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Subject: Computer Science
Title:
基于GPU的分子动力学模拟并行化及实现
Alternative Title: parallel algorithm and implementation for molecular dynamics simulation based on gpu
Author: 费辉 ; 张云泉 ; 王可 ; 许亚武
Keyword: 分子动力学 ; GPU ; OpenCL ; CUDA ; 原子分解法
Source: 计算机科学
Issued Date: 2011
Volume: 38, Issue:9, Pages:275-278,287
Indexed Type: CNKI ; CSCD ; WANFANG
Department: 中国科学院软件研究所并行软件与计算科学实验室;中国科学院软件研究所计算机科学国家重点实验室;中国科学院研究生院;广州大学网络与现代教育技术中心;
Sponsorship: 国家863计划项目(2006AA01A125,2009AA01A129,2009AA01A134)|国家重大专项核高基项目(2009ZX01036-001-002)资助
Abstract: 分子动力学模拟作为获得液体、固体性质的重要计算手段,广泛应用于化学、物理、生物、医药、材料等众多领域。模拟体系的复杂性和精确性的需求,使得计算量巨大,耗费时间长。并行计算是加速大规模分子动力学模拟的重要途径。GPU以几百GFlops甚至上TFlops的运算能力,为分子动力学模拟等的计算密集型应用提供了新的加速方案。提出了一种基于GPU的分子动力学模拟并行算法——oApT-AD,并在OpenCL和CUDA框架下加以实现。性能测试显示,在Tesla C1060显卡上,该算法在OpenCL框架下的实现相对于CPU的串行实现,最高达到120倍加速比。通过对比发现,该算法在CUDA上的性能与OpenCL基本相当。同时,该算法还可以扩展到两块及以上的GPU上,具有良好的可扩展性。
English Abstract: Molecular Dynamics Simulation is an important method for acquiring liquid and solid atomsproperties.This method has been widely used in the fields of chemistry,physics,biology,medicine and materials.The complexity and accuracy demand causes enormous workloads.Parallel computing is a feasible way to speedup large-scale molecular dynamics simulation.With hundreds of GFlops or even TFlops performance,GPU can speed up computing-intensive applications.This paper presented a parallel algorithm named oApT-AD,and we implemented it on GPU under OpenCL and CUDA Framework.The experiment results show that the oApT-AD algorithm can achieve 120speedup on GPU Tesla C1060under OpenCL Framework,compared to that on CPU.And we also implemented the oApT-AD algorithm on GPU under CUDA Framework.The implement under OpenCL Framework provides almost the same performance as the implement under CUDA Framework.Moreover,our algorithm can be extended to two or more GPUs,with good scalability.
Language: 中文
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Content Type: 期刊论文
URI: http://ir.iscas.ac.cn/handle/311060/16040
Appears in Collections:软件所图书馆_期刊论文

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Recommended Citation:
费辉,张云泉,王可,等. 基于GPU的分子动力学模拟并行化及实现[J]. 计算机科学,2011-01-01,38(9):275-278,287.
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