Implementation of Particle-Mesh Ewald(PME) on Graphics Processing Units

CHINESE JOURNAL OF COMPUTATIONAL PHYSICS ›› 2010, Vol. 27 ›› Issue (4): 548-554.

Previous Articles Next Articles

Implementation of Particle-Mesh Ewald(PME) on Graphics Processing Units

XU Ji^1,2, GE Wei¹, REN Ying¹, LI Jinghai¹

1. State Key Laboratory of Multiphase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China;
2. Graduate University of the Chinese Academy of Sciences, Beijing 100039, China

Received:2009-04-30 Revised:2009-09-04 Online:2010-07-25 Published:2010-07-25

Abstract

Abstract: In this article,long range part of electrostatic interaction is accelerated using GPUs in NIVIDIA CUDA programming environment.Particle Mesh Ewald algorithm is adopted and split into 5 procedures:parameters designation,discretization of point charges into grids,Fourier transformation of grids,potential of electrostatic interaction,and force calculation of electrostatic interaction.The codes are tested by seven biomolecular systems with different sizes.Roughly 7-fold speedup over one core of mainstream CPUs is obtained.The codes can be integrated into molecular dynamic simulation software packages that already exst or used as part of GPU codes developed in the future to further speedup traditional MD simulations.

Key words: PME, GPU, CUDA, speedup

CLC Number:

O241

XU Ji, GE Wei, REN Ying, LI Jinghai. Implementation of Particle-Mesh Ewald(PME) on Graphics Processing Units[J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2010, 27(4): 548-554.

[1]	Puyang GAO. Numerical Investigation of Gas Entrapment in Polymer Filling Process [J]. Chinese Journal of Computational Physics, 2021, 38(6): 693-706.
[2]	YUE Junzheng, DONG Hefei, HONG Tao. Three-dimensional Numerical Simulation of Detonation Aftereffect of Suspended Aluminum Dusts in Corner Space [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2020, 37(1): 37-45.
[3]	YAO Mengjun, SHANG Wenqiang, ZHANG Ying, GAO Hui, ZHANG Daoxu, LIU Peiyao. Numerical Analysis of Kelvin-Helmholtz Instability in Inclined Walls [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2019, 36(4): 403-412.
[4]	PENG Hao, SHAN Minglei, ZHU Changping, YAO Cheng. Performance Optimization of 3D Pseudopotential Multi-Relaxation-Time Lattice Boltzmann Model on GPU [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2018, 35(5): 554-562.
[5]	JIANG Dong, LI Yongchi. Embedding of Constitutive Iterative Algorithm in LS-DYNA [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2018, 35(3): 262-268.
[6]	QI Meiling, YANG Qiong, WANG Canglong, TIAN Yuan, YANG Lei. Parallel Algorithm on GPU and Optimization for Molecular Dynamics Simulation of Irradiation Damage of Structure Materials [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2017, 34(4): 461-467.
[7]	LEI Timan, MENG Xuhui, GUO Zhaoli. Lattice Boltzmann Study on Influence of Chemical Reaction on Mixing of Miscible Fluids with Viscous Instability in Porous Media [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2016, 33(4): 399-409.
[8]	JIANG Hua, DONG Gang, CHEN Xiao. A Numerical Study of Interactions Between Shock Waves and Flame with GPU Acceleration [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2016, 33(1): 23-29.
[9]	SHANGGUAN Yanqin, WANG Xian, LI Yueming. High-Performance Numerical Simulation of Jet in Cross-Flow Based on Lattice Boltzmann Method [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2015, 32(6): 669-676.
[10]	CAO Jianwei, XU Xiang, WANG Younian. Parallel Algorithms for Separable Elliptic Equation based on GPU [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2015, 32(4): 475-481.
[11]	ZHANG Rui, WEN Lihua, XIAO Jinyou. GPU-accelerated Boundary Element Method for Large-scale Problems in Acoustics [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2015, 32(3): 299-309.
[12]	HE Yongxiang, LIU Xin, ZHAO Haibo. High Performance GPU Parallel Computing of Gas Dynamic by Direct Simulation Monte Carlo [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2015, 32(2): 169-176.
[13]	ZHU Lianhua, GUO Zhaoli. GPU Accelerated Lattice Boltzmann Simulation of Flow in Porous Media [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2015, 32(1): 20-26.
[14]	WEI Shaolei, CHENG Linsong, HUANG Wenjun, ZHANG Huideng. Prediction of Steam Chamber Development and Production Performance for SAGD in Thin Heavy Oil Reservoirs [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2014, 31(6): 690-698.
[15]	HUANG Shuo, XIAO Jinyou, HU Yucai, WANG Tao. GPU-accelerated Boundary Element Method for Burton-Miller Equation in Acoustics [J]. CHINESE JOURNAL OF COMPUTATIONAL PHYSICS, 2011, 28(4): 481-487.

Implementation of Particle-Mesh Ewald(PME) on Graphics Processing Units

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Authors

Reviewers

Journal Online

About Journal