Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures

BACKGROUND: The hardware accelerators will provide solutions to computationally complex problems in bioinformatics fields. However, the effect of acceleration depends on the nature of the application, thus selection of an appropriate accelerator requires some consideration. RESULTS: In the present s...

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Autores principales: Shimoda, Takehiro, Suzuki, Shuji, Ohue, Masahito, Ishida, Takashi, Akiyama, Yutaka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331681/
https://www.ncbi.nlm.nih.gov/pubmed/25707855
http://dx.doi.org/10.1186/1752-0509-9-S1-S6
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author Shimoda, Takehiro
Suzuki, Shuji
Ohue, Masahito
Ishida, Takashi
Akiyama, Yutaka
author_facet Shimoda, Takehiro
Suzuki, Shuji
Ohue, Masahito
Ishida, Takashi
Akiyama, Yutaka
author_sort Shimoda, Takehiro
collection PubMed
description BACKGROUND: The hardware accelerators will provide solutions to computationally complex problems in bioinformatics fields. However, the effect of acceleration depends on the nature of the application, thus selection of an appropriate accelerator requires some consideration. RESULTS: In the present study, we compared the effects of acceleration using graphics processing unit (GPU) and many integrated core (MIC) on the speed of fast Fourier transform (FFT)-based protein-protein docking calculation. The GPU implementation performed the protein-protein docking calculations approximately five times faster than the MIC offload mode implementation. The MIC native mode implementation has the advantage in the implementation costs. However, the performance was worse with larger protein pairs because of memory limitations. CONCLUSION: The results suggest that GPU is more suitable than MIC for accelerating FFT-based protein-protein docking applications.
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spelling pubmed-43316812015-03-25 Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures Shimoda, Takehiro Suzuki, Shuji Ohue, Masahito Ishida, Takashi Akiyama, Yutaka BMC Syst Biol Proceedings BACKGROUND: The hardware accelerators will provide solutions to computationally complex problems in bioinformatics fields. However, the effect of acceleration depends on the nature of the application, thus selection of an appropriate accelerator requires some consideration. RESULTS: In the present study, we compared the effects of acceleration using graphics processing unit (GPU) and many integrated core (MIC) on the speed of fast Fourier transform (FFT)-based protein-protein docking calculation. The GPU implementation performed the protein-protein docking calculations approximately five times faster than the MIC offload mode implementation. The MIC native mode implementation has the advantage in the implementation costs. However, the performance was worse with larger protein pairs because of memory limitations. CONCLUSION: The results suggest that GPU is more suitable than MIC for accelerating FFT-based protein-protein docking applications. BioMed Central 2015-01-21 /pmc/articles/PMC4331681/ /pubmed/25707855 http://dx.doi.org/10.1186/1752-0509-9-S1-S6 Text en Copyright © 2015 Shimoda et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Shimoda, Takehiro
Suzuki, Shuji
Ohue, Masahito
Ishida, Takashi
Akiyama, Yutaka
Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
title Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
title_full Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
title_fullStr Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
title_full_unstemmed Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
title_short Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
title_sort protein-protein docking on hardware accelerators: comparison of gpu and mic architectures
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331681/
https://www.ncbi.nlm.nih.gov/pubmed/25707855
http://dx.doi.org/10.1186/1752-0509-9-S1-S6
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