Top supercomputing award
22 November 2005
The UCL-led High Performance Computing (HPC) and e-Science project, SPICE, won a top award at SC05, the world's premier supercomputing conference in Seattle this week.
SPICE principle investigator Professor Peter Coveney (UCL Computer Science), said: "SPICE shows how the power of supercomputers on both sides of the Atlantic can be harnessed to simulate and visualise biological processes of unprecedented complexity. We're delighted with this award."
The SPICE team convinced the judges with their simulation of DNA strands passing through a cell membrane. Knowledge of this important biological process is crucial for understanding the transfer of genetic information during cell division, and for applications such as the design of high-throughput DNA screening devices. However, it takes place over a much longer timescale than is possible to simulate using conventional computational methods.
Technical lead on the SPICE project, Dr Shantenu Jha (UCL Chemistry), said: "Many biological processes take longer than a nanosecond - that's what makes them so computationally difficult."
SPICE uses technology developed under Professor Coveney's RealityGrid project, to marshal the resources of supercomputers on the UK National Grid Service (NGS) and the US TeraGrid, connected by dedicated high bandwidth optical channels. Even with resources of this grid-of-grids to hand, the simulation is too large for straight computation. SPICE has overcome this obstacle by dividing the simulation into two stages.
In the first, the researcher gets a rough 'feel' for the DNA's progress from the response of a haptic device, a touch-sensitive joystick, used to pull it through a protein nanopore embedded in the cell membrane. "You try to pull the DNA through the pore and you can feel the strain on it. It's a very smart way of probing the DNA's local energetic environment - and it's fun," said Dr Jha. "In the second stage, insight gained from the first is used to set the parameters for a set of full-scale simulations. "By doing some smart exploration first, we're limiting the computation we need for a detailed, rigorous analysis."
Such complex simulations would not be possible without the use of dedicated optical networks to connect supercomputers in the US and UK. The researchers steer the simulation in real time via the haptic device, each snapshot of the simulation requiring several hundred processors and simultaneous high-end computing and visualisation resources. Standard packet-switched networks, even with high bandwidth, cannot guarantee sufficient quality of service for such interactivity.
Professor Coveney added: "Without dedicated optical networks in the US, UK and across the Atlantic, SPICE would be impossible. There's no loss or re-ordering of data which means that we can steer the simulations interactively." SPICE is one of the first demonstrations of the UK's new, dedicated optical research network, UKLight.
SPICE is jointly funded by the UK Engineering and Physical Sciences Research Council (EPSRC) and the US National Science Foundation (NSF) as one component of a bi-national collaboration to exploit state of the art optical networks to tackle scientific problems that would otherwise remain out of reach. Two US projects, NeKTAR and VORTRONICS, are using the same infrastructure to simulate blood flow through the entire network of human arteries and to tackle computationally intensive problems in turbulent fluid dynamics.