TCB Publications - Abstract

John E. Stone, Barry Isralewitz, and Klaus Schulten. Early experiences scaling VMD molecular visualization and analysis jobs on Blue Waters. In Extreme Scaling Workshop (XSW), 2013, pp. 43-50, Aug. 2013.

STON2013 Petascale molecular dynamics simulations provide a powerful tool for probing the dynamics of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone. Extraction of details about the dynamics of biomolecules from terabytes of simulation output requires powerful user-extensible molecular analysis and visualization tools. Petascale simulation trajectories are so large that it is now necessary to perform many analysis and visualization tasks formerly handled by off-site computational facilities in- place on the supercomputer itself. We report ongoing progress on porting, tuning, and scaling up the popular molecular visualization and analysis program VMD on the NSF Blue Waters petascale supercomputer. We describe key achievements including algorithmic and memory efficiency improvements, hand-vectorization of key CPU algorithms, new and improved GPU analysis and visualization algorithms, and parallel I/O performance results. We evaluate the performance of VMD for user-developed analysis scripts with the Timeline trajectory analysis tool in VMD. Finally, we describe the unique capabilities provided by the Cray XK7 GPU-accelerated compute partition of Blue Waters.

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