Cargando…
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...
Autores principales: | , , , |
---|---|
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 |
_version_ | 1783623422920622080 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7739916 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT kotsaloschristos digitalbloodinmassivelyparallelcpugpusystemsforthestudyofplatelettransport AT lattjonas digitalbloodinmassivelyparallelcpugpusystemsforthestudyofplatelettransport AT benyjoel digitalbloodinmassivelyparallelcpugpusystemsforthestudyofplatelettransport AT chopardbastien digitalbloodinmassivelyparallelcpugpusystemsforthestudyofplatelettransport |