Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound
Full-wave nonlinear ultrasound simulation on distributed clusters with applications in high-intensity focused ultrasound
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DOI：
10.1177/1094342015581024
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发表时间：
2014-08
期刊：
影响因子：
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通讯作者：
J. Jaros;Alistair P. Rendell;B. Treeby
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文献类型：
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作者：
J. Jaros;Alistair P. Rendell;B. Treeby
基于模型的治疗计划和高强度聚焦超声的曝光测量需要通过异质和吸收介质的非线性超声传播的数值模拟。由于超声波相对于最高频率谐波的波长行进的距离很大，这是一个需要计算的问题。在这里，k-空间伪谱方法是用来解决一组耦合偏微分方程相当于一个广义Westerpyruvate方程。该模型在C++中实现，并使用消息传递接口（MPI）并行化，用于解决分布式集群上的大规模问题。使用1D平板分解来划分域，并且使用稀疏通信模式来执行全局通信。在转置空间中执行空间频率域中的操作以减少由3D快速傅立叶变换施加的通信负担。该模型的性能评估使用网格大小高达4096×2048×2048网格点，分布在一个集群使用多达1024个计算核心。考虑到梯度计算的全局性质，该模型显示出良好的强缩放行为，每当内核数量增加一倍时，速度将提高1.7倍。这意味着大规模模拟可以分布在集群上的大量核心上，以相对较小的开销最大限度地减少执行时间。该模型的有效性证明了通过模拟高强度聚焦超声声处理的肾脏的超声波束图案。
Model-based treatment planning and exposimetry for high-intensity focused ultrasound 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 4096×2048×2048 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 efficacy of the model is demonstrated by simulating the ultrasound beam pattern for a high-intensity focused ultrasound sonication of the kidney.