NDLI: GPGPU supported cooperative acceleration in molecular dynamics

Content Provider	IEEE Xplore Digital Library
Author	Gang Chen Guobo Li Songwen Pei Baifeng Wu
Copyright Year	2009
Description	Author affiliation: School of Computer Science, Fudan University, Shanghai 200433, China (Gang Chen; Guobo Li; Songwen Pei; Baifeng Wu)
Abstract	Molecular dynamics simulations have become a significant computational approach to study complicated physical phenomena at the atomic level. Nevertheless, accurate simulations are limited in size and timescale by the available computing resources, which make the simulations very time-consuming. This consequentially leads to tremendous computational requirements. Therefore, the need for speeding up this process is crucial. In this paper, we present a novel implementation to accelerate molecular dynamics simulations with GPGPU (General Purpose Graphics Processing Unit). Our goal is to reduce the total computational time of MD simulations at a very high performance/cost ratio with the introduction of the GPGPU algorithm. This is motivated by their enhanced programmability, attractive cost/performance ratio and incredible growth in speed. To demonstrate that GPGPUs already provide an inexpensive alternative to scientific applications, we have used AMD's Brook+ streaming programming environment to implement a new parallel algorithm. Our experimental results show the novel approach achieves speedup by the factor of fifteen compared to the corresponding sequential implementation.
Starting Page	113
Ending Page	118
File Size	372347
Page Count	6
File Format	PDF
ISBN	9781424435340
DOI	10.1109/CSCWD.2009.4968044
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-04-22
Publisher Place	Chile
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Acceleration Computational modeling Graphics Costs Physics computing Computer simulation High performance computing Parallel algorithms Arithmetic Biomedical computing Brook+ Molecular dynamics (MD) GPU GPGPU
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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