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GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem.

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GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem.

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dc.contributor.author Mena, Andres es_ES
dc.contributor.author Ferrero De Loma-Osorio, José María es_ES
dc.contributor.author Rodriguez Matas, Jose Felix es_ES
dc.date.accessioned 2016-10-11T06:57:29Z
dc.date.available 2016-10-11T06:57:29Z
dc.date.issued 2015-11
dc.identifier.issn 0010-4655
dc.identifier.uri http://hdl.handle.net/10251/71588
dc.description.abstract Solving the electric activity of the heart possess a big challenge, not only because of the structural complexities inherent to the heart tissue, but also because of the complex electric behaviour of the cardiac cells. The multi-scale nature of the electrophysiology problem makes difficult its numerical solution, requiring temporal and spatial resolutions of 0.1 ms and 0.2 mm respectively for accurate simulations, leading to models with millions degrees of freedom that need to be solved for thousand time steps. Solution of this problem requires the use of algorithms with higher level of parallelism in multi-core platforms. In this regard the newer programmable graphic processing units (GPU) has become a valid alternative due to their tremendous computational horsepower. This paper presents results obtained with a novel electrophysiology simulation software entirely developed in Compute Unified Device Architecture (CUDA). The software implements fully explicit and semi-implicit solvers for the monodomain model, using operator splitting. Performance is compared with classical multi-core MPI based solvers operating on dedicated high-performance computer clusters. Results obtained with the GPU based solver show enormous potential for this technology with accelerations over 50× for three-dimensional problems. es_ES
dc.description.sponsorship This project was partially supported by the "VI Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica" from the Ministerio de Economia y Competitividad of Spain (grant numbers TIN2012-37546-C03-01 and TIN2012-37546-C03-03) and the European Commission (European Regional Development Funds - ERDF - FEDER). We also thanks Dr Gunnar Seemann at the Karlsruhe Institute of Technology for providing the tetrahedral model of the human atria. en_EN
dc.language Inglés es_ES
dc.publisher Elsevier es_ES
dc.relation Ministerio de Economia y Competitividad of Spain TIN2012-37546-C03-01 TIN2012-37546-C03-03 es_ES
dc.relation European Commission es_ES
dc.relation.ispartof Computer Physics Communications es_ES
dc.rights Reserva de todos los derechos es_ES
dc.subject GPU es_ES
dc.subject Solver es_ES
dc.subject Reaction-diffusion equations es_ES
dc.subject Computational modelling es_ES
dc.subject Cardiac electrophysiology es_ES
dc.subject.classification TECNOLOGIA ELECTRONICA es_ES
dc.title GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem. es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1016/j.cpc.2015.06.018
dc.rights.accessRights Cerrado es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Interuniversitario de Investigación en Bioingeniería y Tecnología Orientada al Ser Humano - Institut Interuniversitari d'Investigació en Bioenginyeria i Tecnologia Orientada a l'Ésser Humà es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ingeniería Electrónica - Departament d'Enginyeria Electrònica es_ES
dc.description.bibliographicCitation Mena, A.; Ferrero De Loma-Osorio, JM.; Rodriguez Matas, JF. (2015). GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem. Computer Physics Communications. 196:280-289. doi:10.1016/j.cpc.2015.06.018 es_ES
dc.description.accrualMethod Senia es_ES
dc.relation.publisherversion http://dx.doi.org/10.1016/j.cpc.2015.06.018 es_ES
dc.description.upvformatpinicio 280 es_ES
dc.description.upvformatpfin 289 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 196 es_ES
dc.relation.senia 292133 es_ES
dc.identifier.eissn 1879-2944


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