Early experiences scaling VMD molecular visualization and analysis jobs on blue waters

John E. Stone, Barry Isralewitz, Klaus Schulten

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


Pataskala 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 bimolecular from terabytes of simulation output requires powerful user-extensible molecular analysis and visualization tools. Pataskala 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 pet scale 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.

Original languageEnglish (US)
Title of host publicationProceedings - 2013 Extreme Scaling Workshop, XSW 2013
PublisherIEEE Computer Society
Number of pages8
ISBN (Print)9781479936915
StatePublished - 2013
Externally publishedYes
Event2013 7th Extreme Scaling Workshop, XSW 2013 - Boulder, CO, United States
Duration: Aug 15 2013Aug 16 2013

Publication series

NameProceedings - 2013 Extreme Scaling Workshop, XSW 2013


Other2013 7th Extreme Scaling Workshop, XSW 2013
Country/TerritoryUnited States
CityBoulder, CO

ASJC Scopus subject areas

  • Computer Science Applications


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