Publication detail

Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound

JAROŠ, J. RENDELL, A. TREEBY, B.

Original Title

Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound

Type

journal article in Web of Science

Language

English

Original Abstract

Model-based treatment planning and exposimetry for high-intensity focused ultrasound (HIFU) requires the numerical simulation of nonlinear ultrasound propagation through heterogeneous and absorbing media. This is a computationally demanding problem due to the large distances travelled by the ultrasound waves relative to the wavelength of the highest frequency harmonic. Here, the k-space pseudospectral method is used to solve a set of coupled partial differential equations equivalent to a generalised Westervelt equation. The model is implemented in C++ and parallelised using the message passing interface (MPI) for solving large-scale problems on distributed clusters. The domain is partitioned using a 1D slab decomposition, and global communication is performed using a sparse communication pattern. Operations in the spatial frequency domain are performed in transposed space to reduce the communication burden imposed by the 3D fast Fourier transform. The performance of the model is evaluated using grid sizes up to 4096 x 2048 x 2048 grid points distributed over a cluster using up to 1024 compute cores. Given the global nature of the gradient calculation, the model shows good strong scaling behaviour, with a speed-up of 1.7x whenever the number of cores is doubled. This means large-scale simulations can be distributed across high numbers of cores on a cluster to minimise execution times with a relatively small overhead. The effiacy of the model is demonstrated by simulating the ultrasound beam pattern for a HIFU sonication of the kidney.

Keywords

High Intensity Focused Ultrasound, Fourier Pseudospectral Methods, Westervelt Equation, FFTW, Large-Scale Problems, Distributed Computing

Authors

JAROŠ, J.; RENDELL, A.; TREEBY, B.

RIV year

2015

Released

29. 1. 2016

Publisher

SAGE Publications

ISBN

1741-2846

Periodical

International Journal of High Performance Computing Applications

Year of study

30

Number

2

State

United Kingdom of Great Britain and Northern Ireland

Pages from

137

Pages to

155

Pages count

19

URL

http://hpc.sagepub.com/content/early/2015/04/28/1094342015581024.full.pdf

BibTex

@article{BUT119832,
  author="Jiří {Jaroš} and Alistair {Rendell} and Bradley {Treeby}",
  title="Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound",
  journal="International Journal of High Performance Computing Applications",
  year="2016",
  volume="30",
  number="2",
  pages="137--155",
  doi="10.1177/1094342015581024",
  issn="1741-2846",
  url="http://hpc.sagepub.com/content/early/2015/04/28/1094342015581024.full.pdf"
}

Documents

k-Wave-MPI-paper.pdf