This section provides a number of examples of how High End Computing is used, including case studies from HECToR users.
High End Computing Case Studies
Do you have a story?
How has HECToR helped your research? Do you have an interesting case study? The HECToR team are keen to hear how the HECToR facility has had an impact on your research. If you are interested in your research appearing on the HECToR website then please contact us via the HECToR Helpdesk and we will be more than happy to help you write it up.
Case Studies
Virtual palaeontology: gait reconstruction of extinct vertebrates using high performance computing
The team of scientists - from The University of Manchester, University of Oregon and Yale have been using HECToR to understand how dinosaurs moved. They found that hopping hadrosaurs were fastest but, for safety reasons, a two-legged running gait was most likely. In addition the team, funded by National Geographic and The Natural Environment Research Council, has shown how more research can be done to find out how large and fast animals moved, both living and extinct.
Improving the Modelling of Cardiac Arrythmia
Medical science is increasingly turning to computational models to study the possible effects of drugs and surgical interventions, before moving on to patient trials. One active area of research is in heart modelling. Researchers at the Oxford e-Research Centre (OeRC) and EPCC (University of Edinburgh), will be using HECToR to optimise heart-modelling software. If successful, this work will enable much greater integration of computer simulation with the operating theatre and could, ultimately, lead to personalised medicine.
SPRINT - parallel statistics using R
Gene analysis is becoming increasingly complex and can be greatly enhanced by exploiting the power of high-performance computing (HPC), but the software can be difficult for researchers to use. To allow greater access to the benefits of HPC, EPCC and the Division of Pathway Medicine at the University of Edinburgh developed a prototype framework called SPRINT, which allows biostatisticians to more easily exploit HPC systems.
Novel computing in fight against cancer
National Cancer Registration data indicate that some 35,000 people each year are diagnosed with colorectal cancer (cancer of the large bowel and rectum) and 16,000 die from the disease. While the development of effective treatments is clearly important, early identification of patients at risk and prevention is a primary objective of all major cancer agencies and of National Health Service policy. Armed with first access to an unprecedented set of genomic data in colorectal cancer, the University of Edinburgh Colon Cancer Genetics Group (CCGG) and EPCC Supercomputing Centre teamed up to investigate the relationship between genetic markers and colorectal cancer.
Fasten your seatbelts: Turbulent patches in oceans and atmospheres
The presence of patches of turbulent fluid within atmospheric or oceanic flows is well known (not least to aircraft passengers). Wave breaking is a complex phenomenon and has been quite extensively explored. The subsequent breakdown to a fully turbulent patch, along with the latter's development and (perhaps) eventual decay is not, however, well understood. We have been using HECToR resources to compute such flows, analysing both the transition-to-turbulence process and the fully developed turbulence in the patch.
Breakthrough in Fluid Mixing: Simulating Fractal-Generated Turbulent Flows
The first ever successful simulations of turbulence generated by fractal grids (see figure) have been performed on HECToR in 2008 and 2009. The size of these simulations is so large that they are impossible without High Performance Computing. Industries that need to create or minimise turbulence have an interest in this work. They include the chemical and process industries, which use turbulence for mixing, and the aerospace and automotive industries, which need to reduce noise, fuel consumption and pollutant emissions through the control of turbulent flows.
Optimisation of ONETEP Code
ONETEP is currently being used for a wide variety of applications by several UK and international research groups, including studies of protein-ligand interactions and self-assembly in semiconductor nanorods. Recent development work using HECToR and Imperial's CX1 machine has greatly improved the parallel efficiency of ONETEP, especially when studying systems of solids. Recently, calculations involving systems of up to 32,768 of crystalline silicon have been demonstrated and scaling efficiently up to over 256 cores.
CP2K : High Performance Quantum Chemistry on HECToR
CP2K is a freely available, open source application which uses Density Functional Theory (DFT) to perform ab-initio quantum mechanical calculations on a variety of physical systems. CP2K is heavily used on HECToR - around 50,000 CPU hours are used each month. Substantial performance improvements had been achieved: up to 30% on 256 cores for a small benchmark system of liquid water, and up to 300% on 1024 cores for a larger, non-homogenous system. These improvements are already available to users of HECToR and HPCx via the centrally installed versions of CP2K, and are available to CP2K users worldwide through the CVS repository on the CP2K website.
Reducing Noise Pollution from Aircraft
Aircraft pressure relief valves are used to protect the fuel tanks of wide-body civil aircraft from over-pressurization. The relief valve outlet is typically in the shape of a cylindrical hole, or cavity, cut in the underside side of the wing skin. At typical approach speeds of around Mach 0.3, the flow past the cylindrical cavity can become unsteady. This produces an unwanted tonal contribution to the airframe landing noise. A numerical investigation of this phenomenon was performed in consultation with Airbus France, as part of the EU programme AeroTraNet.
Technical Reports
Both the HECToR Computational Science and Engineering (CSE) team and the Cray Centre of Excellence (CoE) have technical reports on work done to enable new science on HECToR.