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

Qing Hou; Min Li; Yulu Zhou; Jiechao Cui; Zhenguo Cui; Jun Wang

doi:10.1016/j.cpc.2013.03.026

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arXiv · 1212.6332

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

Qing Hou·Min Li·Yulu Zhou·Jiechao Cui·Zhenguo Cui·Jun Wang

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Abstract

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 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 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.

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Qing Hou, Min Li, Yulu Zhou, Jiechao Cui, Zhenguo Cui, Jun Wang. 2012-12-27. Molecular dynamics simulations with many-body potentials on multiple GPUs - the implementation, package and performance. https://doi.org/10.1016/j.cpc.2013.03.026

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