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Classical Molecular Dynamics Algorithms for Execution on FPGA with the Use of OpenCL Technology

Student: Parfenov Andrey

Supervisor: Igor Morozov

Faculty: HSE Tikhonov Moscow Institute of Electronics and Mathematics (MIEM HSE)

Educational Programme: Mathematical Methods of Modelling and Computer Technologies (Master)

Final Grade: 9

Year of Graduation: 2017

The aim of this work is the implementation of molecular dynamics and Monte-Carlo algorithms for N-body simulation using Field Programmable Gate Array (FPGA). We’ve considered different kinds of interactions potentials such as: short range Lenard-Jones potential which describes dipole-dipole interaction of uncharged atoms and long-range Coulomb potential which describes interac-tions between ions and electrons for nonideal plasma. In this work OpenCL tech-nology was used for MD\MC implementation. Performance tests were developed and performed for Terasic DE1-SOC board, which based on Altera Cyclone 5 and Arm Cortex A9, Nvidia 960M, Intel HD Graphics 4600 and CPU Haswell i7. We obtained, that for systems included more than 500 uncharged particles GPU usage provides much more better per-formance than CPU implementation. At the same time, as for the Coulomb po-tential, the gain in productivity is observed starting from a smaller number of particles. It was shown that Cyclone 5 FPGA provides performance comparable to Intel HD Graphics 4600 in molecular dynamics problems. Extrapolation of the results to more powerful FPGA models showed that Stratix 5 and Altera 10 fam-ilies FPGA will provide 10 times better performance than Cyclone 5, used in this work. Obtained results indicate that the usage of FPGAs is appropriate in tasks which required a large amount of calculations for systems with a relatively small number of particles.

Full text (added May 10, 2017)

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