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

ABSTRACT: 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.

SUBMITTER: Kotsalos C

PROVIDER: S-EPMC7739916 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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

Kotsalos Christos C Latt Jonas J Beny Joel J Chopard Bastien B

Interface focus 20201211 1

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 in ...[more]

PMID: 33335703

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Dataset Information

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

Publications

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

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