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

Journal Article · Thu Sep 15 04:00:00 EDT 2016 · Journal of Computational Physics

DOI:https://doi.org/10.1016/J.JCP.2016.05.061· OSTI ID:22572352

Trędak, Przemysław ^[1]; Rudnicki, Witold R. ^[2]; Majewski, Jacek A. ^[1]

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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)

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.

• OSTI ID: 22572352
• Journal Information: Journal of Computational Physics, Journal Name: Journal of Computational Physics Vol. 321; ISSN JCTPAH; ISSN 0021-9991
• Country of Publication: United States
• Language: English

Related Subjects

71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
ALGORITHMS
HYDROCARBONS
MANY-BODY PROBLEM
MATERIALS
MATHEMATICAL SOLUTIONS
MOLECULAR DYNAMICS METHOD
POTENTIALS
PROGRAMMING
SYNCHRONIZATION