Modelling & simulation

Macaque cranium
with muscle
wrapping

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.

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 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.

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.

The NESS project is developing next-generation sound synthesis techniques based on physical models of acoustical systems. One key system targeted by NESS is the acoustics of 3D rooms. 

Computer simulation of 3D room acoustics has many practical applications such as the design of concert halls, virtual reality systems, and artificial reverberation effects for electroacoustic music and video games. 

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.

The Nu-FuSE (Nuclear Fusion Simulations at Exascale) project was a 3-year, G8 funded, international research project to investigate the challenges and requirements for fusion simulations at Exascale levels. The project’s aim was to significantly improve computational modelling capabilities for fusion, and fusion-related sciences, enhancing the predictive capabilities needed to address key physics challenges of a new generation of fusion systems. 

Justs Zarins reports on his work to improve the performance of TINKER, a molecular dynamics codebase. This 3-month dissertation project was undertaken as part of his MSc in High Performance Computing at EPCC. Justs has now joined EPCC as a post-graduate researcher.

Every year the British Science Festival (BSF) visits a city in the UK and engages the public with the latest and greatest science, engineering and technology. It is a fantastic opportunity for people to get involved in science and the programme contains a wide variety of activities to ensure the festival appeals to all ages.

This was the third year that EPCC has been involved with the BSF. We travelled down to Birmingham where we held an exhibition entitled “Supercomputing: From dinosaurs to particle physics” on the Saturday, which was aimed primarily at families. We were based in the Library of Birmingham along with a number of other highly-engaging events that all aimed to introduce the public to HPC and to encourage the next generation of computational scientists.