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Digital blood in massively parallel CPU/GPU systems for the study of platelet transport

We propose a highly versatile computational framework for the simulation of cellular blood flow focusing on extreme performance without compromising accuracy or complexity. The tool couples the lattice Boltzmann solver Palabos for the simulation of blood plasma, a novel finite-element method (FEM) s...

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Detalles Bibliográficos
Autores principales: Kotsalos, Christos, Latt, Jonas, Beny, Joel, Chopard, Bastien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7739916/
https://www.ncbi.nlm.nih.gov/pubmed/33335703
http://dx.doi.org/10.1098/rsfs.2019.0116
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author Kotsalos, Christos
Latt, Jonas
Beny, Joel
Chopard, Bastien
author_facet Kotsalos, Christos
Latt, Jonas
Beny, Joel
Chopard, Bastien
author_sort Kotsalos, Christos
collection PubMed
description We propose a highly versatile computational framework for the simulation of cellular blood flow focusing on extreme performance without compromising accuracy or complexity. The tool couples the lattice Boltzmann solver Palabos for the simulation of blood plasma, a novel finite-element method (FEM) solver for the resolution of deformable blood cells, and an immersed boundary method for the coupling of the two phases. The design of the tool supports hybrid CPU–GPU executions (fluid, fluid–solid interaction on CPUs, deformable bodies on GPUs), and is non-intrusive, as each of the three components can be replaced in a modular way. The FEM-based kernel for solid dynamics outperforms other FEM solvers and its performance is comparable to state-of-the-art mass–spring systems. We perform an exhaustive performance analysis on Piz Daint at the Swiss National Supercomputing Centre and provide case studies focused on platelet transport, implicitly validating the accuracy of our tool. The tests show that this versatile framework combines unprecedented accuracy with massive performance, rendering it suitable for upcoming exascale architectures.
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spelling pubmed-77399162020-12-16 Digital blood in massively parallel CPU/GPU systems for the study of platelet transport Kotsalos, Christos Latt, Jonas Beny, Joel Chopard, Bastien Interface Focus Articles We propose a highly versatile computational framework for the simulation of cellular blood flow focusing on extreme performance without compromising accuracy or complexity. The tool couples the lattice Boltzmann solver Palabos for the simulation of blood plasma, a novel finite-element method (FEM) solver for the resolution of deformable blood cells, and an immersed boundary method for the coupling of the two phases. The design of the tool supports hybrid CPU–GPU executions (fluid, fluid–solid interaction on CPUs, deformable bodies on GPUs), and is non-intrusive, as each of the three components can be replaced in a modular way. The FEM-based kernel for solid dynamics outperforms other FEM solvers and its performance is comparable to state-of-the-art mass–spring systems. We perform an exhaustive performance analysis on Piz Daint at the Swiss National Supercomputing Centre and provide case studies focused on platelet transport, implicitly validating the accuracy of our tool. The tests show that this versatile framework combines unprecedented accuracy with massive performance, rendering it suitable for upcoming exascale architectures. The Royal Society 2021-02-06 2020-12-11 /pmc/articles/PMC7739916/ /pubmed/33335703 http://dx.doi.org/10.1098/rsfs.2019.0116 Text en © 2020 The Authors. http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/http://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Articles
Kotsalos, Christos
Latt, Jonas
Beny, Joel
Chopard, Bastien
Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
title Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
title_full Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
title_fullStr Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
title_full_unstemmed Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
title_short Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
title_sort digital blood in massively parallel cpu/gpu systems for the study of platelet transport
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7739916/
https://www.ncbi.nlm.nih.gov/pubmed/33335703
http://dx.doi.org/10.1098/rsfs.2019.0116
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