ROBUST MOLECULAR DYNAMICS SIMULATIONS USING CODED FFT ALGORITHM

Y Wong and YQ Zhang and H Jeong and P Grover, 2019 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP), 8197-8201 (2019).

As error/failure rates in supercomputers are projected to grow, computationally intensive scientific applications that leverage 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 computeintensive 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.

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