Out-of-core macromolecular simulations on multithreaded architectures
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comunitat-uji-handle2:10234/7036
comunitat-uji-handle3:10234/8620
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http://dx.doi.org/10.1002/cpe.3357 |
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Title
Out-of-core macromolecular simulations on multithreaded architecturesAuthor (s)
Date
2015Publisher
WileyISSN
1532-0626; 1532-0634Type
info:eu-repo/semantics/articlePublisher version
http://onlinelibrary.wiley.com/doi/10.1002/cpe.3357/abstractSubject
Abstract
We address the solution of large-scale eigenvalue problems that appear in the motion simulation o f com-
plex macromolecules on multithreaded platforms, consisting of multicore processors and possibly a graphics
p ... [+]
We address the solution of large-scale eigenvalue problems that appear in the motion simulation o f com-
plex macromolecules on multithreaded platforms, consisting of multicore processors and possibly a graphics
processor (graphics processing unit). In particular, we compare specialized implementations of several high-
performance eigensolvers that, by relying on disk storage and out-of-core 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 out-of-core 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 computa-
tion to a graphics processing unit 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. [-]
Is part of
Concurrency and Computation: Practice and Experience, 2015, vol. 27, núm. 6Rights
Published online in Wiley Online Library (wileyonlinelibrary.com).
Copyright © 2014 John Wiley & Sons, Ltd.
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