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Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Feiguo Chen, Wei Ge, Jinghai Li
State Key Laboratory of Multi-Phase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
Science in China Series B: Chemistry, Vol. 52, No. 3. (1 March 2009), pp. 372-380

@article{chen2009molecular,

   title={Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs},

   author={Chen, F.G. and Ge, W. and Li, J.H.},

   journal={Science in China Series B: Chemistry},

   volume={52},

   number={3},

   pages={372–380},

   issn={1006-9291},

   year={2009},

   publisher={Springer}

}

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Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20-60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflops. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered.
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