TY - JOUR
T1 - An FPGA accelerator for molecular dynamics simulation using OpenCL
AU - Waidyasooriya, Hasitha Muthumala
AU - Hariyama, Masanori
AU - Kasahara, Kota
N1 - Publisher Copyright:
© 2017, the Authors. Published by Atlantis Press.
Copyright:
Copyright 2018 Elsevier B.V., All rights reserved.
PY - 2017/1
Y1 - 2017/1
N2 - 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.
AB - 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.
KW - Hardware acceleration
KW - Molecular dynamics simulation
KW - OpenCL for FPGA
KW - Scientific computing
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U2 - 10.2991/ijndc.2017.5.1.6
DO - 10.2991/ijndc.2017.5.1.6
M3 - Article
AN - SCOPUS:85019242936
VL - 5
SP - 52
EP - 61
JO - International Journal of Networked and Distributed Computing
JF - International Journal of Networked and Distributed Computing
SN - 2211-7938
IS - 1
ER -