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Gordon Bell Finalists Achieve 20 Petaflops on Titan

proteinsOver at OLCF, Jennifer Brouner writes that researchers are using the GPU-powered Titan supercomputer at record speeds to monitor proteins responsible for cellular behavior.

A simulation of the internal workings of cells has reached a sustained performance of 20 petaflops on Titan at ORNL. As one of the fastest running codes in the world, this achievment also earned the development team from the National Research Council of Italy a finalist position for the Gordon Bell Prize. The award will be presented at SC13 in Denver.

We are simulating the crowded protein solution that is representative of our cell compartments,” said Simone Melchionna from CNR’s Institute for Chemical and Physical Processes. “If we want to target a specific cell for treatment, we need to understand how that cell works. Proteins are the most crucial cellular agents, and their behavior affects all activities that take place within the human body.”

Scientists are using supercomputers to simulate the hundreds of thousands of proteins that move and interact within cells. The understanding they gain sheds light on the factors that drive the critical activities of cells, which are the most basic units of life.

The research team developed a code called MUPHY, for MUlti PHYsics simulator, to study the two-way interactions that exist between proteins and fluids within a cell. The application accounts for the physical forces that cause protein movement, as well as the forces involved in protein–protein and protein–fluid interactions.

Computation is partitioned among processors so that each node monitored the movement and behavior of a single protein, which minimized memory requirement and helped with load balance.

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