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Proceedings of the 3rd International Conference on Molecular Simulation

An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid

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Pages 801-807 | Received 30 Jan 2014, Accepted 07 May 2014, Published online: 03 Jul 2014
 

Abstract

A new implementation of molecular dynamics simulation is presented. We employed policy-based design to achieve static polymorphism within our simulation programs. This technique provides flexibility and extensibility without additional if-statement branching in the simulation program development. It is shown that policy-based implementation prevents computational performance degradation. We used a fine-grained domain decomposition scheme to parallelise the simulation program. The smaller size decomposition reduces the total amount of inter-processing-core communication and affords good scalability for parallel calculation of short-range forces. The calculation of long-range interactions limits the total scalability. For enhanced performance at high levels of parallelism, the calculation methods for long-range interactions should be improved.

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