Abstract

Molecular Dynamics (MD) simulations executed on state-of-the-art supercomputers are producing data at rates faster than it can be written out to disk. In situ and in transit analysis of data generated by MD simulations reduce the original volume of information by several orders of magnitude, thereby alleviating the negative impact of I/O bottlenecks. This work focuses on characterizing the impact of in situ and in transit analytics on the overall MD workflow performance, and the capability for capturing rapid, rare events in the simulated molecular system. The MD simulation and analysis processes share data via remote direct memory access (RDMA) using DataSpaces. Our metrics of interest are time spent waiting in I/O by the MD simulation, lost frames of the MD simulation, and idle time of the analysis. We measure these metrics for a diverse set of molecular systems and characterize their trends for in situ and in transit …

Date

2019

Authors

Michela Taufer, Stephen Thomas, Michael Wyatt, Tu Mai Anh Do, Loïc Pottier, Rafael Ferreira da Silva, Harel Weinstein, Michel A Cuendet, Trilce Estrada, Ewa Deelman

Conference

2019 15th International Conference on eScience (eScience)

Pages

188-198

Publisher

IEEE