Robust Molecular Dynamics Simulations Using Coded FFT Algorithm

Abstract

As error/failure rates in supercomputers are projected to grow, computationally intensive scientific applications that lever-age large-scale parallelization will suffer from the increased error rate. In this work, we apply coded computing to protein folding simulations in an error-prone environment. We implemented the fast Fourier Poisson method for solving electrostatic equations at each time step of the simulation, and we utilize coded FFT algorithm to protect the compute-intensive FFT algorithm from soft errors. Through experiments on Amazon AWS, we showed that coded protein folding can be implemented with less than 10% overhead in total simulation time, and also showed that coded computing approach is faster than classical checkpointing method when the error rate is high.