Multiscale hemodynamics using GPU clusters

Communications in Computational Physics

Volumn 11, Issue 1, 2012, Pages 48-64

  Bisson, Mauro ^a   Bernaschi, Massimo ^b   Melchionna, Simone ^c,d   Succi, Sauro ^b,e   Kaxiras, Efthimios ^d,f  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b CNR   (Italy)

^c CNR   (Italy)

^d EPFL   (Switzerland)

^e UNIVERSITY OF FREIBURG   (Germany)

^f HARVARD UNIVERSITY   (United States)

Author keywords

Hemodynamics; Irregular domain; Molecular dynamics; Multi GPU computing

Indexed keywords

EID: 84055193478     PISSN: 18152406     EISSN: 19917120     Source Type: Journal    
DOI: 10.4208/cicp.210910.250311a     Document Type: Article

References (16)

1. M. Fyta, S. Melchionna, E. Kaxiras and S. Succi, Multiscale coupling of molecular dynamics and hydrodynamics: applications to DNA translocation through a nanopore, Multiscale Modeling and Simulation, 5(2006), 1156-1173. (Pubitemid 350300982)
2. M. Fyta, S. Melchionna, S. Succi and E. Kaxiras, Multiscale simulation of nanobiological flows, Comput. Sci. Eng., March/April, 2008.
3. R. Benzi, S. Succi and M. Vergassola, The lattice Boltzmann equation: theory and applications, Phys. Rep., 222(3) (1992), 145-197.
4. S. Melchionna, M. Bernaschi, S. Succi, E. Kaxiras, F. J. Rybicki, D. Mitsouras, A. U. Coskun and C. L. Feldman, Hydrokinetic approach to large-scale cardiovascular blood flow, Comput. Phys. Commun., 181(2010), 462-472.
5. Message Passing Interface Forum, MPI: A Message-Passing Interface Standard, 1994.
6. M. Bisson, M. Bernaschi and S. Melchionna, Parallel molecular dynamics with irregular domain decomposition, Commun. Comput. Phys., 10(2011), 1071-1088.
7. J. D. Owens, M. Houston, D. Luebke, S. Green, J. E. Stone and J. C. Phillips, GPU Computing, Proc. IEEE, 96(5) (2008), 879-899.
8. http://glaros.dtc.umn. edu/gkhome/metis/metis/overview.
9. http://www.labri.fr/perso/pelegrin/scotch/.
10. S. Succi, The Lattice Boltzmann Equation for Fluid Dynamics and Beyond, Oxford University Press, USA, 2001
11. J. G. Gay and B. J. Berne, Modification of the overlap potential to mimic a linear site-site potential, J. Chem. Phys., 74(1981), 3316-3319.
12. A. Dullweber, B. Leimkuhler and R. McLachlan, Symplectic splitting methods for rigid body molecular dynamics, J. Chem. Phys., 107(1997), 5840-5851. (Pubitemid 127568823)
13. M. Bernaschi et al., MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations, Comput. Phys. Commun., 180(2009), 1495-1502.
14. http://www.ibm.com/systems/deepcomputing/bluegene/.
15. M. Bernaschi, M. Fatica, S. Melchionna, S. Succi and E. Kaxiras, A flexible high performance Lattice Boltzmann GPU code for the simulations of fluid flows in complex geometries, Concurrency Prac. Ex., DOI: 10.1002/cpe.1466(2009).
16. http://gpgpu.org/developer/cudpp.