Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models

Autores
Rucci, Enzo; Chichizola, Franco; Naiouf, Ricardo Marcelo; de Giusti, Laura Cristina; de Giusti, Armando Eduardo
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
HPC (high perfomance computing) based on clusters of multicores is one of the main research lines in parallel programming. It is important to study the impact of programming paradigms of shared memory, message passing or a combination of both on these architectures in order to efficiently exploit the power of these architectures. The Smith-Waterman algorithm is used as study case for the local alignment of DNA sequences, which allows establishing the similarity degree between two sequences. In this paper, the Smith-Waterman algorithm is parallelized by means of a pipeline scheme due to the data dependencies that are inherent to the problem, using the various communication/synchronization models mentioned above and then carrying out a comparative analysis. Finally, experimental results are presented, as well as future research lines.
Fil: Rucci, Enzo. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Fil: Chichizola, Franco. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Fil: Naiouf, Ricardo Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina
Fil: de Giusti, Laura Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina
Fil: de Giusti, Armando Eduardo. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Materia
CLUSTER OF MULTICORES
COMMUNICATION MODELS
PARALLEL PROGRAMING
PIPELINE
SMITH-WATERMAN
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/271560
Acceder
id CONICETDig_67642d3a24f936ccacbfab7cf56ed663
oai_identifier_str oai:ri.conicet.gov.ar:11336/271560
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication modelsRucci, EnzoChichizola, FrancoNaiouf, Ricardo Marcelode Giusti, Laura Cristinade Giusti, Armando EduardoCLUSTER OF MULTICORESCOMMUNICATION MODELSPARALLEL PROGRAMINGPIPELINESMITH-WATERMANhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1HPC (high perfomance computing) based on clusters of multicores is one of the main research lines in parallel programming. It is important to study the impact of programming paradigms of shared memory, message passing or a combination of both on these architectures in order to efficiently exploit the power of these architectures. The Smith-Waterman algorithm is used as study case for the local alignment of DNA sequences, which allows establishing the similarity degree between two sequences. In this paper, the Smith-Waterman algorithm is parallelized by means of a pipeline scheme due to the data dependencies that are inherent to the problem, using the various communication/synchronization models mentioned above and then carrying out a comparative analysis. Finally, experimental results are presented, as well as future research lines.Fil: Rucci, Enzo. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Chichizola, Franco. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Naiouf, Ricardo Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; ArgentinaFil: de Giusti, Laura Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; ArgentinaFil: de Giusti, Armando Eduardo. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaDavid Publishing Company2012-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/271560Rucci, Enzo; Chichizola, Franco; Naiouf, Ricardo Marcelo; de Giusti, Laura Cristina; de Giusti, Armando Eduardo; Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models; David Publishing Company; Journal of Communication and Computer; 9; 12; 12-2012; 1364-13711930-1553CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.davidpublisher.com/index.php/Home/Article/index?id=8567.htmlinfo:eu-repo/semantics/altIdentifier/doi/10.17265/1548-7709/2012.12 007info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:33:45Zoai:ri.conicet.gov.ar:11336/271560instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:33:45.471CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
title Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
spellingShingle Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
Rucci, Enzo
CLUSTER OF MULTICORES
COMMUNICATION MODELS
PARALLEL PROGRAMING
PIPELINE
SMITH-WATERMAN
title_short Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
title_full Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
title_fullStr Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
title_full_unstemmed Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
title_sort Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models
dc.creator.none.fl_str_mv Rucci, Enzo
Chichizola, Franco
Naiouf, Ricardo Marcelo
de Giusti, Laura Cristina
de Giusti, Armando Eduardo
author Rucci, Enzo
author_facet Rucci, Enzo
Chichizola, Franco
Naiouf, Ricardo Marcelo
de Giusti, Laura Cristina
de Giusti, Armando Eduardo
author_role author
author2 Chichizola, Franco
Naiouf, Ricardo Marcelo
de Giusti, Laura Cristina
de Giusti, Armando Eduardo
author2_role author
author
author
author
dc.subject.none.fl_str_mv CLUSTER OF MULTICORES
COMMUNICATION MODELS
PARALLEL PROGRAMING
PIPELINE
SMITH-WATERMAN
topic CLUSTER OF MULTICORES
COMMUNICATION MODELS
PARALLEL PROGRAMING
PIPELINE
SMITH-WATERMAN
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv HPC (high perfomance computing) based on clusters of multicores is one of the main research lines in parallel programming. It is important to study the impact of programming paradigms of shared memory, message passing or a combination of both on these architectures in order to efficiently exploit the power of these architectures. The Smith-Waterman algorithm is used as study case for the local alignment of DNA sequences, which allows establishing the similarity degree between two sequences. In this paper, the Smith-Waterman algorithm is parallelized by means of a pipeline scheme due to the data dependencies that are inherent to the problem, using the various communication/synchronization models mentioned above and then carrying out a comparative analysis. Finally, experimental results are presented, as well as future research lines.
Fil: Rucci, Enzo. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Fil: Chichizola, Franco. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
Fil: Naiouf, Ricardo Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina
Fil: de Giusti, Laura Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina
Fil: de Giusti, Armando Eduardo. Universidad Nacional de La Plata. Facultad de Informática. Instituto de Investigación en Informática Lidi; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina
description HPC (high perfomance computing) based on clusters of multicores is one of the main research lines in parallel programming. It is important to study the impact of programming paradigms of shared memory, message passing or a combination of both on these architectures in order to efficiently exploit the power of these architectures. The Smith-Waterman algorithm is used as study case for the local alignment of DNA sequences, which allows establishing the similarity degree between two sequences. In this paper, the Smith-Waterman algorithm is parallelized by means of a pipeline scheme due to the data dependencies that are inherent to the problem, using the various communication/synchronization models mentioned above and then carrying out a comparative analysis. Finally, experimental results are presented, as well as future research lines.
publishDate 2012
dc.date.none.fl_str_mv 2012-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/271560
Rucci, Enzo; Chichizola, Franco; Naiouf, Ricardo Marcelo; de Giusti, Laura Cristina; de Giusti, Armando Eduardo; Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models; David Publishing Company; Journal of Communication and Computer; 9; 12; 12-2012; 1364-1371
1930-1553
CONICET Digital
CONICET
url http://hdl.handle.net/11336/271560
identifier_str_mv Rucci, Enzo; Chichizola, Franco; Naiouf, Ricardo Marcelo; de Giusti, Laura Cristina; de Giusti, Armando Eduardo; Parallel pipelines for DNA sequence alignment on a cluster of multicores. A comparison of communication models; David Publishing Company; Journal of Communication and Computer; 9; 12; 12-2012; 1364-1371
1930-1553
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.davidpublisher.com/index.php/Home/Article/index?id=8567.html
info:eu-repo/semantics/altIdentifier/doi/10.17265/1548-7709/2012.12 007
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv David Publishing Company
publisher.none.fl_str_mv David Publishing Company
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1844614353236525056
score 13.069144

Publicaciones similares