Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server

Performance and Accuracy Analysis of Nonlinear k-Wave Simulations Using Local Domain Decomposition with an 8-GPU Server

Scopus Article

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.

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.

k-Wave, Local domain decomposition, Fourier Basis, pseudospectral methods

k-Wave, Local domain decomposition, Fourier Basis, pseudospectral methods

TREEBY, B.; VAVERKA, F.; JAROŠ, J.

2020

22.10.2018

Proceedings of Meetings on Acoustics

1939-800X

Proceedings of Meetings on Acoustics

34

1

United States of America

1

5

5

https://asa.scitation.org/doi/10.1121/2.0000883

published version