Communications of the ACM
Cloud and Supercomputing Cooperate in Molecular Dynamics Research
The director of the biophysics program at Stanford University says cloud and supercomputing technology are both needed in many fields of study.
Vijay Pande, director of the biophysics program at Stanford University, says both cloud computing and supercomputing technologies are necessary for many fields of study, such as molecular dynamics.
Pande uses cloud computing technologies associated with Folding@home and Google Exacycle to run many detailed molecular dynamics simulations. "A lot of what we do is run the raw trajectories on Folding@home, or Google Exacycle, analyze it on [the National Center for Supercomputing Applications' Blue Waters supercomputer], and spit it back out to Folding@home," Pande says. The combination of cloud computing and supercomputing enables experiments at Pande's lab to reach time scales 1,000 times longer than similar experiments.
The lab's researchers aim to discover which protein folding errors lead to disease, how the errors happen, and what kinds of medicine could prevent the folding errors or mitigate their effect. The new experiments rely on more efficient parallelization that avoids communication bottlenecks, as well as a suite of shorter, independent simulations that can run on heterogeneous hardware.
Pande's software completes many short model runs that examine the state of a molecule at various times. In the future, the power of both supercomputers and cloud computing will increase, enabling researchers such as Pande to sample a wider variety of shapes in less time.
From National Center for Supercomputing Applications
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