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.
Download Full Text
The manuscripts available on our site are provided for your personal
use only and may not be retransmitted or redistributed without written
permissions from the paper's publisher and author. You may not upload any
of this site's material to any public server, on-line service, network, or
bulletin board without prior written permission from the publisher and
author. You may not make copies for any commercial purpose. Reproduction
or storage of materials retrieved from this web site is subject to the
U.S. Copyright Act of 1976, Title 17 U.S.C.
