MASA: a multi-platform architecture for sequence aligners with block pruning

Biological sequence alignment is a very popular application in Bioinformatics used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These implementations are platform-specific and porting them to other s...

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Detalles Bibliográficos
Autores: De Sandes, Edans, Miranda, Guillermo, Martorell, Xavier, Ayguadé Parra, Eduard|||0000-0002-5146-103X, Teodoro, George, de Melo, Alba
Tipo de recurso: artículo
Fecha de publicación:2016
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/99739
Acceso en línea:https://hdl.handle.net/2117/99739
https://dx.doi.org/10.1145/2858656
Access Level:acceso abierto
Palabra clave:Parallel programming (Computer science)
Biological Sequence Alignment
Parallel Algorithms
GPU
multicores
Intel Phi
Programació en paral·lel (Informàtica)
Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·leles
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spelling MASA: a multi-platform architecture for sequence aligners with block pruningDe Sandes, EdansMiranda, GuillermoMartorell, XavierAyguadé Parra, Eduard|||0000-0002-5146-103XTeodoro, Georgede Melo, AlbaParallel programming (Computer science)Biological Sequence AlignmentParallel AlgorithmsGPUmulticoresIntel PhiProgramació en paral·lel (Informàtica)Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·lelesBiological sequence alignment is a very popular application in Bioinformatics used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These implementations are platform-specific and porting them to other systems requires considerable programming effort. This paper proposes and evaluates MASA, a flexible and customizable software architecture that enables the execution of biological sequence alignment applications with three variants (local, global and semi-global) in multiple hardware/software platforms with block pruning, which is able to reduce significantly the amount of data processed. To attain our flexibility goals, we also propose a generic version of block pruning and developed multiple parallelization strategies as building blocks, including a new asynchronous dataflow based parallelization, which may be combined to implement efficient aligners in different platforms.We provide four MASA aligner implementations for multicores (OmpSs and OpenMP), GPU (CUDA) and Intel Phi (OpenMP), showing that MASA is very flexible. The evaluation of our generic block pruning strategy shows that it significantly outperforms the previously proposed block pruning, being able to prune up to 66.5% of the cells when using the new dataflow based parallelization strategy.Peer Reviewed20162016-03-0120172017-01-20journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/99739https://dx.doi.org/10.1145/2858656reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/997392026-05-27T15:37:01Z
dc.title.none.fl_str_mv MASA: a multi-platform architecture for sequence aligners with block pruning
title MASA: a multi-platform architecture for sequence aligners with block pruning
spellingShingle MASA: a multi-platform architecture for sequence aligners with block pruning
De Sandes, Edans
Parallel programming (Computer science)
Biological Sequence Alignment
Parallel Algorithms
GPU
multicores
Intel Phi
Programació en paral·lel (Informàtica)
Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·leles
title_short MASA: a multi-platform architecture for sequence aligners with block pruning
title_full MASA: a multi-platform architecture for sequence aligners with block pruning
title_fullStr MASA: a multi-platform architecture for sequence aligners with block pruning
title_full_unstemmed MASA: a multi-platform architecture for sequence aligners with block pruning
title_sort MASA: a multi-platform architecture for sequence aligners with block pruning
dc.creator.none.fl_str_mv De Sandes, Edans
Miranda, Guillermo
Martorell, Xavier
Ayguadé Parra, Eduard|||0000-0002-5146-103X
Teodoro, George
de Melo, Alba
author De Sandes, Edans
author_facet De Sandes, Edans
Miranda, Guillermo
Martorell, Xavier
Ayguadé Parra, Eduard|||0000-0002-5146-103X
Teodoro, George
de Melo, Alba
author_role author
author2 Miranda, Guillermo
Martorell, Xavier
Ayguadé Parra, Eduard|||0000-0002-5146-103X
Teodoro, George
de Melo, Alba
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Parallel programming (Computer science)
Biological Sequence Alignment
Parallel Algorithms
GPU
multicores
Intel Phi
Programació en paral·lel (Informàtica)
Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·leles
topic Parallel programming (Computer science)
Biological Sequence Alignment
Parallel Algorithms
GPU
multicores
Intel Phi
Programació en paral·lel (Informàtica)
Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors::Arquitectures paral·leles
description Biological sequence alignment is a very popular application in Bioinformatics used routinely worldwide. Many implementations of biological sequence alignment algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These implementations are platform-specific and porting them to other systems requires considerable programming effort. This paper proposes and evaluates MASA, a flexible and customizable software architecture that enables the execution of biological sequence alignment applications with three variants (local, global and semi-global) in multiple hardware/software platforms with block pruning, which is able to reduce significantly the amount of data processed. To attain our flexibility goals, we also propose a generic version of block pruning and developed multiple parallelization strategies as building blocks, including a new asynchronous dataflow based parallelization, which may be combined to implement efficient aligners in different platforms.We provide four MASA aligner implementations for multicores (OmpSs and OpenMP), GPU (CUDA) and Intel Phi (OpenMP), showing that MASA is very flexible. The evaluation of our generic block pruning strategy shows that it significantly outperforms the previously proposed block pruning, being able to prune up to 66.5% of the cells when using the new dataflow based parallelization strategy.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016-03-01
2017
2017-01-20
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/99739
https://dx.doi.org/10.1145/2858656
url https://hdl.handle.net/2117/99739
https://dx.doi.org/10.1145/2858656
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,301629

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