GPGPU supported cooperative acceleration in molecular dynamics

Gang Chen, Guobo Li, Songwen Pei, Baifeng Wu
School of Computer Science, Fudan University, Shanghai 200433, China
13th International Conference on Computer Supported Cooperative Work in Design, 2009. CSCWD 2009


   title={GPGPU supported cooperative acceleration in molecular dynamics},

   author={Chen, G. and Li, G. and Pei, S. and Wu, B.},




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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.
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