Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications

摘要

This paper presents Salsa, a novel, decentralized and asynchronous realization of the "replica exchange" algorithm for simulating the structure, function, folding, and dynamics of proteins. Salsa provides a scalable communication and interaction substrate that presents a virtual shared space abstraction and enables the dynamic and asynchronous interactions required by the simulations to be simply and efficiently implemented. The design, implementation and experimental evaluation of Salsa and replica exchange-based simulations using Salsa are presented