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Blood Flow in the Brain, Multi-Scale Modeling and More: Life as an Early-career HPC Researcher

Fri, 04/18/2014 - 2:53pm
Andrew Purcell

"I’m perhaps a bit unusual in having worked with astrophysics, blood flow, and materials applications, but the computing ties everything together." Courtesy of Derek GroeniSGTW speaks to Derek Groen, a post-doctoral researcher from the Centre for Computational Science at University College London (UCL), UK. He’ll be presenting his work into the optimization of hemodynamics simulation code at ISC’14, and he tells iSGTW why the event is not to be missed by early-career researchers.

At ISC’14, you’re going to be giving a presentation in the session on advanced re-engineering of high-performance computing (HPC) applications. Could you tell the iSGTW readers a little about this?

I’m going to present optimization work that we’ve done for a high-performance hemodynamics code named HemeLB. It’s used to model blood flow in blood vessels in the brain and I’ll be talking about work we’ve done to improve this code.

Why is hemodynamics simulation important?

We want to understand blood flow in the brain. It can be very difficult for clinicians to measure things like flow velocity, especially under conditions which may be hard to replicate in a clinical setting, such as when the subject undergoes a change in heart rate or blood pressure. Using the HemeLB code, we’re able to make predictions for flow conditions that are different to those easily observed by clinicians in the hospital. This is where the supercomputers come in: it is not uncommon for us to require at least a few hundred, or even tens of thousands, of cores.

I’ve read that you’re going to be involved in the CER2EBRAL project. What exactly is this?

The CER2EBRAL project, which is funded by the Qatar National Research Fund for three years, will be launching just a few months from now. Nevertheless, we’ve already done some preliminary work and have prepared a conference paper. The idea with the CER2EBRAL project is to create an automatic — or at least semi-automatic — clinical workflow based on the HemeLB code, which aims to help clinicians to predict the outcomes of vascular surgery in the brain.

At the moment, we run HemeLB on large supercomputers, such as ARCHER, and resources from the European Grid Infrastructure (EGI).  So, we need to make HemeLB more suitable for execution within a clinical environment. We intend to optimize the code for running on many-core architectures and then try it out within a clinical environment on a GPU-enabled machine. We’ll also be working on improving the efficiency and accuracy of how 3D models are produced from clinical angiography scans.

ISC’14 will be held in Leipzig, Germany, from 22-26 June, 2014.

Andrew Purcell is the editor of iSGTW and is based at CERN, near Geneva. This article originally appeared in iSGTW on April 16, 2014. Read the full article: Blood flow in the brain, multi-scale modeling, and more — life as an early-career HPC researcher

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