Abstract
This article discusses the implementation of a hybrid algorithm for the parallelization of molecular-dynamics simulations. The hybrid algorithm combines the spatial decomposition method using message passing with a task-based, threaded approach for the parallelization of the workload. Benchmark simulations on a multi-core system and an Intel Xeon Phi co-processor show that the hybrid algorithm provides better performances than the message-passing or threaded approaches alone.
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Acknowledgements
This work has been made possible by generous allocation of computer time on computer systems managed by Calcul Québec, the Shared Hierarchical Academic Research Network (SHARCNET) and Compute/Calcul Canada. Financial support by Laurentian University and the Natural Sciences and Engineering Research Council of Canada (NSERC) is gratefully acknowledged.
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Mangiardi, C.M., Meyer, R. (2016). Molecular-Dynamics Simulations Using Spatial Decomposition and Task-Based Parallelism. In: Bélair, J., Frigaard, I., Kunze, H., Makarov, R., Melnik, R., Spiteri, R. (eds) Mathematical and Computational Approaches in Advancing Modern Science and Engineering. Springer, Cham. https://doi.org/10.1007/978-3-319-30379-6_13
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DOI: https://doi.org/10.1007/978-3-319-30379-6_13
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