A flexible high-performance Lattice Boltzmann GPU code for the simulations of fluid flows in complex geometries

We describe the porting of the Lattice Boltzmann component of MUPHY, a multi-physics-scale simulation software, to multiple graphics processing units using the Compute Unified Device Architecture. The novelty of this work is the development of ad hoc techniques for optimizing the indirect addressing that MUPHY uses for efficient simulations of irregular domains. Copyright © 2009 John Wiley & Sons, Ltd.

[1]  P. Ahlrichs,et al.  Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics , 1999, cond-mat/9905183.

[2]  Sauro Succi,et al.  Massively Parallel Lattice-Boltzmann Simulation of Turbulent Channel Flow , 1997 .

[3]  Sauro Succi,et al.  Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore , 2006, Multiscale Model. Simul..

[4]  Thomas Zeiser,et al.  Performance evaluation of a parallel sparse lattice Boltzmann solver , 2008, J. Comput. Phys..

[5]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics: II. Design considerations for distributed processing , 1991 .

[6]  Burkhard Dünweg,et al.  Lattice Boltzmann Simulation of Polymer-Solvent Systems , 1998 .

[7]  R. Benzi,et al.  The lattice Boltzmann equation: theory and applications , 1992 .

[8]  Sauro Succi,et al.  Applying the lattice Boltzmann equation to multiscale fluid problems , 2001, Comput. Sci. Eng..

[9]  A. Ladd,et al.  Lattice-Boltzmann Simulations of Particle-Fluid Suspensions , 2001 .

[10]  M. Cates,et al.  Fluctuating lattice Boltzmann , 2004, cond-mat/0402598.

[11]  Jay E. Steele,et al.  Parallel processing flow models on desktop hardware , 2008, ACM-SE 46.

[12]  Bastien Chopard,et al.  Lattice Gas: An Efficient and Reusable Parallel Library Based on a Graph Partitioning Technique , 1999, HPCN Europe.

[13]  Gerhard Wellein,et al.  On the single processor performance of simple lattice Boltzmann kernels , 2006 .

[14]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[15]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics I. Design considerations for vector processing , 1991 .

[16]  Takao Yamazaki,et al.  A domain decomposition parallelization strategy for molecular dynamics simulations on distributed memory machines , 1993 .

[17]  G. S. Pawley,et al.  Molecular dynamics of clusters of particles interacting with pairwise forces using a massively parallel computer , 1988 .

[18]  Massimo Bernaschi,et al.  Parallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations , 2007, 0711.2665.

[19]  Berend Smit,et al.  Efficient Parallel Implementation of Molecular Dynamics on a Toroidal Network. Part I. Parallelizing Strategy , 1993 .

[20]  Massimo Bernaschi,et al.  MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations , 2009, Comput. Phys. Commun..

[21]  Arie E. Kaufman,et al.  Implementing lattice Boltzmann computation on graphics hardware , 2003, The Visual Computer.

[22]  D. Wolf-Gladrow Lattice-Gas Cellular Automata and Lattice Boltzmann Models: An Introduction , 2000 .

[23]  Helmut Grubmüller,et al.  Molecular dynamics simulation on a parallel computer. , 1990 .

[24]  L. Nallamshetty,et al.  Prediction of coronary artery plaque progression and potential rupture from 320-detector row prospectively ECG-gated single heart beat CT angiography: Lattice Boltzmann evaluation of endothelial shear stress , 2009, The International Journal of Cardiovascular Imaging.