A group in Trinity College is working to make high performance computing more accessible to Irish researchers, writes Dick Ahlstrom.
If you need a supercomputer there is one waiting for you at Trinity College Dublin. A new initiative hopes to make high-performance computing available to Irish researchers across the State and also to bring down the cost of advanced scientific software.
The project is being run from Trinity's Institute for Information Technology and Advanced Computation (IITAC), which is part of the College's Centre for High Performance Computing (CHPC).
IITAC is a research programme in computational biomolecular science that links researchers in physical science with computer and biological science, explains Trinity's David Lloyd.
"I am a chemist who works in biochemistry using high performance computers," says Lloyd, who is Hitachi lecturer in the department of biochemistry's molecular design group. IITAC shares computing power across a range of science disciplines. "The underpinning link is using supercomputers to solve scientific problems. I co-ordinate the bioscience end of that."
The centre's main activities currently relate to surface science and simulations of molecules and proteins using powerful computer models to provide insights into an otherwise invisible world, he explains.
He started thinking about the high cost of the specialised modelling packages and the lack of access to high performance computing. Earlier this year Science Foundation Ireland (SFI) announced an initiative to make high-cost scientific journals available to all third level colleges through a shared resource. "It occurred to me if you could do it with journals why can't we do it with software."
He negotiated a temporary deal with two software companies - Accelrys and the Chemical Computing Group - and in October he launched an on-line demonstration. Any academic user in need of the modelling packages available at IITAC can use them for free. "Basically they download the software onto their systems and run it while linked to us," Lloyd explains.
The demonstration developed, and since mid-November users can gain access to a cluster of 120 linked computers available at IITAC. Geoff Bradley of the CHPC, Graeme Watson of the department of chemistry and Lloyd co-ordinate the demo.
"It is a fully-functional system. The only thing you can't do is use it for commercial purposes, as it is an academic licence," Lloyd explains.
This means that biochemists trying to understand the activities of a protein or materials scientists trying to visualise the surface of a semi-conductor can use the modelling software and run it on the IITAC cluster.
Modelling how proteins change their shape after binding to other biochemicals is a typical example of what the system can do for the biosciences. In materials science, the system might be used to produce a map of the electron distribution on the surface of a semi-conductor. "If you were going to do that simulation on a single computer it would take weeks. If you did it on the cluster it would be done in a day," he says.
The demonstration runs until the end of December but is already being used by 60 researchers in universities, institutes of technology and the Royal College of Surgeons of Ireland. Lloyd and his collaborators now plan to run another demonstration, this time providing advanced computing to physicists interested in fluid dynamics for the study of, say, aerodynamics.
Trinity and partners, the Dublin Institute for Advanced Studies, NUI Galway, UCD and UCC, the National Microelectronics Research Centre in Cork and NUI Maynooth have joined to bid for the project. It would be modelled on the Centre for Scientific Computing in Finland, Lloyd says. "We are trying to reduce the reproduction of resources."