HPC news
HIGH-PERFORMANCE COMPUTING
Numerical Algorithms Group aids study of egg shell formation
University of Warwick researchers Mark Rodger and David Quigley, in collaboration with colleagues at the University of Sheffi eld, have used molecular dynamics simulation and the HECToR supercomputer – a 12,000 core Cray XT4 – to solve a problem in eggshell formation. Protein ovocledidin-17 (OC-17) is found only in the mineral region of eggs and laboratory results showed that it appeared to infl uence the transformation of calcium carbonate into calcite crystals. Having been unclear as to how this process could be used to form an eggshell, the researchers created a model to show how the protein bound to a calcium carbonate surface. In addition to the Cray
supercomputers managed by the University of Edinburgh, the Research Councils’ HECToR service includes a comprehensive Computational Science and Engineering (CSE) support service provided by the Numerical Algorithms Group (NAG). One of NAG’s HPC experts identifi ed input and especially output (I/O) as the bottleneck for the simulation software,
IN BRIEF
known as DL_POLY_3, originating from Daresbury Laboratories.
A solution was provided for this research and NAG has gone on to optimise all the I/O routines, to assist other users of DL_POLY_3. This was done by reordering data to take advantage of modern fi le systems and then further improved by performing the I/O in parallel. This six months of work has resulted in the I/O for DL_POLY_3 being around 50 times faster on average.
Dr David Quigley from the Department of Physics and Centre
for Scientifi c Computing, University of Warwick, said: ‘Prior to the I/O improvements, DL_POLY_3 was unable to make effective use of the parallel fi le system on HECToR, severely crippling the performance of our simulations. The new code has reduced the time taken to write a single snapshot from three minutes to less than half a second, resulting in an overall factor of 20 improvement in our net performance. Without this development, HECToR would have been effectively useless for our purposes.’
Intel shares HPC predictions
At a briefi ng in London, representatives from Intel commented on the state of high-performance computing (HPC). ‘We are absolutely headed towards multi- and many- core within the next three years,’ said Sean McGuire, director strategic government, HPC programs Emea. ‘HPC is pervasive.’ Stating that the UK leads the way in
certain scientifi c applications of HPC – namely bio sciences and weather forecasting – the company offered details of how HPC is being used for purposes ranging from gaining insight into blood clots, to analysing data within the fi nancial sector. Imperial College London’s Simon Burbidge said that, while it is hard to
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say just how important HPC is, every department at the college uses it as a fundamental part of their research. Installed in 2009, the system in place, dubbed cx2, is an SGI Altix ICE 8200 boasting 3,124 cores, 32.14 Tfl ops of performance and seven Tbytes of memory.
One of the key requirements was that the system be expandable. It was upgraded last year and is offering researchers greater fl exibility by complementing experiments and enabling simulation-based studies, such as observations of blood fl ow through the aortic valve, that are not otherwise possible. The cx2 has reached position 439 in the Top500 list.
Another organisation benefi ting from an HPC facility is the Cambridge Research Institute, part of Cancer Research UK. Commenting that the developments in gene sequencing are changing the way we approach bio science, Peter McCallum, head of IT and scientifi c computing, stated that scientists need local access to HPC as it has become mainstream in this fi eld.
This has thrown up certain issues, however, such as the limitation of IT budgets and the question of whether the processing needs to be done on site or whether it can be pushed into the cloud. The main drawback of pursuing the latter option, said McCallum, is the long-term cost of storing the massive amount of generated data, as well as the time taken to push that data out.
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The US Department of Energy’s Argonne National Laboratory has selected Allinea Software to improve debugging performance and scalability on IBM’s Blue Gene/P system. Bright Computing and Scherm Brazil, a provider of HPC systems, are now partnering to provide CPU and GPU cluster systems to the Brazilian market. CAPS entreprise, a French developer of programming tools for ‘manycore’ systems, has announced the creation of an American subsidiary. Shanghai University has formed a strategic partnership with the Numerical Algorithms Group (NAG), which involves the cooperative development of computational fl uid dynamics (CFD) software.
The US National Science Foundation (NSF) has awarded Syracuse University (SU) in New York $791,000 to build a supercomputer.
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