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 |
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| 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 |
| URI: | http://fulir.irb.hr/id/eprint/2406 |
| DOI: | 10.1016/j.jcp.2016.01.007 |
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