OpenMP parallelization of a mickens time-integration scheme for a mixed-culture biofilm model and its performance on multi-core and multi-processor computers

Authors:
Nasim Muhammad;Hermann J. Eberl
Affiliations:
Dept. of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada;Dept. of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada
Venue:
HPCS'09 Proceedings of the 23rd international conference on High Performance Computing Systems and Applications
Year:
2009

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Abstract

We document and compare the performance of an OpenMP parallelized simulation code for a mixed-culture biofilm model on a desktop workstation with two quad core Xeon processors, and on SGI Altix Systems with single core and dual core Itanium processors. The underlying model is a parabolic system of highly non-linear partial differential equations, which is discretized in time using a non-local Mickens scheme, and in space using a standard finite difference method.