An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara
Graduate School of Information Sciences, Tohoku University, Aoba 6-6-05, Aramaki, Aoba, Sendai, Miyagi 980-8579, Japan
Atlantis Press, International Journal of Networked and Distributed Computing, Vol. 5, No. 1 (January 2017) 52-61, 2017


   title={An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL},

   author={Waidyasooriya, Hasitha Muthumala and Hariyama, Masanori and Kasahara, Kota},



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Molecular dynamics (MD) simulations are very important to study physical properties of the atoms and molecules. However, a huge amount of processing time is required to simulate a few nano-seconds of an actual experiment. Although the hardware acceleration using FPGAs provides promising results, huge design time and hardware design skills are required to implement an accelerator successfully. In this paper, we use a heterogeneous computing system for MD simulations, that can be used in C-based programming environment. We propose an FPGA accelerator designed using C-based OpenCL for the heterogeneous environment. We achieved over 4.6 times of speed-up compared to CPU-based processing, by using only 36% of the Stratix V FPGA resources. We also evaluate the processing times of different tasks in the heterogeneous environment.
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