Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F21%3APU138855" target="_blank" >RIV/00216305:26230/21:PU138855 - isvavai.cz</a>
Result on the web
<a href="https://link.springer.com/chapter/10.1007/978-3-030-67077-1_6" target="_blank" >https://link.springer.com/chapter/10.1007/978-3-030-67077-1_6</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1007/978-3-030-67077-1_6" target="_blank" >10.1007/978-3-030-67077-1_6</a>
Alternative languages
Result language
angličtina
Original language name
Performance Evaluation of Pseudospectral Ultrasound Simulations on a Cluster of Xeon Phi Accelerators
Original language description
The ability to perform large-scale ultrasound simulations has generated significant interest in medical ultrasonics, including for treatment planning in therapeutic ultrasound, and image reconstruction in photoacoustic tomography. However, routine execution of such simulations using traditional computational methods, e.g., finite difference time domain, is considered intractable due to the computational and memory requirements. The k-Wave toolbox alleviates these requirements by employing a k-space corrected pseudospectral method. This significantly reduces the spatial and temporal grid resolution, however, at the cost of introducing global all-to-all communication through the use of the fast Fourier transform. To improve data locality, reduce data movements and allow efficient use of accelerators, we recently implemented a domain decomposition technique based on local Fourier basis. Nowadays, the trend in parallel computing is towards the use of accelerated nodes where computationally intensive tasks are offloaded from processors to accelerators. In this paper, we investigate the performance aspects of the distributed k-Wave implementation running on the Salomon cluster equipped with 864 Intel Xeon Phi (Knight's Corner) accelerators. The paper shows that running large simulations across many accelerators is not a trivial task. The main obstacle is the instability of Intel MPI on Infiniband interconnection once the number of accelerators exceeds 32. Beyond this limit, the use of service 1Gbps interconnection is the only solution. The second problem is low performance of the fast Fourier transforms ranging from 1% to 50% of a single 12-core CPU. Finally, there is no support for fast LustreFS file system. Despite these factors, the observed strong and weak scaling is comparable with a cluster of CPU, but the absolute running time is between 4.3x and 1.8x longer in the worst and best case, respectively. However, the accounting policy for
Czech name
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Czech description
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Classification
Type
D - Article in proceedings
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
Result continuities
Project
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Continuities
R - Projekt Ramcoveho programu EK
Others
Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Article name in the collection
High Performance Computing in Science and Engineering. HPCSE 2019
ISBN
978-3-030-67076-4
ISSN
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e-ISSN
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Number of pages
17
Pages from-to
99-115
Publisher name
Springer Nature Switzerland AG
Place of publication
Cham
Event location
Hotel Soláň
Event date
May 20, 2019
Type of event by nationality
WRD - Celosvětová akce
UT code for WoS article
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