Digital Commons Network^™

Efficient Replica-Exchange Across Distributed Production Infrastructure, Abhinav S. Thota

LSU Master's Theses

Replica-Exchange (RE) methods represent a class of algorithms that involve a large number of loosely-coupled ensembles and are used to understand physical phenomena -- ranging from protein folding dynamics to binding affinity calculations. We develop a framework for RE that supports different replica pairing and coordination mechanisms, that can use a wide range of production cyberinfrastructure concurrently. Additionally, our framework uses a flexible pilot-job implementation, which enables effective resource allocation for multiple replicas. We characterize the performance of two different RE algorithms - synchronous and asynchronous - at unprecedented scales on production distributed infrastructure (Teragrid and LONI). The synchronous RE …