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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. (2016) Fast band-Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors. Journal of computational physics, 309 . pp. 314-323. ISSN 0021-9991

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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.

Item Type: Article
Uncontrolled Keywords: Computational biology; macromolecular machines; eigenvalue problems; Krylov subspace methods; multicore processors; graphics processors
Subjects: NATURAL SCIENCES > Biology > Biochemistry and Molecular Biology
TECHNICAL SCIENCES > Computing
TECHNICAL SCIENCES > Computing > Process Computing
Divisions: Center for Informatics and Computing
Depositing User: Davor Davidović
Date Deposited: 19 Jan 2016 15:52
Last Modified: 16 Mar 2018 00:15
URI: http://fulir.irb.hr/id/eprint/2406
DOI: 10.1016/j.jcp.2016.01.007

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