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P-Aevol: an OpenMP Parallelization of a Biological Evolution Simulator, Through Decomposition in Multiple Loops

Laurent Turpin 1, 2 Jonathan Rouzaud-Cornabas 3, 1, 4 Thierry Gautier 2 Christian Pérez 2
1 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
2 AVALON - Algorithms and Software Architectures for Distributed and HPC Platforms
Inria Grenoble - Rhône-Alpes, LIP - Laboratoire de l'Informatique du Parallélisme
Abstract : This paper presents how we have achieved the parallelization of Aevol, a biological evolution simulator, on multi-core architecture using the OpenMP standard. While it looks like a simple for-loop problem with independent iterations, the stochastic nature of Aevol makes the duration of the iterations unpredictable and it conveys a high irregularity. Classical scheduling algorithms of OpenMP runtimes turn out to be inecient. By analysing the origin of this irregularity, this paper present how to transform the highly irregular Aevol for-loop to a sequence composed by a small duration irregular for-loop followed by work intensive for-loop easy to schedule using classical LPT algorithm. This method leads to a gain up to 27% from the best OpenMP loop schedule.
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https://hal.inria.fr/hal-02962838
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Submitted on : Friday, October 9, 2020 - 3:11:12 PM
Last modification on : Saturday, September 11, 2021 - 3:18:29 AM
Long-term archiving on: : Sunday, January 10, 2021 - 6:47:14 PM

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Laurent Turpin, Jonathan Rouzaud-Cornabas, Thierry Gautier, Christian Pérez. P-Aevol: an OpenMP Parallelization of a Biological Evolution Simulator, Through Decomposition in Multiple Loops. 16th International Workshop on OpenMP, Sep 2020, Austin, United States. pp.52-66, ⟨10.1007/978-3-030-58144-2_4⟩. ⟨hal-02962838⟩

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