High Performance Adaptive Physics Refinement to Enable Large-Scale Tracking of Cancer Cell Trajectory

Daniel F. Puleri, Sayan Roychowdhury, Peter Balogh, John Gounley, Erik W. Draeger, Jeff Ames, Adebayo Adebiyi, Simbarashe Chidyagwai, Benjamin Hernandez, Seyong Lee, Shirley V. Moore, Jeffrey S. Vetter, Amanda Randles

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Scopus citations

Abstract

The ability to track simulated cancer cells through the circulatory system, important for developing a mechanistic understanding of metastatic spread, pushes the limits of today's supercomputers by requiring the simulation of large fluid volumes at cellular-scale resolution. To overcome this challenge, we introduce a new adaptive physics refinement (APR) method that captures cellular-scale interaction across large domains and leverages a hybrid CPU-GPU approach to maximize performance. Through algorithmic advances that integrate multi-physics and multi-resolution models, we establish a finely resolved window with explicitly modeled cells coupled to a coarsely resolved bulk fluid domain. In this work we present multiple validations of the APR framework by comparing against fully resolved fluid-structure interaction methods and employ techniques, such as latency hiding and maximizing memory bandwidth, to effectively utilize heterogeneous node architectures. Collectively, these computational developments and performance optimizations provide a robust and scalable framework to enable system-level simulations of cancer cell transport.

Original languageEnglish
Title of host publicationProceedings - 2022 IEEE International Conference on Cluster Computing, CLUSTER 2022
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages230-242
Number of pages13
ISBN (Electronic)9781665498562
DOIs
StatePublished - 2022
Event2022 IEEE International Conference on Cluster Computing, CLUSTER 2022 - Heidelberg, Germany
Duration: Sep 6 2022Sep 9 2022

Publication series

NameProceedings - IEEE International Conference on Cluster Computing, ICCC
Volume2022-September
ISSN (Print)1552-5244

Conference

Conference2022 IEEE International Conference on Cluster Computing, CLUSTER 2022
Country/TerritoryGermany
CityHeidelberg
Period09/6/2209/9/22

Funding

This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/ doe-public-access-plan). Research reported in this publication was supported by the National Science Foundation under Award Number 1943036 and National Institutes of Health under Award Number U01-CA253511. Computing support for this work came from the DOE INCITE program and the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program.

Keywords

  • cancer metastasis
  • deformable cells
  • heterogeneous architectures
  • immersed boundary
  • multiphysics

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