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).

References

[1]	Zhang M K, Chen S, Shang Z 2012 Acta Phys. Sin. 61 034701 (in Chinese) [张明焜, 陈硕, 尚智 2012 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 62 064705]
[3]	Xu S F, Wang J G 2013 Acta Phys. Sin. 62 124701 (in Chinese) [许少锋, 汪久根 2013 62 124701]
[4]	Chang J Z, Liu M B 2010 Acta Phys. Sin. 59 7556 (in Chinese) [常建忠, 刘谋斌 2010 59 7556]
[5]	Wang X L, Chen S 2010 Acta Phys. Sin. 59 6778 (in Chinese) [王晓亮, 陈硕 2010 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 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 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 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

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 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 62 064705]
[3]	Xu S F, Wang J G 2013 Acta Phys. Sin. 62 124701 (in Chinese) [许少锋, 汪久根 2013 62 124701]
[4]	Chang J Z, Liu M B 2010 Acta Phys. Sin. 59 7556 (in Chinese) [常建忠, 刘谋斌 2010 59 7556]
[5]	Wang X L, Chen S 2010 Acta Phys. Sin. 59 6778 (in Chinese) [王晓亮, 陈硕 2010 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 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 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 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

[1]	Yang Wei-Tao, Hu Zhi-Liang, He Huan, Mo Li-Hua, Zhao Xiao-Hong, Song Wu-Qing, Yi Tian-Cheng, Liang Tian-Jiao, He Chao-Hui, Li Yong-Hong, Wang Bin, Wu Long-Sheng, Liu Huan, Shi Guang. Neutron induced single event effects on near-memory computing architecture AI chips. Acta Physica Sinica, 2024, 73(13): 138502. doi: 10.7498/aps.73.20240430
[2]	Shao Xu-Qiang, Mei Peng, Chen Wen-Xin. Real-time simulation of realistic fluid animation based on stable SPH-SWE numerical model. Acta Physica Sinica, 2021, 70(23): 234701. doi: 10.7498/aps.70.20211251
[3]	Zhang Ren-Qiang, Jiang Xiang-Yu, Yu Jiong-Chi, Zeng Chong, Gong Ming, Xu Shun. Calculation and optimization of correlation function in distillation method of lattice quantum chromodynamcis. Acta Physica Sinica, 2021, 70(16): 161201. doi: 10.7498/aps.70.20210030
[4]	Yang Ying, Song Jun-Jie, Wan Ming-Wei, Gao Liang-Hui, Fang Wei-Hai. Morphologies of self-assembled gold nanorod-surfactant-lipid complexes at molecular level. Acta Physica Sinica, 2020, 69(24): 248701. doi: 10.7498/aps.69.20200979
[5]	Tang Fu-Ming, Liu Kai, Yang Yi, Tu Qian, Wang Feng, Wang Zhe, Liao Qing. Numerical solution of three-dimensional time-dependent Schrödinger equation based on graphic processing unit acceleration. Acta Physica Sinica, 2020, 69(23): 234202. doi: 10.7498/aps.69.20200700
[6]	Lin Chen-Sen, Chen Shuo, Xiao Lan-Lan. New dissipative particle dynamics boundary condition for complex geometry. Acta Physica Sinica, 2019, 68(14): 140204. doi: 10.7498/aps.68.20190533
[7]	Xu Shao-Feng, Lou Ying-Hou, Wu Yao-Feng, Wang Xiang-Yang, He Ping. Fluid slip over hydrophobic surfaces in microchannels: a dissipative particle dynamics study. Acta Physica Sinica, 2019, 68(10): 104701. doi: 10.7498/aps.68.20182002
[8]	Dai Wei, Liu Qing-Quan, Yang Jie, Su Kai-Feng, Han Shang-Bang, Shi Jia-Chi. Computational fluid dynamics analysis and experimental study of sounding temperature sensor. Acta Physica Sinica, 2016, 65(11): 114701. doi: 10.7498/aps.65.114701
[9]	Xiao Jun, Li Deng-Yu, Wang Ya-Li, Shi Yi-Shi. Ptychographical algorithm of the parallel scheme. Acta Physica Sinica, 2016, 65(15): 154203. doi: 10.7498/aps.65.154203
[10]	Zhang Yi-Zhao, Bao Yun. Direct solution method of efficient large-scale parallel computation for 3D turbulent Rayleigh-Bénard convection. Acta Physica Sinica, 2015, 64(15): 154702. doi: 10.7498/aps.64.154702
[11]	Lei Juan-Mian, Huang Can. An improved pre-processing method for somooth particle hydrodynamics. Acta Physica Sinica, 2014, 63(14): 144702. doi: 10.7498/aps.63.144702
[12]	Han Ya-Wei, Qiang Hong-Fu, Zhao Jiu-Ling, Gao Wei-Ran. A new repulsive model for solid boundary condition in smoothed particle hydrodynamics. Acta Physica Sinica, 2013, 62(4): 044702. doi: 10.7498/aps.62.044702
[13]	Huang Pei-Pei, Liu Da-Gang, Liu La-Qun, Wang Hui-Hui, Xia Meng-Ju, Chen Ying. Three-dimensional numerical simulation of the single-channel pulsed-power vacuum device. Acta Physica Sinica, 2013, 62(19): 192901. doi: 10.7498/aps.62.192901
[14]	Liu Han-Tao, Liu Mou-Bin, Chang Jian-Zhong, Su Tie-Xiong. Dissipative particle dynamics simulation of multiphase flow through a mesoscopic channel. Acta Physica Sinica, 2013, 62(6): 064705. doi: 10.7498/aps.62.064705
[15]	Xu Shao-Feng, Wang Jiu-Gen. Dissipative particle dynamics simulation of macromolecular solutions under Poiseuille flow in microchannels. Acta Physica Sinica, 2013, 62(12): 124701. doi: 10.7498/aps.62.124701
[16]	Chang Jian-Zhong, Liu Han-Tao, Liu Mou-Bin, Su Tie-Xiong. Dissipative particle dynamics simulation of flow around a mesoscopic sphere with different Reynolds numbers. Acta Physica Sinica, 2012, 61(6): 064704. doi: 10.7498/aps.61.064704
[17]	Zhou Qing, He Xiao-Dong, Hu Yue. A universal cryptosystem based on two simple physical models. Acta Physica Sinica, 2011, 60(9): 094701. doi: 10.7498/aps.60.094701
[18]	Wang Xiao-Liang, Chen Shuo. Simulation of vapor-liquid coexistence using dissipative particle dynamics. Acta Physica Sinica, 2010, 59(10): 6778-6785. doi: 10.7498/aps.59.6778
[19]	Chang Jian-Zhong, Liu Mou-Bin. A new boundary treatment algorithm for dissipative particle dynamics. Acta Physica Sinica, 2010, 59(11): 7556-7563. doi: 10.7498/aps.59.7556
[20]	Liao Chen, Liu Da-Gang, Liu Sheng-Gang. Three-dimensional electromagnetic particle-in-cell simulation by parallel computing. Acta Physica Sinica, 2009, 58(10): 6709-6718. doi: 10.7498/aps.58.6709

Catalog

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

Metrics

Abstract views: 7325
PDF Downloads: 583
Cited By: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

Search

Article

留言板