Molecular dynamics simulations with many-body potentials on multiple GPUs-The implementation, package and performance

Q Hou and M Li and YL Zhou and JC Cui and ZG Cui and J Wang, COMPUTER PHYSICS COMMUNICATIONS, 184, 2091-2101 (2013).

DOI: 10.1016/j.cpc.2013.03.026

Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of MD usually run in a one-host-process- one-GPU (OHPOG) scheme. This scheme may pose a limitation on the system size that an implementation can handle due to the small device memory relative to the host memory. In this paper, we present a one-host- process-multiple-GPU (OHPMG) implementation of MD with embedded-atom- model or semi-empirical tight-binding many-body potentials. Because more device memory is available in an OHPMG process, the system size that can be handled is increased to a few million or more atoms. In comparison with the serial CPU implementation, in which Newton's third law is applied to improve the computational efficiency, our OHPMG implementation has achieved a 28.9x-86.0x speedup in double precision, depending on the system size, the cut-off ranges and the number of GPUs. The implementation can also handle a group of small simulation boxes in one run by combining the small boxes into a large box. This approach greatly improves the GPU computing efficiency when a large number of MD simulations for small boxes are needed for statistical purposes. (C) 2013 Elsevier B.V. All rights reserved.

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