Parallel Pipelines for DNA Sequence Alignment on a Cluster of Multicores: A Comparison of Communication Models

Autores
Rucci, Enzo; Chichizola, Franco; De Giusti, Laura Cristina; Naiouf, Marcelo; 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.
Facultad de Informática
Materia
Ciencias Informáticas
Cluster of multicores
communication models
Parallel programming languages
Pipeline computing
Smith-Waterman
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/80063
Acceder
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network_acronym_str SEDICI
repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling Parallel Pipelines for DNA Sequence Alignment on a Cluster of Multicores: A Comparison of Communication ModelsRucci, EnzoChichizola, FrancoDe Giusti, Laura CristinaNaiouf, MarceloDe Giusti, Armando EduardoCiencias InformáticasCluster of multicorescommunication modelsParallel programming languagesPipeline computingSmith-WatermanHPC (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.Facultad de Informática2012-09-15info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdf1364-1371http://sedici.unlp.edu.ar/handle/10915/80063enginfo:eu-repo/semantics/altIdentifier/issn/1930-1553info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc/4.0/Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-10-15T11:06:33Zoai:sedici.unlp.edu.ar:10915/80063Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-10-15 11:06:34.131SEDICI (UNLP) - Universidad Nacional de La Platafalse
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
Ciencias Informáticas
Cluster of multicores
communication models
Parallel programming languages
Pipeline computing
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
De Giusti, Laura Cristina
Naiouf, Marcelo
De Giusti, Armando Eduardo
author Rucci, Enzo
author_facet Rucci, Enzo
Chichizola, Franco
De Giusti, Laura Cristina
Naiouf, Marcelo
De Giusti, Armando Eduardo
author_role author
author2 Chichizola, Franco
De Giusti, Laura Cristina
Naiouf, Marcelo
De Giusti, Armando Eduardo
author2_role author
author
author
author
dc.subject.none.fl_str_mv Ciencias Informáticas
Cluster of multicores
communication models
Parallel programming languages
Pipeline computing
Smith-Waterman
topic Ciencias Informáticas
Cluster of multicores
communication models
Parallel programming languages
Pipeline computing
Smith-Waterman
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.
Facultad de Informática
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 2012-09-15
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
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://sedici.unlp.edu.ar/handle/10915/80063
url http://sedici.unlp.edu.ar/handle/10915/80063
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/1930-1553
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc/4.0/
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/4.0/
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
dc.format.none.fl_str_mv application/pdf
1364-1371
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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score 13.22299

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