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Out-of-core macromolecular simulations on multithreaded architectures

Aliaga, José Ignacio; Badia, Jose M.; Castillo, Maribel; Davidović, Davor; Mayo, Rafael; Quintana-Ortí, Enrique S. (2015) Out-of-core macromolecular simulations on multithreaded architectures. Concurrency and Computation: Practice and Experience, 27 (6). pp. 1540-1550. ISSN 1532-0626

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Abstract

We address the solution of large-scale eigenvalue problems that appear in the motion simulation of complex macromolecules on multithreaded platforms, consisting of multicore processors and possibly a graphics processor (GPU). In particular, we compare specialized implementations of several high- performance eigensolvers that, by relying on disk storage and out-of-core (OOC) techniques, can in principle tackle the large memory requirements of these biological problems, which in general do not fit into the main memory of current desktop machines. All these OOC eigensolvers, except for one, are composed of compute-bound (i.e., arithmetically-intensive) operations, which we accelerate by exploiting the performance of current multicore processors and, in some cases, by additionally off-loading certain parts of the computation to a GPU accelerator. One of the eigensolvers is a memory-bound algorithm, which strongly constrains its performance when the data is on disk. However, this method exhibits a much lower arithmetic cost compared with its compute- bound alternatives for this particular application. Experimental results on a desktop platform, representative of current server technology, illustrate the potential of these methods to address the simulation of biological activity.

Item Type: Article
Additional Information: This is the peer reviewed version of the following article: Aliaga, J. I., Badía, J. M., Castillo, M., Davidović, D., Mayo, R. and Quintana-Ortí, E. S. (2015), Out-of-core macromolecular simulations on multithreaded architectures. Concurrency Computat.: Pract. Exper., 27: 1540–1550, which has been published in final form at http://dx.doi.org/10.1002/cpe.3357. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
Uncontrolled Keywords: Macromolecular motion simulation; eigenvalue problems; out-of-core computing; multicore processors; GPUs
Subjects: NATURAL SCIENCES > Mathematics > Algebra
NATURAL SCIENCES > Mathematics > Numerical Mathematics
NATURAL SCIENCES > Chemistry
TECHNICAL SCIENCES > Computing
Divisions: Center for Informatics and Computing
Depositing User: Davor Davidović
Date Deposited: 22 May 2015 15:25
Last Modified: 26 Apr 2016 23:15
URI: http://fulir.irb.hr/id/eprint/1964
DOI: 10.1002/cpe.3357

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