Vaverka, F;
Treeby, BE;
Jaros, J;
(2021)
Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators.
In: Kozubek, T and Arbenz, P and Jaros, J and Ríha, L and Sístek, J and Tichý, P, (eds.)
HPCSE 2019: High Performance Computing in Science and Engineering.
(pp. pp. 99-115).
Springer: Cham, Switzerland.
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Abstract
The rapid development of novel procedures in medical ultrasonics, including treatment planning in therapeutic ultrasound and image reconstruction in photoacoustic tomography, leads to increasing demand for large-scale ultrasound simulations. However, routine execution of such simulations using traditional methods, e.g., finite difference time domain, is expensive and often considered intractable due to the computational and memory requirements. The k-space corrected pseudospectral time domain method used by the k-Wave toolbox allows for significant reductions in spatial and temporal grid resolution. These improvements are achieved at the cost of all-to-all communication, which are inherent to the multi-dimensional fast Fourier transforms. To improve data locality, reduce communication and allow efficient use of accelerators, we recently implemented a domain decomposition technique based on a local Fourier basis. In this paper, we investigate whether it is feasible to run the distributed k-Wave implementation on the Salomon cluster equipped with 864 Intel Xeon Phi (Knight’s Corner) accelerators. The results show the immaturity of the KNC platform with issues ranging from limited support of Infiniband and LustreFS in Intel MPI on this platform to poor performance of 3D FFTs achieved by Intel MKL on the KNC architecture. Yet, we show that it is possible to achieve strong and weak scaling comparable to CPU-only platforms albeit with the runtime 1.8× to 4.3× longer. However, the accounting policy for Salomon’s accelerators is far more favorable and thus their employment reduces the computational cost significantly.
| Type: | Proceedings paper |
|---|---|
| Title: | Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators |
| Event: | International Conference on High Performance Computing in Science and Engineering |
| ISBN-13: | 978-3-030-67076-4 |
| Open access status: | An open access version is available from UCL Discovery |
| Publisher version: | https://doi.org/10.1007/978-3-030-67077-1_6 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| Keywords: | Ultrasound simulations · Local Fourier basis decomposition · Pseudospectral methods · Ultrasound · k-Wave toolbox · Intel Xeon Phi · Knight’s Corner · MKL · MPI · OpenMP. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Med Phys and Biomedical Eng |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10121054 |
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