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

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 t...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Rucci, Enzo, Chichizola, Franco, De Giusti, Laura Cristina, Naiouf, Marcelo, De Giusti, Armando Eduardo
Formato:	Articulo
Lenguaje:	Inglés
Publicado:	2012
Materias:	Ciencias Informáticas Cluster of multicores communication models Parallel programming languages Pipeline computing Smith-Waterman
Acceso en línea:	http://sedici.unlp.edu.ar/handle/10915/80063
Aporte de:	SEDICI (UNLP) de Universidad Nacional de La Plata

id	I19-R120-10915-80063
record_format	dspace
institution	Universidad Nacional de La Plata
institution_str	I-19
repository_str	R-120
collection	SEDICI (UNLP)
language	Inglés
topic	Ciencias Informáticas Cluster of multicores communication models Parallel programming languages Pipeline computing Smith-Waterman
spellingShingle	Ciencias Informáticas Cluster of multicores communication models Parallel programming languages Pipeline computing Smith-Waterman Rucci, Enzo Chichizola, Franco De Giusti, Laura Cristina Naiouf, Marcelo De Giusti, Armando Eduardo Parallel Pipelines for DNA Sequence Alignment on a Cluster of Multicores: A Comparison of Communication Models
topic_facet	Ciencias Informáticas Cluster of multicores communication models Parallel programming languages Pipeline computing Smith-Waterman
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.
format	Articulo Articulo
author	Rucci, Enzo Chichizola, Franco De Giusti, Laura Cristina Naiouf, Marcelo De Giusti, Armando Eduardo
author_facet	Rucci, Enzo Chichizola, Franco De Giusti, Laura Cristina Naiouf, Marcelo De Giusti, Armando Eduardo
author_sort	Rucci, Enzo
title	Parallel Pipelines for DNA Sequence Alignment on a Cluster of Multicores: A Comparison of Communication Models
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
publishDate	2012
url	http://sedici.unlp.edu.ar/handle/10915/80063
work_keys_str_mv	AT ruccienzo parallelpipelinesfordnasequencealignmentonaclusterofmulticoresacomparisonofcommunicationmodels AT chichizolafranco parallelpipelinesfordnasequencealignmentonaclusterofmulticoresacomparisonofcommunicationmodels AT degiustilauracristina parallelpipelinesfordnasequencealignmentonaclusterofmulticoresacomparisonofcommunicationmodels AT naioufmarcelo parallelpipelinesfordnasequencealignmentonaclusterofmulticoresacomparisonofcommunicationmodels AT degiustiarmandoeduardo parallelpipelinesfordnasequencealignmentonaclusterofmulticoresacomparisonofcommunicationmodels
bdutipo_str	Repositorios
_version_	1764820487541620736

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

Ejemplares similares