Systems and Means of Informatics
2017, Volume 27, Issue 4, pp 109-121
EFFECTIVE USE OF PROGRAMMABLE GRAPHICS PROCESSING UNITS IN PROBLEMS OF MOLECULAR DYNAMICS SIMULATION
- S. A. Semenov
- D. L. Reviznikov
Abstract
Graphics processing units (GPU) make it possible to expand significantly the capabilities of computing systems. The article discusses the use of graphics processors in problems of molecular dynamics modeling with a complex particle interaction potential. In order to improve the performance of calculations on the GPU, the following methods are implemented: reduction of the number of requests to the global memory; reduction of the number of branches; selection of the optimal load of multiprocessors; and use of equivalent mathematical expressions that perform functions for faster code execution. Parallel execution of the program is realized by partitioning the space into cells, compiling and updating the list of neighboring atoms in order to minimize memory collisions, distribution of operations over computational flows, and allocation of additional memory for creating copies of the coordinates of interacting atoms. Several examples illustrating the computational complexity of the algorithms are considered.
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[+] About this article
Title
EFFECTIVE USE OF PROGRAMMABLE GRAPHICS PROCESSING UNITS IN PROBLEMS OF MOLECULAR DYNAMICS SIMULATION
Journal
Systems and Means of Informatics
Volume 27, Issue 4, pp 109-121
Cover Date
2017-10-30
DOI
10.14357/08696527170408
Print ISSN
0869-6527
Publisher
Institute of Informatics Problems, Russian Academy of Sciences
Additional Links
Key words
high-performance computing; graphics processors; shared memory; molecular dynamics simulation; nanomaterials
Authors
S. A. Semenov  and D. L. Reviznikov , 
Author Affiliations
Moscow Aviation Institute (National Research University), 4 Volokolamskoe Av., Moscow 125993, Russian Federation
A. A. Dorodnicyn Computing Center, Federal Research Center "Computer Science and Control" of the Russian Academy of Sciences, 40 Vavilov Str., Moscow 119333, Russian Federation
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