计算机工程与科学2009，Vol.31Issue(z1)：46-49,132,5.DOI:10.3969/j.issn.1007-130X.2009.A1.015
使用GPU加速分子动力学模拟中的非绑定力计算
GPU Acceleration of Nonbonded Forces for Molecular Dynamics Simulation
摘要
Abstract
The most costly computation required by molecular dynamics (MD) is the calculation of non-bonded forces. This paper presents two algorithms based on CUDA and Brook+ to accelerate the calculation of non-bonded forces and then examines them on two popular GPUs of NVIDIA and AMD. The algorithms enable fine-grained task decomposition and spatial decomposition of forces that map efficiently to the compute units of GPU. They also present optimization methods such as use of shared memory between threads and strip-mined. We then test our implementations for 432 thousand atoms. Our code executed on Tesla C1060 runs 6.5 times faster than the original application running on single core of Intel Intel Xeon 2.6GHZ CPU, while on HD4870 it runs 4.8 times faster.关键词
GPU/分子动力学模拟/CUDA/Brook+Key words
GPU/molecular dynamics simulation/CUDA/Brook+分类
信息技术与安全科学引用本文复制引用
吴强,杨灿群,葛振,陈娟..使用GPU加速分子动力学模拟中的非绑定力计算[J].计算机工程与科学,2009,31(z1):46-49,132,5.基金项目
国家863计划资助项目(2008AA01Z110) （2008AA01Z110）
国家自然科学基金资助项目(60673150,60903044) （60673150,60903044）
