Simulações computacionais de arritmias cardíacas em ambientes de computação de alto desempenho do tipo Multi-GPU

Abstract

Computer models have become valuable tools for the study and comprehension of the complex phenomena of cardiac electrophysiology. However, the high complexity of the biophysical processes and the microscopic level of details demand complex mathematical and computational models. Key aspects of cardiac electrophysiology, such as slow conduction, conduction block and saltatory effects have been the research topic of many studies since they are strongly related to cardiac arrhythmia. However, to reproduce these phenomena the numerical models need to use sub-cellular discretization for the solution of the PDEs and nonuniform, heterogeneous tissue electric conductivity. Due to the high computational costs of simulations that reproduce the fine microstructure of cardiac tissue, previous studies have considered tissue experiments of small or moderate sizes and used simple cardiac cell models. In this work we develop a cardiac electrophysiology model (microscopic model) that captures the microstructure of cardiac tissue by using a very fine spatial discretization (8µm) and uses a very modern and complex cell model based on Markov Chains for the characterization of ion channel's structure and dynamics. To cope with the computational challenges, the model was parallelized using a hybrid approach: cluster computing and GPGPUs (General-purpose computing on graphics processing units). Our parallel implementation of this model using a Multi-GPU platform was able to reduce the execution times of the simulations from more than 6 days (on a single processor) to 21 minutes (on a small 8-node cluster equipped with 16 GPUs). Furthermore, in order to decrease further the computational cost we have developed a discrete model equivalent to the microscopic one. This new model was also parallelized using the same approach as the microscopic model and was able to perform simulations that took 21 minutes to be executed in just 65 seconds. We believe that this new parallel implementation paves the way for the investigation of many open questions associated