A fast band–Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors
- Departamento de Sistemas Informáticos y Computación, Universitat Politècnica de València (Spain)
- Depto. Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón (Spain)
- Dept. Biological Chemical Physics, Rocasolano Physics and Chemistry Institute, CSIC, Madrid (Spain)
- Rudjer Bošković Institute, Centar za Informatiku i Računarstvo – CIR, Zagreb (Croatia)
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.
- OSTI ID:
- 22570235
- Journal Information:
- Journal of Computational Physics, Vol. 309; Other Information: Copyright (c) 2016 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9991
- Country of Publication:
- United States
- Language:
- English
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