Multiscale simulation of cardiovascular flows on the IBM Blue Gene/P: Full heart-circulation system at near red-blood cell resolution

2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2010

Volumn , Issue , 2010, Pages

  Peters, Amanda ^a   Melchionna, Simone ^a,b   Kaxiras, Efthimios ^a,b   Lätt, Jonas ^b   Sircar, Joy ^a   Bernaschi, Massimo ^c   Bisson, Mauro ^c   Succi, Sauro ^a,c,d  

^a HARVARD UNIVERSITY   (United States)

^b EPFL   (Switzerland)

^c CNR   (Italy)

^d UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

10 MICRON; ARTERIAL GEOMETRY; ATHEROSCLEROTIC PLAQUE; BLOOD CELLS; BLOOD FLOW; BOUNDING SPACE; CARDIOVASCULAR FLOW; CIRCULATION SYSTEMS; COMPUTATIONAL CORE; HEART MUSCLES; LARGE SCALE SIMULATIONS; LEVEL OF DETAIL; MULTI-SCALE SIMULATION; RED BLOOD CELL; SPATIAL RESOLUTION; VOLUME UNITS;

BLOOD VESSELS; CELLS; HEMOGLOBIN OXYGEN SATURATION; SUPERCOMPUTERS;

BLOOD;

EID: 78650813616     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/SC.2010.33     Document Type: Conference Paper

References (34)

