UK e-Science project wins top supercomputing award

Issued by EPSRC on behalf of the UK e-Science Programme

A UK e-Science project has won a top award at SC05, the world’s premier supercomputing conference in Seattle this week. SPICE (Simulated Pore Interactive Computing Environment) achieved success in the HPC Analytics Challenge for demonstrating the use of innovative techniques in rigorous data analysis and high-end visualisation to solve a complex, real-world problem.

“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,” says Professor Peter Coveney, principal investigator for the SPICE project from University College London.

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.

“Many biological processes take longer than a nanosecond – that’s what makes them so computationally difficult,” says Dr Shantenu Jha, technical lead on the SPICE team.

SPICE uses technology developed under another UK e-Science project, RealityGrid, 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 (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,” says 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,” says Dr Jha.

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 compute and visualization resources. Standard packet-switched networks, even with high bandwidth, cannot guarantee sufficient quality of service for such interactivity.

“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,” says Professor Coveney. 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 (lambda) 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 highly computationally-intensive problems in turbulent fluid dynamics.