High performance molecular visualization: In-situ and parallel rendering with EGL

John E. Stone, Peter Messmer, Robert Sisneros, Klaus Schulten

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

Abstract

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications.

Original languageEnglish (US)
Title of host publicationProceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1014-1023
Number of pages10
ISBN (Electronic)9781509021406
DOIs
StatePublished - Jul 18 2016
Event30th IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2016 - Chicago, United States
Duration: May 23 2016May 27 2016

Publication series

NameProceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016

Other

Other30th IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2016
CountryUnited States
CityChicago
Period5/23/165/27/16

Keywords

  • In-situ visualization
  • Molecular visualization
  • Parallel rendering
  • Remote visualization

ASJC Scopus subject areas

  • Computer Networks and Communications

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  • Cite this

    Stone, J. E., Messmer, P., Sisneros, R., & Schulten, K. (2016). High performance molecular visualization: In-situ and parallel rendering with EGL. In Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016 (pp. 1014-1023). [7529973] (Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/IPDPSW.2016.127