Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
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Multi-core processors introduce many challenges both at the systemand 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 inthe context of two scalable, production-level molecular dynamics simulationframeworks. Experimental analysis and observations in this paper provide for abetter understanding of the interactions between the application and the underlyingsystem features such as memory bandwidth, architectural optimization,and communication library implementation. In particular, we observe that parallelefficiencies could be as low as 50% on quad-core systems while a set ofdual-core processors connected with a high speed interconnect can easily outperformthe same number of cores on a socket or in a package. This indicates thatcertain modifications to the software stack and application implementations arenecessary in order to fully exploit the performance of multi-core based systems.