Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System

Xiaojun Zhao, Minsi Chen, Sahar Soheilian Esfahani, Abbes Amira, Faycal Bensaali, Julien AbiNahed, Sarada Dakua, Robin Richardson, Peter Coveney

Research output: Contribution to journalArticle

Abstract

Cerebral aneurysm is a cerebrovascular disorder caused by a weakness in the wall of an artery or vein, that causes a localised dilation or ballooning of the blood vessel. It is life-threatening, hence an early and accurate diagnosis would be a great aid to medical professionals in making the correct choice of treatment. HemeLB is a massively parallel latticeBoltzmann simulation software which is designed to provide
the radiologist with estimates of flow rates, pressures and shear stresses throughout the relevant vascular structures, intended to eventually permit greater precision in the choice of therapeutic intervention. However, in order to allow surgeries and doctors to view and visualise the results in real-time at medical environments, a cost-efficient, practical platform is needed. In this paper, we have developed and evaluated a version of HemeLB on various heterogeneous system-on-chip platforms, allowing users to run HemeLB on a low cost embedded platform and to visualise the simulation results in real-time. A comprehensive evaluation of implementation on the Zynq SoC and Jetson TX1 embedded graphic processing unit platforms are reported. The achieved results show that the proposed Jetson TX1 implementation outperforms the Zynq implementation by a factor of 19 in terms of site updates per second.
Original languageEnglish
Number of pages10
JournalIEEE Systems Journal
Publication statusAccepted/In press - 4 Nov 2019

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Blood vessels
Surgery
Costs
Shear stress
Flow rate
System-on-chip
Graphics processing unit

Cite this

Zhao, X., Chen, M., Esfahani, S. S., Amira, A., Bensaali, F., AbiNahed, J., ... Coveney, P. (Accepted/In press). Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System. IEEE Systems Journal.
Zhao, Xiaojun ; Chen, Minsi ; Esfahani, Sahar Soheilian ; Amira, Abbes ; Bensaali, Faycal ; AbiNahed, Julien ; Dakua, Sarada ; Richardson, Robin ; Coveney, Peter. / Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System. In: IEEE Systems Journal. 2019.
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abstract = "Cerebral aneurysm is a cerebrovascular disorder caused by a weakness in the wall of an artery or vein, that causes a localised dilation or ballooning of the blood vessel. It is life-threatening, hence an early and accurate diagnosis would be a great aid to medical professionals in making the correct choice of treatment. HemeLB is a massively parallel latticeBoltzmann simulation software which is designed to providethe radiologist with estimates of flow rates, pressures and shear stresses throughout the relevant vascular structures, intended to eventually permit greater precision in the choice of therapeutic intervention. However, in order to allow surgeries and doctors to view and visualise the results in real-time at medical environments, a cost-efficient, practical platform is needed. In this paper, we have developed and evaluated a version of HemeLB on various heterogeneous system-on-chip platforms, allowing users to run HemeLB on a low cost embedded platform and to visualise the simulation results in real-time. A comprehensive evaluation of implementation on the Zynq SoC and Jetson TX1 embedded graphic processing unit platforms are reported. The achieved results show that the proposed Jetson TX1 implementation outperforms the Zynq implementation by a factor of 19 in terms of site updates per second.",
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Zhao, X, Chen, M, Esfahani, SS, Amira, A, Bensaali, F, AbiNahed, J, Dakua, S, Richardson, R & Coveney, P 2019, 'Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System', IEEE Systems Journal.

Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System. / Zhao, Xiaojun; Chen, Minsi; Esfahani, Sahar Soheilian; Amira, Abbes; Bensaali, Faycal; AbiNahed, Julien; Dakua, Sarada; Richardson, Robin; Coveney, Peter.

In: IEEE Systems Journal, 04.11.2019.

Research output: Contribution to journalArticle

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T1 - Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System

AU - Zhao, Xiaojun

AU - Chen, Minsi

AU - Esfahani, Sahar Soheilian

AU - Amira, Abbes

AU - Bensaali, Faycal

AU - AbiNahed, Julien

AU - Dakua, Sarada

AU - Richardson, Robin

AU - Coveney, Peter

PY - 2019/11/4

Y1 - 2019/11/4

N2 - Cerebral aneurysm is a cerebrovascular disorder caused by a weakness in the wall of an artery or vein, that causes a localised dilation or ballooning of the blood vessel. It is life-threatening, hence an early and accurate diagnosis would be a great aid to medical professionals in making the correct choice of treatment. HemeLB is a massively parallel latticeBoltzmann simulation software which is designed to providethe radiologist with estimates of flow rates, pressures and shear stresses throughout the relevant vascular structures, intended to eventually permit greater precision in the choice of therapeutic intervention. However, in order to allow surgeries and doctors to view and visualise the results in real-time at medical environments, a cost-efficient, practical platform is needed. In this paper, we have developed and evaluated a version of HemeLB on various heterogeneous system-on-chip platforms, allowing users to run HemeLB on a low cost embedded platform and to visualise the simulation results in real-time. A comprehensive evaluation of implementation on the Zynq SoC and Jetson TX1 embedded graphic processing unit platforms are reported. The achieved results show that the proposed Jetson TX1 implementation outperforms the Zynq implementation by a factor of 19 in terms of site updates per second.

AB - Cerebral aneurysm is a cerebrovascular disorder caused by a weakness in the wall of an artery or vein, that causes a localised dilation or ballooning of the blood vessel. It is life-threatening, hence an early and accurate diagnosis would be a great aid to medical professionals in making the correct choice of treatment. HemeLB is a massively parallel latticeBoltzmann simulation software which is designed to providethe radiologist with estimates of flow rates, pressures and shear stresses throughout the relevant vascular structures, intended to eventually permit greater precision in the choice of therapeutic intervention. However, in order to allow surgeries and doctors to view and visualise the results in real-time at medical environments, a cost-efficient, practical platform is needed. In this paper, we have developed and evaluated a version of HemeLB on various heterogeneous system-on-chip platforms, allowing users to run HemeLB on a low cost embedded platform and to visualise the simulation results in real-time. A comprehensive evaluation of implementation on the Zynq SoC and Jetson TX1 embedded graphic processing unit platforms are reported. The achieved results show that the proposed Jetson TX1 implementation outperforms the Zynq implementation by a factor of 19 in terms of site updates per second.

KW - Zynq

KW - GPU

KW - HemeLB

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Zhao X, Chen M, Esfahani SS, Amira A, Bensaali F, AbiNahed J et al. Heterogeneous System-on-Chip based Lattice-Boltzmann Visual Simulation System. IEEE Systems Journal. 2019 Nov 4.