Title :
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications
Author :
Zhang, Li ; Parashar, Manish ; Gallicchio, Emilio ; Levy, Ronald M.
Author_Institution :
Dept. of Electr. & Comput. Eng., Rutgers Univ., Piscataway, NJ
Abstract :
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
Keywords :
chemistry computing; molecular dynamics method; parallel processing; proteins; Salsa; parallel molecular dynamics application; replica exchange algorithm; scalable asynchronous replica exchange; virtual shared space abstraction; Algorithm design and analysis; Application software; Biological system modeling; Biology computing; Computational biology; Concurrent computing; Drugs; Dynamic programming; Proteins; Temperature;
Conference_Titel :
Parallel Processing, 2006. ICPP 2006. International Conference on
Conference_Location :
Columbus, OH
Print_ISBN :
0-7695-2636-5
DOI :
10.1109/ICPP.2006.63
