Commun. Comput. Phys., 11 (2012), pp. 48-64.


Multiscale Hemodynamics Using GPU Clusters

Mauro Bisson 1*, Massimo Bernaschi 2, Simone Melchionna 3, Sauro Succi 4, Efthimios Kaxiras 5

1 Department of Computer Science, University of Rome "Sapienza", Italy.
2 Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche, Rome, Italy.
3 Istituto Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche, Rome, Italy; and Institute of Material Sciences and Engineering, Ecole Polytechnique Federale de Lausanne, Switzerland.
4 Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche, Rome, Italy; and Freiburg Institute for Advanced Studies, School of Soft Matter Research, Albertstr. 19, 79104 Freiburg, Germany.
5 Institute of Material Sciences and Engineering, Ecole Polytechnique Federale de Lausanne, Switzerland; and Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.

Received 21 September 2010; Accepted (in revised version) 25 March 2011
Available online 5 September 2011
doi:10.4208/cicp.210910.250311a

Abstract

The parallel implementation of MUPHY, a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries, for multi-GPU platforms is presented. Performance tests show excellent results, with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration, all across the range of GPUs. The basic MUPHY scheme combines a hydrokinetic (Lattice Boltzmann) representation of the blood plasma, with a Particle Dynamics treatment of suspended biological bodies, such as red blood cells. To the best of our knowledge, this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries. This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.


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PACS: 02.70.Ns
Key words: Multi-GPU computing, hemodynamics, molecular dynamics, irregular domain.

*Corresponding author.
Email: bisson@di.uniroma1.it (M. Bisson), massimo@iac.rm.cnr.it (M. Bernaschi), simone.melchionna@epfl.ch (S. Melchionna), succi@iac.cnr.it (S. Succi), efthimios.kaxiras@epfl.ch (E. Kaxiras)
 

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