Biomolecular Path Sampling Enabled by Processing in Network Storage

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.

• Type: Conference
• Year: 2007
• Where: IPPS
• Authors: Paul Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, J. W. Peng, Jesús A. Izaguirre
• Keywords: Biomolecular Simulation, Data Generation, Distributed And Parallel Computing, IPPS 2007, Scale Biomolecular Simulation