Parallel performance analysis of bacterial biofilm simulation models
Modelling and simulation of bacterial biofilms is a computationally expen-sive process necessitating use of parallel computing. Fluid dynamics and ad-vection-consumption models can be decoupled and solved to handle the flu-id-solute-bacterial interactions. Data exchange between the two processes add...
| Main Authors: | , |
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| Other Authors: | |
| Format: | Conference Paper |
| Language: | English |
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2019
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| Online Access: | https://hdl.handle.net/10356/88884 http://hdl.handle.net/10220/49205 |
| _version_ | 1811685103450980352 |
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| author | Sheraton, Muniraj Vivek Sloot, Peter M. A. |
| author2 | International Conference On Computational Science (ICCS 2018) |
| author_facet | International Conference On Computational Science (ICCS 2018) Sheraton, Muniraj Vivek Sloot, Peter M. A. |
| author_sort | Sheraton, Muniraj Vivek |
| collection | NTU |
| description | Modelling and simulation of bacterial biofilms is a computationally expen-sive process necessitating use of parallel computing. Fluid dynamics and ad-vection-consumption models can be decoupled and solved to handle the flu-id-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 dis-tribution in the parallel system. We study the effect of load imbalance and communication overheads on the overall performance of simulation at dif-ferent stages of biofilm growth. We develop a model to optimize the parallel-ization procedure for computing the growth dynamics of bacterial biofilms. |
| first_indexed | 2024-10-01T04:39:12Z |
| format | Conference Paper |
| id | ntu-10356/88884 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:39:12Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | ntu-10356/888842020-11-01T04:43:21Z Parallel performance analysis of bacterial biofilm simulation models Sheraton, Muniraj Vivek Sloot, Peter M. A. International Conference On Computational Science (ICCS 2018) HealthTech NTU Complexity Institute DRNTU::Science::Chemistry Load Imbalance Communication Overhead Modelling and simulation of bacterial biofilms is a computationally expen-sive process necessitating use of parallel computing. Fluid dynamics and ad-vection-consumption models can be decoupled and solved to handle the flu-id-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 dis-tribution in the parallel system. We study the effect of load imbalance and communication overheads on the overall performance of simulation at dif-ferent stages of biofilm growth. We develop a model to optimize the parallel-ization procedure for computing the growth dynamics of bacterial biofilms. Accepted version 2019-07-09T05:30:12Z 2019-12-06T17:13:03Z 2019-07-09T05:30:12Z 2019-12-06T17:13:03Z 2018 Conference Paper Sheraton, M. V., & Sloot, P. M. A. (2018). Parallel performance analysis of bacterial biofilm simulation models. International Conference On Computational Science (ICCS 2018). doi:10.1007/978-3-319-93698-7_38 https://hdl.handle.net/10356/88884 http://hdl.handle.net/10220/49205 10.1007/978-3-319-93698-7_38 en © 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. The published version is available at: https://doi.org/10.1007/978-3-319-93698-7_38 11 p. application/pdf |
| spellingShingle | DRNTU::Science::Chemistry Load Imbalance Communication Overhead Sheraton, Muniraj Vivek Sloot, Peter M. A. Parallel performance analysis of bacterial biofilm simulation models |
| title | Parallel performance analysis of bacterial biofilm simulation models |
| title_full | Parallel performance analysis of bacterial biofilm simulation models |
| title_fullStr | Parallel performance analysis of bacterial biofilm simulation models |
| title_full_unstemmed | Parallel performance analysis of bacterial biofilm simulation models |
| title_short | Parallel performance analysis of bacterial biofilm simulation models |
| title_sort | parallel performance analysis of bacterial biofilm simulation models |
| topic | DRNTU::Science::Chemistry Load Imbalance Communication Overhead |
| url | https://hdl.handle.net/10356/88884 http://hdl.handle.net/10220/49205 |
| work_keys_str_mv | AT sheratonmunirajvivek parallelperformanceanalysisofbacterialbiofilmsimulationmodels AT slootpeterma parallelperformanceanalysisofbacterialbiofilmsimulationmodels |