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A fast band-Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors

AuthorsAliaga, Jose I.; Alonso, P.; Badía, J.M.; Chacón, Pablo ; Davidović , D.; López-Blanco, José R.; Quintana-Ortí, Enrique S.
Issue Date2016
PublisherAcademic Press
CitationJournal of Computational Physics 309: 314- 323 (2016)
AbstractWe 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.
Identifiersdoi: 10.1016/j.jcp.2016.01.007
issn: 1090-2716
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