Accelerating dissipative particle dynamics with graphic processing unit

Lin Chen-Sen; Chen Shuo; Li Qi-Liang; Yang Zhi-Gang

doi:10.7498/aps.63.104702

Abstract

In this paper, the graphic processing unit (GPU) parallel computing of dissipative particle dynamics (DPD) based on compute unified device architecture is carried out. Some issues involved, such as thread mapping, parallel cell-list array updating, generating pseudo-random number on GPU, memory access optimization and loading balancing are discussed in detail. Furthermore, Poiseuille flow and suddenly contracting and expanding flow are simulated to verify the correctness of GPU parallel computing. The results of GPU parallel computing of DPD show that the speedup ratio is about 20 times compared with central processing unit serial computing.

Keywords:

Authors and contacts

1.
School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai 200092, China;
2.
Shanghai Automotive Wind Tunnel Center, Tongji University, Shanghai 201804, China
Funds: Project supported by the Fundamental Scientific Research Foundation for the Central Universities of China (Grant No. 125065), the National Natural Science Foundation of China (Grant Nos. 51276130, 10872152), and the Specialized Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20120072110037).

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[28]	Fan X J, Nhan P T, Yong N T, Wu X H, Xu D 2003 Phys. Fluids 15 11

Cited By

[1]	Zhang M K, Chen S, Shang Z 2012 Acta Phys. Sin. 61 034701 (in Chinese) [张明焜, 陈硕, 尚智 2012 物理学报 61 034701]
[2]	Liu H T, Liu M B, Chang J Z, Su T X 2013 Acta Phys. Sin. 62 064705 (in Chinese) [刘汉涛, 刘谋斌, 常建忠, 苏铁熊 2013 物理学报 62 064705]
[3]	Xu S F, Wang J G 2013 Acta Phys. Sin. 62 124701 (in Chinese) [许少锋, 汪久根 2013 物理学报 62 124701]
[4]	Chang J Z, Liu M B 2010 Acta Phys. Sin. 59 7556 (in Chinese) [常建忠, 刘谋斌 2010 物理学报 59 7556]
[5]	Wang X L, Chen S 2010 Acta Phys. Sin. 59 6778 (in Chinese) [王晓亮, 陈硕 2010 物理学报 59 6778]
[6]	Wu S F, Li X F 2007 Chin. Phys. Lett. 25 184
[7]	He L L, Zhang R F, Ji Y Y 2012 Chin. Phys. B 21 088301
[8]	Liu C F, Ni Y S 2008 Chin. Phys. B 17 4554
[9]	Zhong C W, Xie J F, Zhuo C S, Xiong S W, Yin D C 2009 Chin. Phys. B 18 4083
[10]	Li Q D, Tan Y L, Yang F Y 2011 Acta Phys. Sin. 60 030206 (in Chinese) [李清都, 谭宇玲, 杨芳艳 2011 物理学报 60 030206]
[11]	Li Q D, Zhou H W, Yang X S 2012 Acta Phys. Sin. 61 040503 (in Chinese) [李清都, 周红伟, 杨晓松 2012 物理学报 61 040503]
[12]	Wang X C, Yan B, Liu H K, Li L, Wei X, Hu G E 2013 Acta Phys. Sin. 62 098702 (in Chinese) [汪先超, 闫镔, 刘宏奎, 李磊, 魏星, 胡国恩 2013 物理学报 62 098702]
[13]	Huang C S, Zhang W H, Hou Z M, Chen J H, Li M J, He N Z, Shi B C 2011 Chin. Sci. Bull. 56 2829 (in Chinese) [黄昌盛, 张文欢, 侯志敏, 陈俊辉, 李明晶, 何南忠, 施保昌 2011 科学通报 56 2829]
[14]	Zheng Y C, Liu S, Xiong S W, Zhou J F 2010 Sci. Tech. Eng. 7 1684 (in Chinese) [郑彦奎, 刘沙, 熊生伟, 周季夫 2010 科学技术与工程 7 1684]
[15]	Zhang D D, Xu Y, Xu L 2012 Comput. Sci. 39 296 (in Chinese) [张丹丹, 徐莹, 徐磊 2012 计算机科学 39 296]
[16]	Li C G, Maa Jerome P Y, Kang H G 2012 Sci. China: Phys. Mech. Astron. 55 1894
[17]	Januszewski M, Kostur M 2010 Comput. Phys. Commun. 181 183
[18]	Yuen D A, Wang L 2013 GPU Solutions to Multi-scale Problems in Science and Engineering (Berlin: Springer-Verlag) p143
[19]	Wu H, Xu J B, Zhang S F, Wen H 2011 IEIT J. Adapt. Dyn. Comput. 4 26
[20]	Wang S B, Xua J B, Wen H 2013 Comput. Phys. Commun. 184 2454
[21]	Chen S, Jin Y B, Zhang M K, Shang Z 2012 J. Tongji Univ. (Natural Science) 40 137 (in Chinese) [陈硕, 金亚斌, 张明焜, 尚智 2012 同济大学学报 (自然科学版) 40 137]
[22]	Phillips C L, Andersonb J A, Glotzer S C 2011 J. Comput. Phys. 230 7191
[23]	Howes L, Thomas D 2007 Efficient Random Number Generation and Application Using CUDA (Boston: Addison-Wesley Professional) p370
[24]	Nandapalan N, Brent R P, Murray L M, Rendell A 2012 Parallel Processing and Applied Mathematics (Berlin: Springer-Verlag) p609
[25]	Rose G 2011 IACR Cryptology ePrint Archive 2011 7
[26]	Wheeler D J, Needham R M 1995 Fast Software Encryption (Berlin: Springer-Verlag) p363
[27]	Yao P 2010 M. S. Dissertation (Hefei: University of Science and Technology of China) (in Chinese) [姚平 2010 硕士学位论文 (合肥: 中国科学技术大学)]
[28]	Fan X J, Nhan P T, Yong N T, Wu X H, Xu D 2003 Phys. Fluids 15 11

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Vol. 63, Issue 10 - 2014-05-20

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