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FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations

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Abstract

In the molecular dynamics simulation, an important step is the establishment of neighbor list for each particle, which involves the distance calculation for each particle pair in the simulation space. However, the distance calculation will cause costly floating-point operations. In this paper, we propose a novel algorithm, called Fast Neighbor List, which establishes the neighbor lists mainly using the bitwise operations. Firstly, we design a data layout, which uses an integer value to represent the three-dimensional coordinates of a particle. Then, a bunch of bitwise operations and two subtraction operations are used to judge whether the distance between a pair of particles is within the cutoff radius. We demonstrate that our algorithm can deal with the periodic boundary seamlessly. We also use single instruction multiple data (SIMD) instructions to further improve the performance. We implement our algorithm on Intel Xeon E5-2670, ARM v8, and Sunway many-core processors, respectively. Compared with the traditional method, our algorithm achieves on average 1.79x speedup on Intel Xeon E5-2670 processor, 3.43x speedup on ARM v8 processor, and 4.03x speedup on Sunway many-core processor. After using SIMD instructions, our algorithm achieves on average 2.64x speedup and 14.43x speedup on Intel Xeon E5-2670 and ARM v8 processors, respectively.

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  • 26 July 2019

    The first main paragraph of the paper contains errors. The correct wording is given below.

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Acknowledgements

This work was supported by National Natural Science Foundation of China under Grant Nos. 61502450 and 61432018; National Key R&D Program of China under Grant Nos. 2017YFB0202302 and 2016YFB0200800; State Key Laboratory of Computer Architecture Foundation under Grant No. CARCH3504.

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Authors and Affiliations

  1. State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

    Kun Li, Shigang Li, Shan Huang & Yunquan Zhang

  2. School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China

    Kun Li & Shan Huang

  3. HCST Key Lab at School of EECS, Peking University, Beijing, China

    Yifeng Chen

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  1. Kun Li
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  2. Shigang Li
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  3. Shan Huang
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  5. Yunquan Zhang
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Correspondence to Shigang Li.

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Li, K., Li, S., Huang, S. et al. FastNBL: fast neighbor lists establishment for molecular dynamics simulation based on bitwise operations. J Supercomput 76, 5501–5520 (2020). https://doi.org/10.1007/s11227-019-02860-3

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