PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs
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DOI：
10.1016/j.jcp.2014.04.035
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发表时间：
2014-09-01
影响因子：
4.1
通讯作者：
Grama, A. Y.
中科院分区：
文献类型：
--
作者：
Kylasa, S. B.;Aktulga, H. M.;Grama, A. Y.
我们提出了一个高效和高精度的GP-GPU实现我们的社区代码，PuReMD，用于反应分子动力学模拟使用ReaxFF力场。PuReMD及其与LAMMPS的结合(REAX/C)被世界各地的大量研究小组用来在原子级别详细地模拟从生物膜到炸药(RDX)的各种系统。与ReaxFF相关的亚飞秒时间步长通过有效使用GPU，极大地促进了每时间步长模拟时间的显著改进。本文详细介绍了能够在GPU上进行ReaxFF模拟的PuReMD-GPU的设计和实现，以及我们为在最先进的硬件上获得高性能而开发的各种性能优化技术。在模型系统(大块水和无定形二氧化硅)上进行了全面的实验，以量化PuReMD-GPU的性能改进并验证其准确性。特别是，我们的实验表明，与高度优化的仅使用CPU的单核ReaxFF实现相比，运行时最多可提高16倍。PuReMD-GPU是一个独特的产品代码，目前可应作者的要求提供。(C)2014 Elsevier Inc.保留所有权利。
We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16 x improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors. (C) 2014 Elsevier Inc. All rights reserved.