New Stanford software takes Folding@home’s biological research to supercomputers

Stanford researchers, who made impossible protein-folding simulations routine with Folding@home, bring the technology to supercomputing.

The vast computing resources of Folding@home have been available to Pande and his collaborators. With open-source Copernicus software, other researchers can run simulations, including molecular models, using processer time on multiple supercomputers or computing clusters, rather than home computers.

"It opens the door to huge crowds of people using these methods, which have matured with Folding@home," Pande said.

With an interest in solving protein structures and having large computing clusters on hand, pharmaceutical companies are an example of one potential Copernicus user-group.

The advantage of Copernicus comes from how it uses the fast communication available between supercomputers, combined with statistical sampling techniques, to run parallel simulations within or between computing clusters or between supercomputers.

Copernicus allows for each additional processor in the system to aid the calculation to run faster and faster, something known as strong scaling. Previously, when using supercomputers to understand molecular dynamics, it has been very difficult to achieve strong scaling on a single machine.

"This method should be able to use any supercomputer on the planet completely," Pande said. "Strong scaling to these extremes is unusual."

Folding@home is useful for molecular simulations that take place on relatively long timescales. But Copernicus will be a tool for shorter problems where researchers want a quick solution.

Computationally, using Copernicus is like taking a Lamborghini to run out for milk. Folding@home, on the other hand, "is kind of like a rocket. It takes a big deal to launch it and once you launch, it goes really far," Pande said. "You don’t use it to go to the corner store."

Sarah Jane Keller is a science-writing intern at the Stanford News Service.

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Vijay Pande, Department of Chemistry: pande [a] stanford (p) edu

Dan Stober, Stanford News Service: (650) 721-6965, dstober [a] stanford (p) edu