Journal article

TREEBY Bradley E., VAVERKA Filip and JAROŠ Jiří. Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server. Proceedings of Meetings on Acoustics. 2018, vol. 34, no. 022002, pp. 1-5. ISSN 1939-800X. Available from: https://asa.scitation.org/doi/10.1121/2.0000883
Publication language:english
Original title:Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server
Title (cs):Analýza výkonnosti a přesnosti nelineárních simulací k-Wave na 8-GPU serveru
Pages:1-5
Place:US
Year:2018
URL:https://asa.scitation.org/doi/10.1121/2.0000883
Journal:Proceedings of Meetings on Acoustics, Vol. 34, No. 022002, US
ISSN:1939-800X
DOI:10.1121/2.0000883
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Keywords
k-Wave, Local domain decomposition, Fourier Basis, pseudospectral methods
Annotation

Large-scale nonlinear ultrasound simulations using the open-source k-Wave toolbox are now routinely performed using the MPI version of k-Wave running on traditional CPU-based clusters. However, the allto-all communications required by the 3D fast Fourier transform (FFT) severely impact performance when scaling to large numbers of compute cores. This can be overcome by using a domain decomposition strategy based on a local Fourier basis. In this work, we analyse the performance and accuracy of using local domain decomposition for running a high-intensity focused ultrasound (HIFU) simulation in the kidney on a single server containing eight NVIDIA P40 graphical processing units (GPUs). Different decompositions and overlap sizes are investigated and compared to a global MPI simulation running on a CPU-based supercomputer using 1280 cores. For a grid size of 960 × 960 × 1280 grid points and an overlap size of 4 grid points, the error in the simulation using local domain decomposition is on the order of 0.1% compared to the global simulation, which is sufficient for most applications. The financial cost for running the simulation is also reduced by more than an order of magnitude.
BibTeX:
@ARTICLE{
   author = {E. Bradley Treeby and Filip Vaverka and
	Ji{\v{r}}{\'{i}} Jaro{\v{s}}},
   title = {Performance and Accuracy Analysis of Nonlinear
	k-Wave Simulations Using Local Domain
	Decomposition with an 8-GPU Server},
   pages = {1--5},
   journal = {Proceedings of Meetings on Acoustics},
   volume = {34},
   number = {022002},
   year = {2018},
   ISSN = {1939-800X},
   doi = {10.1121/2.0000883},
   language = {english},
   url = {http://www.fit.vutbr.cz/research/view_pub.php?id=11779}
}

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