Performance analysis and qualitative results of an efficient parallel stochastic simulator for a marine host-parasite system

Michel Langlais (1) , Guillaume Latu (2) , Jean Roman (3) , Patrick Silan (4)

1 IMB - Institut de Mathématiques de Bordeaux
2 IRFM - Institut de Recherche sur la Fusion par confinement Magnétique
3 HiePACS - High-End Parallel Algorithms for Challenging Numerical Simulations
4 MIO - Institut méditerranéen d'océanologie

We are interested in a host-parasite system, i.e. the sea bass-Diplectanum aequans system. A discrete mathematical model is used to describe the dynamics of both populations. Our goal is notably to validate the model in the context of aquaculture. A deterministic numerical simulator and, recently, a stochastic simulator were developed to study this biological system. Parallelization is required because the execution times are too long. The Monte Carlo algorithm of the stochastic simulator and its three levels of parallelism are described. Analysis and performances, up to 256 processors, of a hybrid MPI/OpenMP code are then presented for a cluster of symmetric multi-processor (SMP) nodes. Qualitative results are given for the host-macroparasite system simulation.

Mots clés: Fish; Dicentrachus labrax; Monogenea; parallel algorithmics; numerical simulation; stochastic simulation; host-parasite system; Population dynamics

Domaines: Modélisation et simulation; Parasitologie; Interactions entre organismes; Mathématique discrète [cs.DM]; Calcul parallèle, distribué et partagé [cs.DC]; Algorithme et structure de données [cs.DS]; Médecine vétérinaire et santé animale

Michel Langlais, Guillaume Latu, Jean Roman, Patrick Silan. Performance analysis and qualitative results of an efficient parallel stochastic simulator for a marine host-parasite system. Concurrency and Computation: Practice and Experience, 2003, 15 (11-12), pp.1133-1150. ⟨10.1002/cpe.784⟩. ⟨hal-01336781⟩