John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
GPU-accelerated molecular visualization on petascale supercomputing
platforms.
In Proceedings of the 8th International Workshop on Ultrascale
Visualization, UltraVis '13, pp. 6:1-6:8, New York, NY, USA, 2013. ACM.
STON2013A
Petascale supercomputers create new opportunities for the study
of the structure and function of large biomolecular complexes
such as viruses and photosynthetic organelles,
permitting all-atom molecular dynamics
simulations of tens to hundreds of millions of atoms.
Together with simulation and analysis, visualization
provides researchers with a powerful ``computational microscope''.
Petascale molecular dynamics simulations produce tens to hundreds of
terabytes of data that can be impractical to transfer to remote
facilities, making it necessary to perform visualization
and analysis tasks in-place on the supercomputer where the data
are generated. We describe the adaptation of key visualization
features of VMD, a widely used molecular visualization and
analysis tool, for GPU-accelerated petascale computers.
We discuss early experiences adapting ray tracing
algorithms for GPUs, and compare rendering performance
for recent petascale molecular simulation test cases
on Cray XE6 (CPU-only) and XK7 (GPU-accelerated) compute nodes.
Finally, we highlight opportunities for further
algorithmic improvements and optimizations.
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.
