Practical algorithms to facilitate large-scale first-principles molecular dynamics
François Gygi, Ivan Duchemin, Davide Donadio, Giulia Galli · Journal of Physics Conference Series · 2009
Running First-Principles Molecular Dynamics (FPMD) simulations on large parallel platforms presents a number of practical challenges related to the large size of the datasets generated during simulations and to the lack of flexibility of parallel FPMD codes for the implementation of new algorithms. In this paper, we present two approaches implemented in the Qbox code, that alleviate these problems and facilitate large-scale FPMD simulations. We first describe a parallel I/O strategy based on MPI-IO that fully exploits the performance of parallel file systems. We also describe the implementation of a client-server interface that enables coupled quantum-classical computations in which the quantum simulation run by Qbox is "driven" by another application. This feature can be used to couple FPMD simulations with other simulation methods such as e.g. Path Integral Monte Carlo, thermodynamic integration or replica exchange dynamics.