3 Apr 2015 | 14:30
EPCC will be exhibiting at this year’s Supercomputing in Engineering Show at the Derby Roundhouse on the 15th and 16th April. The show is run in parallel with the Engineering Simulation Show and attendance is free, so this is an ideal opportunity for you to come and talk to us about how we can help transform your simulation and modeling activities using High Performance Computing.
Posted: 5 Mar 2015 | 09:36
Earlier this month we held the second annual CP2K User Group Meeting at King's College London, in the shadow of London's iconic 'Shard'. The meeting was even more popular than last year's, with around 60 people coming along to learn about the latest new features available in CP2K, and to hear from a wide range of existing users what they are doing with the code.
Posted: 27 Jan 2015 | 22:16
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.
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.
Posted: 23 Jan 2015 | 14:58
The Auditory pilot project, involving EPCC and the University’s Acoustics and Audio Group, sought to use HPC to enable faster run times for computational models of the human hearing organ. Dr Michael Newton of the Group explains the work.
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.