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Title: Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU

Abstract

The second generation Reactive Bond Order (REBO) empirical potential is commonly used to accurately model a wide range hydrocarbon materials. It is also extensible to other atom types and interactions. REBO potential assumes complex multi-body interaction model, that is difficult to represent efficiently in the SIMD or SIMT programming model. Hence, despite its importance, no efficient GPGPU implementation has been developed for this potential. Here we present a detailed description of a highly efficient GPGPU implementation of molecular dynamics algorithm using REBO potential. The presented algorithm takes advantage of rarely used properties of the SIMT architecture of a modern GPU to solve difficult synchronizations issues that arise in computations of multi-body potential. Techniques developed for this problem may be also used to achieve efficient solutions of different problems. The performance of proposed algorithm is assessed using a range of model systems. It is compared to highly optimized CPU implementation (both single core and OpenMP) available in LAMMPS package. These experiments show up to 6x improvement in forces computation time using single processor of the NVIDIA Tesla K80 compared to high end 16-core Intel Xeon processor.

Authors:
 [1];  [2];  [3];  [1]
  1. Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw (Poland)
  2. Institute of Informatics, University of Białystok, ul. Konstantego Ciołkowskiego 1M, 15-245 Białystok (Poland)
  3. (Poland)
Publication Date:
OSTI Identifier:
22572352
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Computational Physics; Journal Volume: 321; Other Information: Copyright (c) 2016 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ALGORITHMS; HYDROCARBONS; MANY-BODY PROBLEM; MATERIALS; MATHEMATICAL SOLUTIONS; MOLECULAR DYNAMICS METHOD; POTENTIALS; PROGRAMMING; SYNCHRONIZATION

Citation Formats

Trędak, Przemysław, E-mail: przemyslaw.tredak@fuw.edu.pl, Rudnicki, Witold R., Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Pawińskiego 5a, 02-106 Warsaw, and Majewski, Jacek A. Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU. United States: N. p., 2016. Web. doi:10.1016/J.JCP.2016.05.061.
Trędak, Przemysław, E-mail: przemyslaw.tredak@fuw.edu.pl, Rudnicki, Witold R., Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Pawińskiego 5a, 02-106 Warsaw, & Majewski, Jacek A. Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU. United States. doi:10.1016/J.JCP.2016.05.061.
Trędak, Przemysław, E-mail: przemyslaw.tredak@fuw.edu.pl, Rudnicki, Witold R., Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Pawińskiego 5a, 02-106 Warsaw, and Majewski, Jacek A. Thu . "Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU". United States. doi:10.1016/J.JCP.2016.05.061.
@article{osti_22572352,
title = {Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU},
author = {Trędak, Przemysław, E-mail: przemyslaw.tredak@fuw.edu.pl and Rudnicki, Witold R. and Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Pawińskiego 5a, 02-106 Warsaw and Majewski, Jacek A.},
abstractNote = {The second generation Reactive Bond Order (REBO) empirical potential is commonly used to accurately model a wide range hydrocarbon materials. It is also extensible to other atom types and interactions. REBO potential assumes complex multi-body interaction model, that is difficult to represent efficiently in the SIMD or SIMT programming model. Hence, despite its importance, no efficient GPGPU implementation has been developed for this potential. Here we present a detailed description of a highly efficient GPGPU implementation of molecular dynamics algorithm using REBO potential. The presented algorithm takes advantage of rarely used properties of the SIMT architecture of a modern GPU to solve difficult synchronizations issues that arise in computations of multi-body potential. Techniques developed for this problem may be also used to achieve efficient solutions of different problems. The performance of proposed algorithm is assessed using a range of model systems. It is compared to highly optimized CPU implementation (both single core and OpenMP) available in LAMMPS package. These experiments show up to 6x improvement in forces computation time using single processor of the NVIDIA Tesla K80 compared to high end 16-core Intel Xeon processor.},
doi = {10.1016/J.JCP.2016.05.061},
journal = {Journal of Computational Physics},
number = ,
volume = 321,
place = {United States},
year = {Thu Sep 15 00:00:00 EDT 2016},
month = {Thu Sep 15 00:00:00 EDT 2016}
}