Experimental Evaluation of Molecular Dynamics Simulations on Multi-core Systems

SR Alam and PK Agarwal and SS Hampton and H Ong, High Performance Computing - HiPC 2008, Proceedings, 5374, 131-141 (2008).

DOI: 10.1007/978-3-540-89894-8_15

Multi-core processors introduce many challenges both at the system and application levels that need to be addressed in order to attain the best performance. In this paper, we study the impact of the multi-core technologies in the context of two scalable, production-level molecular dynamics simulation frameworks. Experimental analysis and observations in this paper provide for a better understanding of the interactions between the application and the underlying system features such as memory bandwidth, architectural optimization. and communication library implementation. In particular, we observe that parallel efficiencies could be as low as 50% on quad-core systems while a set of dual-core processors connected with a high speed interconnect can easily outperform the same number of cores on a socket or in a package. This indicates that certain modifications to the software stack and application implementations are necessary in order to fully exploit the performance of multi-core based systems.

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