Naslov
Out-of-Core Macromolecular Simulations on Multithreaded Architectures

Autori
Aliaga, Jose I. ; Badia. Jose ́M. ; Castillo, Maribel ; Davidović, Davor ; Mayo, Rafael ; Quintana-Orti, Enrique S.

Izvornik
Concurrency and computation (1532-0626) 27 (2015), 6; 1540-1550

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
macromolecular motion simulation; eigenvalue problems; out-of-core computing; multicore processors; GPUs

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Matematika, Kemija, Računarstvo

Napomena
Combined Special Issues on International conference on enabling technologies : Infrastructure for collaborative enterprises(WETICE) and Parallel computing on graphics processing units and heterogeneous platforms.

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