Alya Red CCM: HPC-Based Cardiac Computational Modelling - Selected Topics of Computational and Experimental Fluid Mechanics - page 183

Alya Red CCM: HPC-Based Cardiac
Computational Modelling

M. Vázquez, R. Arís, J. Aguado-Sierra, G. Houzeaux, A. Santiago,
M. López, P. Córdoba, M. Rivero and J.C. Cajas

Abstract This paper describes Alya Red CCM, a cardiac computational modelling
tool for supercomputers. It is based on Alya, a parallel simulation code for mul-
tiphysics and multiscale problems, which can deal with all the complexity of bio-
logical systems simulations. The final goal is to simulate the pumping action of
the heart: the model includes the electrical propagation, the mechanical contrac-
tion and relaxation and the blood flow in the heart cavities and main vessels. All
sub-problems are treated as fully transient and solved in a staggered fashion. Elec-
trophysiology and mechanical deformation are solved on the same mesh, with
no interpolation. Fluid flow is simulated on a moving mesh using an Arbitrary
Lagrangian-Eulerian (ALE) strategy, being the mesh deformation computed through
an anisotropic Laplacian equation. The parallel strategy is based on an automatic
mesh partition using Metis and MPI tasks. When required and in order to take
profit of multicore clusters, an additional OpenMP parallelization layer is added.
The paper describes the tool and its different parts. Alya's flexibility allows to eas-
ily program a large variety of physiological models for each of the sub-problems,
including the mutual coupling. This flexibility, added to the parallel efficiency
to solve multiphysics problems in complex geometries render Alya Red CCM a
well suited tool for cardiac biomedical research at either industrial or academic
environments.