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Pregled bibliografske jedinice broj: 793409

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

Aliaga, José I.; Alonso, Pedro; Badía, José M.; Chacón, Pablo; Davidović, Davor; López-Blanco, José R.; Quintana-Ortí, Enrique S.
Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors // Journal of computational physics, 309 (2016), 314-323 doi:10.1016/j.jcp.2016.01.007 (međunarodna recenzija, članak, znanstveni)

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

Autori
Aliaga, José I. ; Alonso, Pedro ; Badía, José M. ; Chacón, Pablo ; Davidović, Davor ; López-Blanco, José R. ; Quintana-Ortí, Enrique S.

Izvornik
Journal of computational physics (0021-9991) 309 (2016); 314-323

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Computational biology; macromolecular machines; eigenvalue problems; Krylov subspace methods; multicore processors; graphics processors

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Matematika, Kemija, Računarstvo



POVEZANOST RADA

Ustanove:
Institut "Ruđer Bošković", Zagreb

Profili:

Avatar Url Davor Davidović (autor)

Poveznice na cjeloviti tekst rada:

doi fulir.irb.hr www.sciencedirect.com dx.doi.org

Citiraj ovu publikaciju:

Aliaga, José I.; Alonso, Pedro; Badía, José M.; Chacón, Pablo; Davidović, Davor; López-Blanco, José R.; Quintana-Ortí, Enrique S.
Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors // Journal of computational physics, 309 (2016), 314-323 doi:10.1016/j.jcp.2016.01.007 (međunarodna recenzija, članak, znanstveni)
Aliaga, J., Alonso, P., Badía, J., Chacón, P., Davidović, D., López-Blanco, J. & Quintana-Ortí, E. (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.
@article{article, author = {Aliaga, Jos\'{e} I. and Alonso, Pedro and Bad\'{\i}a, Jos\'{e} M. and Chac\'{o}n, Pablo and Davidovi\'{c}, Davor and L\'{o}pez-Blanco, Jos\'{e} R. and Quintana-Ort\'{\i}, Enrique S.}, year = {2016}, pages = {314-323}, DOI = {10.1016/j.jcp.2016.01.007}, keywords = {Computational biology, macromolecular machines, eigenvalue problems, Krylov subspace methods, multicore processors, graphics processors}, journal = {Journal of computational physics}, doi = {10.1016/j.jcp.2016.01.007}, volume = {309}, issn = {0021-9991}, title = {Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors}, keyword = {Computational biology, macromolecular machines, eigenvalue problems, Krylov subspace methods, multicore processors, graphics processors} }
@article{article, author = {Aliaga, Jos\'{e} I. and Alonso, Pedro and Bad\'{\i}a, Jos\'{e} M. and Chac\'{o}n, Pablo and Davidovi\'{c}, Davor and L\'{o}pez-Blanco, Jos\'{e} R. and Quintana-Ort\'{\i}, Enrique S.}, year = {2016}, pages = {314-323}, DOI = {10.1016/j.jcp.2016.01.007}, keywords = {Computational biology, macromolecular machines, eigenvalue problems, Krylov subspace methods, multicore processors, graphics processors}, journal = {Journal of computational physics}, doi = {10.1016/j.jcp.2016.01.007}, volume = {309}, issn = {0021-9991}, title = {Fast Band--Krylov Eigensolver for Macromolecular Functional Motion Simulation on Multicore Architectures and Graphics Processors}, keyword = {Computational biology, macromolecular machines, eigenvalue problems, Krylov subspace methods, multicore processors, graphics processors} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus

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