Biomolecular committor probability calculation enabled by processing in network storage

Authors:
P. Brenner;J. M. Wozniak;D. Thain;A. Striegel;J. W. Peng;J. A. Izaguirre
Affiliations:
Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA;Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA;Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA;Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA;Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA;Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
Venue:
Parallel Computing
Year:
2008

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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, organizational, and security challenges inherent to the wide-area computation and storage grid. PINS is presented as an effective and scalable scientific simulation framework to meet the unbounded requirements of a 'user of infinite need'. The novel hybrid database-filesystem architecture enables the high throughput computation and data generation required by our scientific target. Biomolecular simulation methods are correlated with the primary PINS components, including: client tools, hybrid database/file management service (GEMS), computation engine (Condor), virtual file system adapter (Parrot), and local file servers (Chirp). Performance for the PINS prototype is reported for the committor probability calculation of a solvated protein domain requiring 500 independent simulations and the generation of over 1,000,000 output files.