Modelling & simulation

The MPI 3.1 standard, a minor update to the existing MPI 3.0 Standard, was ratified last week at the latest MPI Forum meeting. 

Last week I took part in a Mini-Symposium at the University's School of Engineering to mark the 2.0 release of TPLS, a high-resolution 3D Direct Numerical Simulation code for two-phase flows that we have developed in collaboration with Dr Prash Valluri and Dr. Lennon Ó Náraigh.

EPCC will be exhibiting at this year’s Supercomputing in Engineering Show at the Derby Roundhouse on the 15^th and 16^th 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.

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.  

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.