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 publicationParallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings
Pages143-150
Number of pages8
DOIs
Publication statusPublished - 2008
Event9th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2008 - Dunedin, Otago, New Zealand
Duration: 2008 Dec 12008 Dec 4

Other

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

Fingerprint

Graphics Processing Unit
Molecular Dynamics Simulation
Molecular dynamics
Computer simulation
Program processors
Van Der Waals Force
Van der Waals forces
Computer games
Video Games
Cost-effectiveness
Cost effectiveness
Computer hardware
Exceed
Graphics processing unit
Hardware
kernel
Atoms
Costs
Range of data

ASJC Scopus subject areas

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

Cite this

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

Overheads in accelerating molecular dynamics simulations with GPUs. / Narumi, Tetsu; Sakamaki, Ryuji; Kameoka, Shun; Yasuoka, Kenji.

Parallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings. 2008. p. 143-150 4710974.

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

Narumi, T, Sakamaki, R, Kameoka, S & Yasuoka, K 2008, Overheads in accelerating molecular dynamics simulations with GPUs. in Parallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings., 4710974, pp. 143-150, 9th International Conference on Parallel and Distributed Computing, Applications and Technologies, PDCAT 2008, Dunedin, Otago, New Zealand, 08/12/1. https://doi.org/10.1109/PDCAT.2008.68
Narumi T, Sakamaki R, Kameoka S, Yasuoka K. Overheads in accelerating molecular dynamics simulations with GPUs. In Parallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings. 2008. p. 143-150. 4710974 https://doi.org/10.1109/PDCAT.2008.68
Narumi, Tetsu ; Sakamaki, Ryuji ; Kameoka, Shun ; Yasuoka, Kenji. / Overheads in accelerating molecular dynamics simulations with GPUs. Parallel and Distributed Computing, Applications and Technologies, PDCAT Proceedings. 2008. pp. 143-150
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