Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA

Autores
Rucci, Enzo; García Sanchez, Carlos; Botella, Guillermo; De Giusti, Armando Eduardo; Naiouf, Marcelo; Prieto-Matias, Manuel
Año de publicación
2017
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.
Publicado en Lecture Notes in Computer Science book series (LNCS, vol. 10209).
Facultad de Informática
Materia
Ciencias Informáticas
Field Programmable Gate Array
Graphic Processor Unit
Field Programmable Gate Array Implementation
Latency Memory Access
Dedicated Memory
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-nd/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/82872
Acceder
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network_name_str SEDICI (UNLP)
spelling Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGARucci, EnzoGarcía Sanchez, CarlosBotella, GuillermoDe Giusti, Armando EduardoNaiouf, MarceloPrieto-Matias, ManuelCiencias InformáticasField Programmable Gate ArrayGraphic Processor UnitField Programmable Gate Array ImplementationLatency Memory AccessDedicated MemoryWith the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.Publicado en <i>Lecture Notes in Computer Science</i> book series (LNCS, vol. 10209).Facultad de Informática2017-04-27info:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionObjeto de conferenciahttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdf500-511http://sedici.unlp.edu.ar/handle/10915/82872enginfo:eu-repo/semantics/altIdentifier/isbn/978-3-319-56154-7info:eu-repo/semantics/altIdentifier/doi/10.1007/978-3-319-56154-7_45info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0/Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:15:36Zoai:sedici.unlp.edu.ar:10915/82872Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:15:37.197SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
spellingShingle Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
Rucci, Enzo
Ciencias Informáticas
Field Programmable Gate Array
Graphic Processor Unit
Field Programmable Gate Array Implementation
Latency Memory Access
Dedicated Memory
title_short Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_full Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_fullStr Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_full_unstemmed Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
title_sort Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
dc.creator.none.fl_str_mv Rucci, Enzo
García Sanchez, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author Rucci, Enzo
author_facet Rucci, Enzo
García Sanchez, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author_role author
author2 García Sanchez, Carlos
Botella, Guillermo
De Giusti, Armando Eduardo
Naiouf, Marcelo
Prieto-Matias, Manuel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Ciencias Informáticas
Field Programmable Gate Array
Graphic Processor Unit
Field Programmable Gate Array Implementation
Latency Memory Access
Dedicated Memory
topic Ciencias Informáticas
Field Programmable Gate Array
Graphic Processor Unit
Field Programmable Gate Array Implementation
Latency Memory Access
Dedicated Memory
dc.description.none.fl_txt_mv With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.
Publicado en <i>Lecture Notes in Computer Science</i> book series (LNCS, vol. 10209).
Facultad de Informática
description With the greater importance of parallel architectures such as GPUs or Xeon Phi accelerators, the scientific community has developed efficient solutions in the bioinformatics field. In this context, FPGAs begin to stand out as high performance devices with moderate power consumption. This paper presents and evaluates a parallel strategy of the well-known Smith-Waterman algorithm using OpenCL on Intel/Altera’s FPGA for long DNA sequences. We efficiently exploit data and pipeline parallelism on a Intel/Altera Stratix V FPGA reaching upto 114 GCUPS in less than 25 watt power requirements.
publishDate 2017
dc.date.none.fl_str_mv 2017-04-27
dc.type.none.fl_str_mv info:eu-repo/semantics/conferenceObject
info:eu-repo/semantics/publishedVersion
Objeto de conferencia
http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
format conferenceObject
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/82872
url http://sedici.unlp.edu.ar/handle/10915/82872
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/isbn/978-3-319-56154-7
info:eu-repo/semantics/altIdentifier/doi/10.1007/978-3-319-56154-7_45
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
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500-511
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repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
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