SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations
SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations
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DOI：
10.1016/j.cpc.2012.09.022
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发表时间：
2013-02-01
影响因子：
6.3
通讯作者：
Walker, Ross C.
中科院分区：
文献类型：
--
作者：
Le Grand, Scott;Goetz, Andreas W.;Walker, Ross C.
提出了一种新的基于图形处理器（GPU）的全原子经典分子动力学（MD）模拟加速精度模型。与先前介绍的使用混合单/双精度算法的模型相比，该精度模型用定点整数算法代替双精度算法来累积力分量。这显著提升了现代GPU硬件的性能，而不会牺牲数值精度。我们提出了一个实现的NVIDIA GPU的广义玻恩隐式溶剂模拟以及显式溶剂模拟使用粒子网格埃瓦尔德（PME）算法的远程静电使用这种精确的模型。测试证明了这种实现的性能以及其数值稳定性为恒定能量和恒定温度的生物分子MD相比，双精度CPU实现和双和混合单/双精度GPU实现。(C)2012爱思唯尔有限公司版权所有。
A new precision model is proposed for the acceleration of all-atom classical molecular dynamics (MD) simulations on graphics processing units (GPUs). This precision model replaces double precision arithmetic with fixed point integer arithmetic for the accumulation of force components as compared to a previously introduced model that uses mixed single/double precision arithmetic. This significantly boosts performance on modern GPU hardware without sacrificing numerical accuracy. We present an implementation for NVIDIA GPUs of both generalized Born implicit solvent simulations as well as explicit solvent simulations using the particle mesh Ewald (PME) algorithm for long-range electrostatics using this precision model. Tests demonstrate both the performance of this implementation as well as its numerical stability for constant energy and constant temperature biomolecular MD as compared to a double precision CPU implementation and double and mixed single/double precision GPU implementations. (C) 2012 Elsevier B.V. All rights reserved.