دورية أكاديمية
Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors
| العنوان: | Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors |
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| المؤلفون: | Aliaga, Jose I., Alonso Jordá, Pedro, Badía Contelles, José Manuel, Chacon, Pablo, Davidovic, Davo, Lopez-Blanco, Jose R., Quintana-Orti, Enrique S |
| المساهمون: | Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació, Universitat Politècnica de València. Escola Tècnica Superior d'Enginyeria Informàtica, Ministerio de Economía y Competitividad, Universitat Jaume I, Fundació Caixa Castelló - Bancaixa |
| بيانات النشر: | Elsevier |
| سنة النشر: | 2016 |
| المجموعة: | Universitat Politécnica de Valencia: RiuNet / Politechnical University of Valencia |
| مصطلحات موضوعية: | Computational biology, Macromolecular machines, Eigenvalue problems, Krylov subspace methods, Multicore processors, Graphics processors, CIENCIAS DE LA COMPUTACION E INTELIGENCIA ARTIFICIAL, LENGUAJES Y SISTEMAS INFORMATICOS |
| الوصف: | 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. ; 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. ; 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. https://doi.org/10.1016/j.jcp.2016.01.007Test ; S ; 314 ; 323 ; 309 |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| تدمد: | 0021-9991 |
| العلاقة: | Journal of Computational Physics; info:eu-repo/grantAgreement/MINECO//TIN2014-53495-R/ES/COMPUTACION HETEROGENEA DE BAJO CONSUMO/; info:eu-repo/grantAgreement/UJI//P1·1B2013-20/; info:eu-repo/grantAgreement/MINECO//TIN2011-23283/ES/POWER-AWARE HIGH PERFORMANCE COMPUTING/; http://dx.doi.org/10.1016/j.jcp.2016.01.007Test; urn:issn:0021-9991; http://hdl.handle.net/10251/82822Test |
| DOI: | 10.1016/j.jcp.2016.01.007 |
| الإتاحة: | https://doi.org/10.1016/j.jcp.2016.01.007Test http://hdl.handle.net/10251/82822Test |
| حقوق: | http://rightsstatements.org/vocab/InC/1.0Test/ ; info:eu-repo/semantics/closedAccess |
| رقم الانضمام: | edsbas.76C174D9 |
| قاعدة البيانات: | BASE |
| تدمد: | 00219991 |
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| DOI: | 10.1016/j.jcp.2016.01.007 |