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Development and performance of a HemeLB GPU code for human-scale blood flow simulation



Zacharoudiou, I;

McCullough, JWS;

Coveney, PV;

(2023)

Development and performance of a HemeLB GPU code for human-scale blood flow simulation.

Computer Physics Communications
, 282


, Article 108548. 10.1016/j.cpc.2022.108548.

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    Abstract

    In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture – typically in the form of GPU accelerators. In some machines these are isolated within a dedicated partition, whilst in others they are integral to all compute nodes – often with multiple GPUs per node – and provide the majority of a machine’s compute performance. In light of this trend, it is becoming essential that codes deployed on HPC are updated to execute on accelerator hardware. In this paper we introduce a GPU implementation of the 3D blood flow simulation code HemeLB that has been developed using CUDA C++. We demonstrate how taking advantage of NVIDIA GPU hardware can achieve significant performance improvements compared to the equivalent CPU only code on which it has been built whilst retaining the excellent strong scaling characteristics that have been repeatedly demonstrated by the CPU version. With HPC positioned on the brink of the exascale era, we use HemeLB as a motivation to provide a discussion on some of the challenges that many users will face when deploying their own applications on upcoming exascale machines.

    Type: Article

    Title: Development and performance of a HemeLB GPU code for human-scale blood flow simulation
    Open access status: An open access version is available from UCL Discovery
    DOI: 10.1016/j.cpc.2022.108548
    Publisher version: https://doi.org/10.1016/j.cpc.2022.108548
    Language: English
    Additional information: This work is licensed under a Creative Commons Attribution 4.0 International License. The images
    or other third-party material in this article are included in the Creative Commons license,
    unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license,
    users will need to obtain permission from the license holder to reproduce the material. To view a copy of this
    license, visit http://creativecommons.org/licenses/by/4.0/
    Keywords: Blood flow modelling, Lattice Boltzmann method, High performance computing
    UCL classification: UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
    UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry
    UCL > Provost and Vice Provost Offices > UCL BEAMS
    UCL
    URI: https://discovery.ucl.ac.uk/id/eprint/10156618

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