SC is the International Conference for
 High Performnance Computing, Networking, Storage and Analysis

SCHEDULE: NOV 13-19, 2010

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

SESSION: GPGPU Performance


TIME: 2:30PM - 3:00PM

SESSION CHAIR: Gerhard Wellein

AUTHOR(S):Scott Hampton, Sadaf Alam, Paul Crozier, Pratul Agarwal


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.

Chair/Author Details:

Gerhard Wellein (Chair) - Erlangen Regional Computing Center

Scott Hampton - Oak Ridge National Laboratory

Sadaf Alam - Swiss National Supercomputing Centre

Paul Crozier - Sandia National Laboratories

Pratul Agarwal - Oak Ridge National Laboratory

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The full paper can be found in the ACM Digital Library and IEEE Computer Society

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