Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis on - SC '11, 2011
Interfacing atomistic-based with continuum-based simulation codes is now required in many multisc... more Interfacing atomistic-based with continuum-based simulation codes is now required in many multiscale physical and biological systems. We present the computational advances that have enabled the first multiscale simulation on 131,072 processors by coupling a high-order (spectral element) Navier-Stokes solver with a stochastic (coarse-grained) Molecular Dynamics solver based on Dissipative Particle Dynamics (DPD). The key contributions are proper interface conditions for overlapped domains, topology-aware communication, SIMDization of all basic operations, and multiscale visualization. We study blood flow in a patient-specific cerebrovasculature with a brain aneurysm, and analyze the interaction of blood cells with the arterial walls that lead to thrombus formation and eventual aneurysm rupture. The macro-scale dynamics (about 3 billion unknowns) are resolved by N εκT αr -a multi-level parallel spectral element solver -while the micro-scale flow and cell dynamics within the aneurysm are resolved by an in-house version of DPD-LAMMPS (for an equivalent of about 8 billion molecules).
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Papers by Michael Papka