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. 2013 Oct 21;13:25. doi: 10.1186/1472-6807-13-25

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Copyright © 2013 Hoang et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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The hierarchical parallel structure of gEMpicker. At the top level of the hierarchy, the MPI parallel processing library is used to distribute the calculation over multiple processes on the nodes of a CPU or GPU cluster. On each node, the Boost.Thread library is used to synchronise multiple coarse-grained CPU threads which cooperate using the producer-consumer programming model. During the reduction step, fine-grained parallelisation using OpenMP is used to combine the process-level correlation maps from the CPU nodes, and the MPI_Reduce function is used to propagate the results in parallel towards the master node.