NDLI: Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Content Provider	IEEE Xplore Digital Library
Author	Hampton, S.S. Alam, S.R. Crozier, P.S. Agarwal, P.K.
Copyright Year	2010
Abstract	Biomolecular simulations have traditionally benefited from increases in the processor clock speed and coarse-grain inter-node parallelism on large-scale clusters. With stagnating clock frequencies, the evolutionary path for performance of microprocessors is maintained by virtue of core multiplication. Graphical processing units (GPUs) offer revolutionary performance potential at the cost of increased programming complexity. Furthermore, it has been extremely challenging to effectively utilize heterogeneous resources (host processor and GPU cores) for scientific simulations, as underlying systems, programming models and tools are continually evolving. In this paper, we present a parametric study demonstrating approaches to exploit resources of heterogeneous systems to reduce time-to-solution of a production-level application for biological simulations. By overlapping and pipelining computation and communication, we observe up to 10-fold application acceleration in multi-core and multi-GPU environments illustrating significant performance improvements over code acceleration approaches, where the host-to-accelerator ratio is static, and is constrained by a given algorithmic implementation.
Starting Page	1
Ending Page	11
File Size	1750852
Page Count	11
File Format	PDF
ISBN	9781424475575
e-ISBN	9781424475599
e-ISBN	9781424475582
DOI	10.1109/SC.2010.37
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-11-13
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Graphics processing unit Biological system modeling Computational modeling Programming Performance evaluation Kernel Acceleration
Content Type	Text
Resource Type	Article

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