Smith-Waterman Protein Search with OpenCL on an FPGA

Autores
Rucci, Enzo; De Giusti, Armando Eduardo; Naiouf, Marcelo; García Sanchez, Carlos; Botella, Juan Guillermo; Prieto-Matias, Manuel
Año de publicación
2015
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.
Facultad de Informática
Materia
Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
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:10915/82865
Acceder
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oai_identifier_str oai:sedici.unlp.edu.ar:10915/82865
network_acronym_str SEDICI
repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling Smith-Waterman Protein Search with OpenCL on an FPGARucci, EnzoDe Giusti, Armando EduardoNaiouf, MarceloGarcía Sanchez, CarlosBotella, Juan GuillermoPrieto-Matias, ManuelCiencias InformáticasBioinformaticsSmith-WatermanFPGAAlteraOpenCLThe well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.Facultad de Informática2015-08-22info:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionObjeto de conferenciahttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfhttp://sedici.unlp.edu.ar/handle/10915/82865enginfo:eu-repo/semantics/altIdentifier/isbn/978-1-4673-7952-6info:eu-repo/semantics/altIdentifier/doi/10.1109/Trustcom.2015.634info: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:10915/82865Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:15:37.195SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Smith-Waterman Protein Search with OpenCL on an FPGA
title Smith-Waterman Protein Search with OpenCL on an FPGA
spellingShingle Smith-Waterman Protein Search with OpenCL on an FPGA
Rucci, Enzo
Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
title_short Smith-Waterman Protein Search with OpenCL on an FPGA
title_full Smith-Waterman Protein Search with OpenCL on an FPGA
title_fullStr Smith-Waterman Protein Search with OpenCL on an FPGA
title_full_unstemmed Smith-Waterman Protein Search with OpenCL on an FPGA
title_sort Smith-Waterman Protein Search with OpenCL on an FPGA
dc.creator.none.fl_str_mv Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sanchez, Carlos
Botella, Juan Guillermo
Prieto-Matias, Manuel
author Rucci, Enzo
author_facet Rucci, Enzo
De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sanchez, Carlos
Botella, Juan Guillermo
Prieto-Matias, Manuel
author_role author
author2 De Giusti, Armando Eduardo
Naiouf, Marcelo
García Sanchez, Carlos
Botella, Juan Guillermo
Prieto-Matias, Manuel
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
topic Ciencias Informáticas
Bioinformatics
Smith-Waterman
FPGA
Altera
OpenCL
dc.description.none.fl_txt_mv The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.
Facultad de Informática
description The well-known Smith-Waterman (SW) algorithm is a high-sensitivity method for local alignments. Unfortunately, SW is expensive in terms of both execution time and memory usage, which makes it impractical in many scenarios. Previous research has shown that massively parallel architectures such as GPUs and FPGAs are able to mitigate the computational problems and achieve impressive speedups. In this paper we explore SW acceleration on an FPGA with OpenCL. We efficiently exploit data and thread-level parallelism on an Altera Stratix V FPGA, obtaining up to 39 GCUPS with less than 25 watt of power consumption.
publishDate 2015
dc.date.none.fl_str_mv 2015-08-22
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/10915/82865
url http://sedici.unlp.edu.ar/handle/10915/82865
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/isbn/978-1-4673-7952-6
info:eu-repo/semantics/altIdentifier/doi/10.1109/Trustcom.2015.634
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)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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