1. D.A. Vorp, D.A. Steinman, C.R. Ethier, "Computational Modeling of Arterial Biomechanics", Comput. Sci. Eng., vol. 3, 2001, pp. 51-64.
2. A. Quarteroni, A. Veneziani, P. Zunino, "Mathematical and numerical modeling of solute dynamics in blood flow and arterial walls", SIAM J. Num. Analysis, vol. 39, no. 5, 2002, pp. 1488-1511.
3. L. Grinberg, T. Anor, E. Cheever, et al., "Simulation of the human intracranial arterial tree", Phil. Trans. Royal Soc. A, vol. 367, no. 1896, Jan. 2009, pp. 2371-2386.
4. R. Ouared and B. Chopard, "Lattice Boltzmann Simulations of Blood Flow, Non-Newtonian Rheology and Clotting Processes", J. Stat. Phys. vol. 121, Oct. 2005, pp. 209-221.
5. D.J.W. Evans, P.V. Lawford, J. Gunn, D. Walker, D.R. Hose, R.H. Smallwood, B. Chopard, M. Krafczyk, J. Bernsdorf, A. Hoekstra, "The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery", Phil. Trans. R. Soc. A, vol. 366, no. 1879, Sept. 2008, pp. 3343-3360.
6. I.V. Pivkin, P. Richardson and G. Karniadakis, "Blood flow velocity effects on role of activation delay time on growth and form of platelet thrombi", Proc.Natl.Acad.Sci., vol. 103, no. 46, Nov. 2006, pp. 17164- 17169.
7. J.L. McWhirter, H, Noguchi and G. Gompper, "Flow-induced clustering and alignment of vesicles and red blood cells in microcapillaries, Proc.Natl.Acad.Sci., vol. 106, no. 15, April 2009, pp. 6039-6043.
8. S.K. Veerapaneni, D. Gueyffier, G. Biros, and D. Zorin, "A numerical method for simulating the dynamics of 3D axisymmetric vesicles suspended in viscous flows", J. Comp. Phys., vol. 228, Oct. 2009, pp. 7233-7249.
9. M. Bernaschi, S. Melchionna, S. Succi et al. MUPHY:"A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations", Comp. Phys. Comm., vol. 180, Sept. 2009, pp. 1495-1502.
10. S. Melchionna, M. Bernaschi, S. Succi et al, "Hydrokinetic approach to large-scale cardiovascular flows", Comp. Phys. Comm., vol. 181, 462, (2010).
11. J. C. Phillips, G. Zheng, S. Kumar, and L. V. Kal. NAMD: Biomolecular Simulation on Thousands of Processors. Proc. IEEE/ACM SC2002 Conf. IEEE Press, 2002. Technical Paper 277.
12. J. C. Phillips, G. Zheng, S. Kumar, and L. V. Kal."NAMD: Biomolecular Simulation on Thousands of Processors". Proc. IEEE/ACM SC2002 Conf. IEEE Press, 2002. Technical Paper 277.
13. LB simulations with coupled bodies, even deformable ones, are available in the literature, see for instance M. Dupin et al, Phys. Rev. E, 75, 6, (2007).
14. but we are not aware of any massively parallel implementation of this method to tackle full heart-circulation problems. Parallel LBM applications to complex geometries have been performed by L. Axner et al, J. Comp. Phys., 227, 4895, (2008).
15. but on much smaller sizes (order of ten million cells) and with no suspended particles. Computational fluid dyamics with multi-body dynamics are also available, see J. Gotz et al, Parallel Computing, 36, 142, (2010).
16. but on a much smaller number of nodes (8192). Larger Lattice Boltzmann simulations, with up to 150 billions cells and 260 million suspended particles, have been recently presented (J. Gotz et al, Supercomputing 2010). However, these simulations only deal with idealized cartesian geometries.
17. C. S. Peskin, "Accurate coarse-grained modeling of red blood cells", Acta Numer. 2002, vol. 479.
18. I. Pivkin and G.E. Karniadakis, "Accurate coarse-grained modeling of red blood cells", Phys. Rev. Letts., vol. 101, 2008, 118105.
19. S. Melchionna, in preparation.
20. S. Succi, The Lattice Boltzmann Equation for Fluid Dynamics and Beyond, Oxford University Press, USA, 2001.
21. Q. Zou and X. He, Phys. Fluids, 9, 1591 (1997).
22. C. Chevalier and F. Pellegrini, "PT-Scotch: A tool for efficient parallel graph ordering." Parallel Computing, Jan. 2008, pp. 318-331.
23. S. Succi, The Lattice Boltzmann Equation for Fluid Dynamics and Beyond, Oxford University Press, USA, 2001.
24. Q. Zou and X. He, "On pressure and velocity boundary conditions for the lattice Boltzmann BGK model, "Phys. Fluids, vol. 9, 1997, pp. 1591.
25. G Karypis, V Kumar, "METIS 3.0: Unstructured graph partitioning and sparse matrix ordering system". Dept. Computer Sci., Univ. Minnesota, Tech. Rep., 1997.
26. R. Benzi, S. Succi and M. Vergassola, "The Lattice Boltzmann equation: Theory and applications". Phys. Rep. vol. 222, 1992, pp. 145.
27. J.G. Gay, B.J. Berne, J. Chem. Phys, 74, 3316 (1981).
28. A. Gara et. al, "Overview of the Blue Gene/L system architecture". IBM Journal of Research and Development, vol. 49, issue 2, March 2005, pp. 195-212.
29. 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 and Computation: Practice and Experience, 2009, DOI: 10.1002/cpe.1466.
30. K. Mattila, J. Hyväluoma, T. Rossi, M Aspnäs, J. Westerholm, "An efficient swap algorithm for the lattice Boltzmann method", Comp. Phys. Comm., vol. 176, 2007, pp. 200.
31. MD Mazzeo, PV Coveney PV, "HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries", Comp. Phys. Comm., vol. 178, 2008, pp. 894.
32. JR Clausen, DA Reasor Jr., CK Aidun, "Parallel performance of a lattice- Boltzmann/finite element cellular blood flow solver on the IBM Blue Gene/P architecture", Comp. Phys. Comm. (in press, 2010).
33. A. Dullweber, B. Leimkuhler, R. McLachlan, "Symplectic splitting methods for rigid body molecular dynamics", J. Chem. Phys., vol. 107, 1997, pp. 5840.
34. G. Lakner, I.-H. Chung, G. Cong, S. Fadden, N. Goracke, D. Klepacki, J. Lien, C.Posiech, S.R. Seelam and H.-F. Wen. IBM System Blue Gene Solution: Performance Analysis Tools. IBM Redpaper Publication, Nov. 2008.