Parallel Simulation of Sinoatrial Node Cells Synchronization

• Main Authors: Mata Aurelio, Nicolas, Abrego Norma Pilar, Castellanos, Alonso Graciela, Roman, Garcia Miguel Alfonso, Castro, Garza Gabriel, Lopez, Fernandez Jose Rafael, Godinez
• Format: Conference Proceeding
• Language: English
• Subjects: Computational modeling; CUDA programming; Electric potential; Gap junction channels; Graphics processing units; Heart; HPC; Junctions; Mathematical model; MPI application; OpenMP; Synchronization
• ISSN: 2377-5750
• DOI: 10.1109/PDP2018.2018.00025

The sinoatrial node (SAN) has the function of initiating a depolarizing wave that runs throughout the heart. This wave produces the muscular contraction necessary to blood pumping in animals. In recent years different works have been proposed to simulate the electric potential behaviour of a single sinoatrial cell (SANC) and groups of cells, hence a set of differential equations needs to be solved for each microsecond of simulation. An important drawback comes up when the synchronization of millions of SANCs is required involving a huge processing time. Since the simulation of the behavior of a set of cells is an open research topic, it is important to propose efficient tools to reduce response times; unfortunately, because the complexity of the existent models of SANC, very scarce work has been done to this end. This paper proposes three parallel algorithms to simulate the synchronization of a set of SANCs based on the model of Severi (2012). The proposed approaches are built using OpenMP, MPI, and CUDA, in order to compare the benefits given by different computing platforms. We found that all parallel versions perform better when defining a cell per processing unit; however the CUDA version gives the best results in scalability and performance.