Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines

被引：337

作者：

Jia, Weile ^{[1
,2
]}

Fu, Jiyun ^{[1
,2
]}

Cao, Zongyan ^{[1
]}

Wang, Long ^{[1
]}

Chi, Xuebin ^{[1
]}

Gao, Weiguo ^{[3
,4
]}

Wange, Lin-Wang ^{[5
]}

机构：

[1] Chinese Acad Sci, Comp Network Informat Ctr, Supercomp Ctr, Beijing 100190, Peoples R China

[2] Univ Chinese Acad Sci, Beijing, Peoples R China

[3] Fudan Univ, Sch Math Sci, Shanghai 200433, Peoples R China

[4] Fudan Univ, MOE Key Lab Computat Phys Sci, Shanghai 200433, Peoples R China

[5] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Sci Mat, Berkeley, CA 94720 USA

来源：

JOURNAL OF COMPUTATIONAL PHYSICS | 2013年 / 251卷

关键词：

Molecular dynamics; Electronic structure; First-principles; Density functional theory; Plane wave pseudopotential; GPU;

D O I：

10.1016/j.jcp.2013.05.005

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

Plane wave pseudopotential (PWP) density functional theory (DFT) calculation is the most widely used method for material simulations, but its absolute speed stagnated due to the inability to use large scale CPU based computers. By a drastic redesign of the algorithm, and moving all the major computation parts into GPU, we have reached a speed of 12 s per molecular dynamics (MD) step for a 512 atom system using 256 GPU cards. This is about 20 times faster than the CPU version of the code regardless of the number of CPU cores used. Our tests and analysis on different GPU platforms and configurations shed lights on the optimal GPU deployments for PWP-DFT calculations. An 1800 step MD simulation is used to study the liquid phase properties of GaInP. (C) 2013 Elsevier Inc. All rights reserved.

引用

页码：102 / 115

页数：14

共 25 条

[1] SPONTANEOUS ORDERING IN GAINP2 - A POLARIZED-PIEZOMODULATED-REFLECTIVITY STUDY
ALONSO, RG
MASCARENHAS, A
HORNER, GS
BERTNESS, KA
KURTZ, SR
OLSON, JM
[J]. PHYSICAL REVIEW B, 1993, 48 (16): : 11833 - 11837
[2] LANGEVIN MOLECULAR-DYNAMICS WITH QUANTUM FORCES - APPLICATION TO SILICON CLUSTERS
BINGGELI, N
CHELIKOWSKY, JR
[J]. PHYSICAL REVIEW B, 1994, 50 (16) : 11764 - 11770
[3] UNIFIED APPROACH FOR MOLECULAR-DYNAMICS AND DENSITY-FUNCTIONAL THEORY
CAR, R
PARRINELLO, M
[J]. PHYSICAL REVIEW LETTERS, 1985, 55 (22) : 2471 - 2474
[4] Challenges in modeling materials properties without experimental input
Carter, Emily A.
[J]. SCIENCE, 2008, 321 (5890) : 800 - 803
[5] Accelerated Block Preconditioned Gradient method for large scale wave functions calculations in Density Functional Theory
Fattebert, J. -L.
[J]. JOURNAL OF COMPUTATIONAL PHYSICS, 2010, 229 (02) : 441 - 452
[6] Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures
Genovese, Luigi
Ospici, Matthieu
Deutsch, Thierry
Mehaut, Jean-Francois
Neelov, Alexey
Goedecker, Stefan
[J]. JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (03)
[7] Götz AW, 2010, ANN REP COMP CHEM, V6, P21, DOI 10.1016/S1574-1400(10)06002-0
[8] Architecture of Qbox: A scalable first-principles molecular dynamics code
Gygi, F.
[J]. IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 2008, 52 (1-2) : 137 - 144
[9] Gygi F., 2005, P 2005 ACM IEEE SC 0
[10] Simple reversible molecular dynamics algorithms for Nose-Hoover chain dynamics
Jang, S
Voth, GA
[J]. JOURNAL OF CHEMICAL PHYSICS, 1997, 107 (22) : 9514 - 9526

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