Alya red CCM: HPC-Based cardiac computational modelling

Abstract

This paper describes Alya Red CCM, a cardiac computational modelling tool for supercomputers. It is based on Alya, a parallel simulation code for multiphysics and multiscale problems, which can deal with all the complexity of biological systems simulations. The final goal is to simulate the pumping action of the heart: the model includes the electrical propagation, the mechanical contraction 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. Electrophysiology 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 easily 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.