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Parallel Performance Analysis of Bacterial Biofilm Simulation Models

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10860)

Abstract

Modelling and simulation of bacterial biofilms is a computationally expensive process necessitating use of parallel computing. Fluid dynamics and advection-consumption models can be decoupled and solved to handle the fluid-solute-bacterial interactions. Data exchange between the two processes add up to the communication overheads. The heterogenous distribution of bacteria within the simulation domain further leads to non-uniform load distribution in the parallel system. We study the effect of load imbalance and communication overheads on the overall performance of simulation at different stages of biofilm growth. We develop a model to optimize the parallelization procedure for computing the growth dynamics of bacterial biofilms.

Keywords

Load imbalance Communication overhead Biofilm 

Notes

Acknowledgment

P.S. acknowledges the Russian Science Foundation for support under RSCF #14-21-00137.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Interdisciplinary Graduate SchoolHealthTech NTU, Nanyang Technological UniversitySingaporeSingapore
  2. 2.Complexity InstituteNanyang Technological UniversitySingaporeSingapore
  3. 3.Institute for Advanced StudiesUniversity of AmsterdamAmsterdamNetherlands
  4. 4.National Research University ITMOSt. PetersburgRussia

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