Overheads in accelerating molecular dynamics simulations with GPUs

Tetsu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka

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

6 Citations (Scopus)

Abstract

Molecular Dynamics (MD) simulation requires huge computational power, as each atom interacts with the others by long range forces such as the Coulomb or van der Waals forces. Recently, a video game computer, such as SONY PLAYSTATION 3 (PS3) or NVIDIA's Graphics Processing Unit (GPU) has become a candidate hardware for accelerating MD simulations as well as an MDGRAPE-3 special-purpose computer for their better performance than current CPU of the PC, and also for their cost-effectiveness. Especially the latest GPU has much more peak performance than a CPU of the PC or an MDGRAPE-3, though a GPU has much more overheads in accelerating MD simulations. When the number of particles is small or the calculation kernel becomes complicated, the performance of the GPU drops dramatically as low as that of the MDGRAPE-3. However, the acceleration ratio of the GPU and the PS3 per cost exceeds that of the MDGRAPE-3.

Original languageEnglish
Title of host publicationProceedings - 9th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2008
Pages143-150
Number of pages8
DOIs
Publication statusPublished - 2008 Dec 1
Event9th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2008 - Dunedin, Otago, New Zealand
Duration: 2008 Dec 12008 Dec 4

Publication series

NameParallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings

Other

Other9th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2008
CountryNew Zealand
CityDunedin, Otago
Period08/12/108/12/4

ASJC Scopus subject areas

  • Software
  • Theoretical Computer Science
  • Hardware and Architecture
  • Computer Science Applications

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  • Cite this

    Narumi, T., Sakamaki, R., Kameoka, S., & Yasuoka, K. (2008). Overheads in accelerating molecular dynamics simulations with GPUs. In Proceedings - 9th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2008 (pp. 143-150). [4710974] (Parallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings). https://doi.org/10.1109/PDCAT.2008.68