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Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors

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Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors

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dc.contributor.author Aliaga, Jose I. es_ES
dc.contributor.author Alonso Jordá, Pedro es_ES
dc.contributor.author Badía Contelles, José Manuel es_ES
dc.contributor.author Chacon, Pablo es_ES
dc.contributor.author Davidovic, Davo es_ES
dc.contributor.author Lopez-Blanco, Jose R. es_ES
dc.contributor.author Quintana-Orti, Enrique S es_ES
dc.date.accessioned 2017-06-14T08:17:25Z
dc.date.available 2017-06-14T08:17:25Z
dc.date.issued 2016-03-15
dc.identifier.issn 0021-9991
dc.identifier.uri http://hdl.handle.net/10251/82822
dc.description.abstract We introduce a new iterative Krylov subspace-based eigensolver for the simulation of macromolecular motions on desktop multithreaded platforms equipped with multicore processors and, possibly, a graphics accelerator (GPU). The method consists of two stages, with the original problem first reduced into a simpler band-structured form by means of a high-performance compute-intensive procedure. This is followed by a memory-intensive but low-cost Krylov iteration, which is off-loaded to be computed on the GPU by means of an efficient data-parallel kernel. The experimental results reveal the performance of the new eigensolver. Concretely, when applied to the simulation of macromolecules with a few thousands degrees of freedom and the number of eigenpairs to be computed is small to moderate, the new solver outperforms other methods implemented as part of high-performance numerical linear algebra packages for multithreaded architectures. © 2016 Elsevier Inc. All rights reserved. es_ES
dc.description.sponsorship This work was supported by the CICYT projects TIN2011-23283 and TIN2014-53495-R of the MINECO and FEDER, and project P1-1B2013-20 of the Fundacio Caixa Castello-Bancaixa and UJI. en_EN
dc.language Inglés es_ES
dc.publisher Elsevier es_ES
dc.relation MINECO & FEDER/ CICYT/ TIN2011-23283 and TIN2014-53495-R es_ES
dc.relation Fundacio Caixa Castello-Bancaixa and UJI/ P1-1B2013-20 es_ES
dc.relation.ispartof Journal of Computational Physics es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject Computational biology es_ES
dc.subject Macromolecular machines es_ES
dc.subject Eigenvalue problems es_ES
dc.subject Krylov subspace methods es_ES
dc.subject Multicore processors es_ES
dc.subject Graphics processors es_ES
dc.subject.classification CIENCIAS DE LA COMPUTACION E INTELIGENCIA ARTIFICIAL es_ES
dc.subject.classification LENGUAJES Y SISTEMAS INFORMATICOS es_ES
dc.title Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1016/j.jcp.2016.01.007
dc.rights.accessRights Cerrado es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació es_ES
dc.contributor.affiliation Universitat Politècnica de València. Escola Tècnica Superior d'Enginyeria Informàtica es_ES
dc.description.bibliographicCitation Aliaga, JI.; Alonso Jordá, P.; Badía Contelles, JM.; Chacon, P.; Davidovic, D.; Lopez-Blanco, JR.; Quintana-Orti, ES. (2016). Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors. Journal of Computational Physics. 309:314-323. doi:10.1016/j.jcp.2016.01.007 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1016/j.jcp.2016.01.007 es_ES
dc.description.upvformatpinicio 314 es_ES
dc.description.upvformatpfin 323 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 309 es_ES
dc.relation.senia 298898 es_ES


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