LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors

被引：7

作者：

Gao, Ping ^{[1
,6
]}

Duan, Xiaohui ^{[2
,6
]}

Guo, Jiaxu ^{[3
,6
]}

Wang, Jin ^{[7
]}

Song, Zhenya ^{[8
,9
]}

Cui, Lizhen ^{[1
,10
]}

Meng, Xiangxu ^{[1
,11
]}

Liu, Xin ^{[6
]}

Zhang, Wusheng ^{[2
,6
]}

Ma, Ming ^{[7
]}

Li, Guohui ^{[12
]}

Chen, Dexun ^{[2
,6
]}

Fu, Haohuan ^{[4
,5
,6
]}

Xue, Wei ^{[2
,6
]}

Liu, Weiguo ^{[1
,6
]}

Yang, Guangwen ^{[2
,4
,5
,6
]}

机构：

[1] Shandong Univ, Sch Software, Jinan, Peoples R China

[2] Tsinghua Univ, Dept Comp Sci & Technol, Beijing, Peoples R China

[3] Jilin Univ, Coll Comp Sci & Technol, Changchun, Peoples R China

[4] Tsinghua Univ, Minist Educ, Key Lab Earth Syst Modeling, Beijing, Peoples R China

[5] Tsinghua Univ, Dept Earth Syst Sci, Beijing, Peoples R China

[6] Natl Supercomp Ctr Wuxi, Wuxi, Jiangsu, Peoples R China

[7] Tsinghua Univ, Ctr Nano & Micro Mech, Dept Engn Mech, Beijing, Peoples R China

[8] Minist Nat Resources, Inst Oceanog 1, Qingdao, Peoples R China

[9] Minist Nat Resources, Key Lab Marine Sci & Numer Modeling, Qingdao, Peoples R China

[10] Joint SDU NTU Ctr Artificial Intelligence Res C F, Jinan, Peoples R China

[11] Minist Educ, Engn Res Ctr Digital Media Technol, Jinan, Peoples R China

[12] Chinese Acad Sci, Dalian Inst Chem Phys, Dalian, Peoples R China

来源：

SC21: INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS | 2021年

基金：

国家重点研发计划;

关键词：

High Performance Computing; Molecular Dynamics; LAMMPS; Inter-Layer Potential (IP); Tersoff; Hybrid Potentials Simulation; Computational Science; next -generation Sunway Supercomputer; MOLECULAR-DYNAMICS SIMULATIONS; ENERGY; GPU; POTENTIALS;

D O I：

10.1145/3458817.3476137

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

LAMMPS is one of the most popular Molecular Dynamic (MD) packages and is widely used in the field of physics, chemistry and materials simulation. Layered Materials Force Field (LIMIT) is our expansion of the LAMMPS potential function based on the Tersoff potential and inter-layer potential (ILP) in LAMMPS. 1","MIT is designed to study layered materials such as graphene and boron hexanitride. It is universal and does not depend on any platform. We have also carried out a series of optimizations on LMFF and the optimization work is carried out on the new generation of Sunway supercomputer, called SWIAlPb. Experiments show that our implementation is efficient, scalable and portable. When generic UWE is ported to Intel Xeon Gold 6278C, 2x performance improvement is achieved. For the optimized SWLMFF, the overall performance improvement is nearly 200-330x compared to the original ILP and 7fersoff potentials. And SWLMFF has good parallel efficiency of 95%-100% under weak scaling with 2.7 million atoms on a single process. The maximum atomic system simulated by SWIA4LF is

引用

页数：16

共 43 条

[1] Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques [J].

Aktulga, H. M. ;

Fogarty, J. C. ;

Pandit, S. A. ;

Grama, A. Y. .

PARALLEL COMPUTING, 2012, 38 (4-5) :245-259

[2] Optimizing the performance of reactive molecular dynamics simulations for many-core architectures [J].

Aktulga, Hasan Metin ;

Knight, Chris ;

Coffman, Paul ;

O'Hearn, Kurt A. ;

Shan, Tzu-Ray ;

Jiang, Wei .

INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 2019, 33 (02) :304-321

[3] STUDIES IN MOLECULAR DYNAMICS .1. GENERAL METHOD [J].

ALDER, BJ ;

WAINWRIGHT, TE .

JOURNAL OF CHEMICAL PHYSICS, 1959, 31 (02) :459-466

[4] GROMACS - A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION [J].

BERENDSEN, HJC ;

VANDERSPOEL, D ;

VANDRUNEN, R .

COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) :43-56

[5] A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons [J].

Brenner, DW ;

Shenderova, OA ;

Harrison, JA ;

Stuart, SJ ;

Ni, B ;

Sinnott, SB .

JOURNAL OF PHYSICS-CONDENSED MATTER, 2002, 14 (04) :783-802

[6] CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].

BROOKS, BR ;

BRUCCOLERI, RE ;

OLAFSON, BD ;

STATES, DJ ;

SWAMINATHAN, S ;

KARPLUS, M .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217

[7] Optimizing legacy molecular dynamics software with directive-based offload [J].

Brown, W. Michael ;

Carrillo, Jan-Michael Y. ;

Gavhane, Nitin ;

Thakkar, Foram M. ;

Plimpton, Steven J. .

COMPUTER PHYSICS COMMUNICATIONS, 2015, 195 :95-101

[8] The Amber biomolecular simulation programs [J].

Case, DA ;

Cheatham, TE ;

Darden, T ;

Gohlke, H ;

Luo, R ;

Merz, KM ;

Onufriev, A ;

Simmerling, C ;

Wang, B ;

Woods, RJ .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1668-1688

[9]

Dong WQ, 2016, PROCEEDINGS OF 2016 IEEE 18TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING AND COMMUNICATIONS

[10]

IEEE 14TH INTERNATIONAL CONFERENCE ON SMART CITY

← 1 2 3 4 5 →