Accelerated molecular dynamics simulation using multi-core CPU and GPU

doi:10.3724/SP.J.1087.2011.00843

Journal of Computer Applications ›› 2011, Vol. 31 ›› Issue (03): 843-847.DOI: 10.3724/SP.J.1087.2011.00843

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Accelerated molecular dynamics simulation using multi-core CPU and GPU

LIN Jiang-hong¹,LIN Jin-xian²,LV Tun³

1. College of Mathematics and Computer Science, Fuzhou University, Fuzhou Fujian 350108, China
2. College of Mathematics and Computer Science, Fuzhou University, Fuzhou Fujian 350108, China; Fujian Supercomputing Center, Fuzhou University, Fuzhou Fujian 350108, China
3. Fujian Supercomputing Center, Fuzhou University, Fuzhou Fujian 350108, China; College of Biological Science and Technology, Fuzhou University, Fuzhou Fujian 350108, China

Received:2010-08-16 Revised:2010-11-04 Online:2011-03-03 Published:2011-03-01
Contact: LIN Jiang-hong

多核CPU和GPU加速分子动力学模拟

林江宏¹,林锦贤²,吕暾³

1. 福州大学数学与计算机科学学院,福州350108
2. 福州大学数学与计算机科学学院，福州350108; 福州大学福建省超级计算中心，福州350108
3. 福州大学福建省超级计算中心，福州350108；福州大学生物科学与工程学院，福州350108

通讯作者: 林江宏
作者简介:林江宏(1986-)，男，福建宁德人，硕士研究生，主要研究方向：分子动力学并行算法；林锦贤(1957-)，男，福建福州人，副教授，主要研究方向：高性能计算；吕暾(1973-)，男，福建厦门人，研究员，主要研究方向：计算生物学。
基金资助:
福建省高校科研专项重点项目(JK2009002);福建省科技厅青年人才基金资助项目（2008F306010107）

Abstract

Abstract: On the heterogeneous architecture of multi-core Central Processing Unit (CPU) and Graphic Processing Unit (GPU), the Open Multi-Processing (OpenMP) and the programming interfaces of Compute Unified Device Architecture (CUDA) were used to implement a molecular dynamics simulation program based on AMBER force field. In order to efficiently use computer processing power, the program was divided into different parts which were processed by CPU single-thread, CPU multi-thread and GPU multi-thread respectively. The experimental results show that compared with the optimized CPU-based implementations, the heterogeneous parallel computing model based on multi-core CPU-GPU gets powerful performance advantage. Especially, the calculations of forces, which account for more than 90% of processing time, get at most 12 times faster than CPU-based implementations while being implemented on GPU.

Key words: Molecular Dynamics (MD), Graphic Processing Unit (GPU), multi-core Central Processing Unit (CPU), AMBER force field, Compute Unified Device Architecture (CUDA), Open Multi-Processing (OpenMP)

摘要： 在多核中央处理器(CPU)—图形处理器(GPU)异构并行体系结构上，采用OpenMP和计算统一设备架构(CUDA)编程实现了基于AMBER力场的蛋白质分子动力学模拟程序。通过合理地将程序划分为CPU单线程、CPU多线程和GPU多线程执行部分，高效地利用了计算机的处理能力。性能测试结果表明，相对于优化后的CPU串行计算，多核CPU-GPU异构并行计算模型有强大的性能优势，特别是将占整个程序执行时间90%的作用力的计算移植到GPU上执行，获得了最高可达12倍的计算加速比。

关键词: 分子动力学, 图形处理器, 多核中央处理器, AMBER力场, 计算统一设备架构, OpenMP

CLC Number:

TP399
O641

LIN Jiang-hong LIN Jin-xian LV Tun. Accelerated molecular dynamics simulation using multi-core CPU and GPU[J]. Journal of Computer Applications, 2011, 31(03): 843-847.

林江宏林锦贤吕暾. 多核CPU和GPU加速分子动力学模拟[J]. 计算机应用, 2011, 31(03): 843-847.

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Accelerated molecular dynamics simulation using multi-core CPU and GPU

多核CPU和GPU加速分子动力学模拟

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