Towards Efficient Short-Range Pair Interaction on Sunway Many-Core Architecture |
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| Authors: | Chen Jun-Shi An Hong Han Wen-Ting Lin Zeng Liu Xin |
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| Affiliation: | 1.School of Computer Science and Technology, University of Science and Technology of China, Hefei 230026, China;2.National Research Center of Parallel Computer Engineering and Technology, Beijing 100080, China |
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| Abstract: | The short-range pair interaction consumes most of the CPU time in molecular dynamics(MD)simulations.The inherent computation sparsity makes it challenging to achieve high-performance kernel on the emerging many-core ar-chitecture.In this paper,we present a highly efficient short-range force kernel on the Sunway,a novel many-core architecture with many unique features.The parallel efficiency of this algorithm on the Sunway many-core processor is strongly limited by the poor data locality and write conflicts.To enhance the data locality,we adopt a super cluster based neighbor list with an appropriate granularity that fits in the local memory of computing cores.In the absence of a low overhead locking mechanism,using data-privatization force array is a more feasible method to avoid write conflicts,but results in the large overhead of data reduction.We adopt a dual-slice partitioning scheme for both hardware resources and computing tasks,which utilizes the on-chip data communication to reduce data reduction overhead and provide load balancing.Moreover,we exploit the single instruction multiple data(SIMD)parallelism and perform instruction reordering of the force kernel on this many-core processor.The experimental results show that the optimized force kernel obtains a performance speedup of 226x compared with the reference implementation and achieves 20％of peak flop rate on the Sunway many-core processor. |
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| Keywords: | molecular dynamics sunway many-core pair interaction parallel algorithm |
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