GPU-accelerated molecular visualization on petascale supercomputing platforms

John E. Stone, Kirby L. Vandivort, Klaus Schulten

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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 petas-cale 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.

Original languageEnglish (US)
Title of host publicationProc. of UltraVis 2013
Subtitle of host publication8th Int. Workshop on Ultrascale Visualization - Held in Conjunction with SC 2013: The Int. Conference for High Performance Computing, Networking, Storage and Analysis
DOIs
StatePublished - 2013
Event8th International Workshop on Ultrascale Visualization, UltraVis 2013 - Held in Conjunction with the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2013 - Denver, CO, United States
Duration: Nov 17 2013Nov 17 2013

Publication series

NameProc. of UltraVis 2013: 8th Int. Workshop on Ultrascale Visualization - Held in Conjunction with SC 2013: The Int. Conference for High Performance Computing, Networking, Storage and Analysis

Other

Other8th International Workshop on Ultrascale Visualization, UltraVis 2013 - Held in Conjunction with the International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2013
Country/TerritoryUnited States
CityDenver, CO
Period11/17/1311/17/13

Keywords

  • GPU
  • Many-core
  • Molecular surface
  • Molecular visualization
  • Parallel rendering
  • Ray tracing

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Computer Science Applications

Fingerprint

Dive into the research topics of 'GPU-accelerated molecular visualization on petascale supercomputing platforms'. Together they form a unique fingerprint.

Cite this