Title :
Biomolecular Path Sampling Enabled by Processing in Network Storage
Author :
Brenner, P. ; Wozniak, J.M. ; Thain, D. ; Striegel, A. ; Peng, J.W. ; Izaguirre, J.A.
Author_Institution :
Dept. of Comput. Sci. & Eng., Notre Dame Univ.
Abstract :
Computationally complex and data intensive atomic scale biomolecular simulation is enabled via processing in network storage (PINS): a novel distributed system framework to overcome bandwidth, compute, storage, and security challenges inherent to the wide area computation and storage grid. High throughput data generation requirements for our scientific target are overcome through novel aggregate bandwidth capabilities. Biomolecular simulation methods are correlated with the client tools, hybrid database/file server (GEMS), computation engine (Condor), virtual file system adapter (Parrot), and local file servers (Chirp). PINS performance is reported for the path sampling of a solvated protein domain requiring over 1000 simulations with total output data generation on the order of 1TB.
Keywords :
biology computing; client-server systems; digital simulation; distributed databases; file servers; grid computing; molecular biophysics; molecular dynamics method; network operating systems; proteins; sampling methods; virtual storage; atomic scale biomolecular simulation; bandwidth capabilities; biomolecular path sampling; computation engine; data generation requirements; distributed system framework; file server; hybrid database; network storage; proteins; virtual file system adapter; Bandwidth; Computational modeling; Computer networks; Data security; Distributed computing; File servers; Grid computing; Pins; Sampling methods; Secure storage;
Conference_Titel :
Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International
Conference_Location :
Long Beach, CA
Print_ISBN :
1-4244-0910-1
Electronic_ISBN :
1-4244-0910-1
DOI :
10.1109/IPDPS.2007.370446
