Department of Computer Systems

Journal article

JAROŠ Jiří, RENDELL Alistair P. and TREEBY Bradley E. Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound. The International Journal of High Performance Computing Applications. 2455 Teller Road Thousand Oaks, CA 91320: SAGE Publications, 2016, vol. 2016, no. 2, pp. 137-155. ISSN 1741-2846. Available from: http://hpc.sagepub.com/content/early/2015/04/28/1094342015581024.full.pdf
Publication language:english
Original title:Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound
Title (cs):Celovlnové nelineární ultrazvukov simulace prováděné na distribuovaných clusterech aplikované v ultrazuvku o vysoké intenzitě
Pages:137-155
Book:The International Journal of High Performance Computing Applications
Place:US
Year:2016
URL:http://hpc.sagepub.com/content/early/2015/04/28/1094342015581024.full.pdf
Journal:The International Journal of High Performance Computing Applications, Vol. 2016, No. 2, 2455 Teller Road Thousand Oaks, CA 91320, US
ISSN:1741-2846
Publisher:SAGE Publications
Keywords
High Intensity Focused Ultrasound, Fourier Pseudospectral Methods, Westervelt Equation, FFTW, Large-Scale Problems, Distributed Computing
Annotation
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.
BibTeX:
@ARTICLE{
   author = {Ji{\v{r}}{\'{i}} Jaro{\v{s}} and P. Alistair Rendell and E.
	Bradley Treeby},
   title = {Full-wave nonlinear ultrasound simulation on distributed
	clusters with applications in high-intensity focused
	ultrasound},
   pages = {137--155},
   booktitle = {The International Journal of High Performance Computing
	Applications},
   journal = {The International Journal of High Performance Computing
	Applications},
   volume = {2016},
   number = {2},
   year = {2016},
   publisher = {SAGE Publications},
   ISSN = {1741-2846},
   language = {english},
   url = {http://www.fit.vutbr.cz/research/view_pub.php.en.iso-8859-2?id=10833}
}

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