title: Folding Proteins at 500 ns/hour with Work Queue.
abstract: Molecular modeling is a field that traditionally has large computational costs. Until recently, most simulation techniques relied on long trajectories, which inherently have poor scalability. A new class of methods is proposed that requires only a large number of short calculations, and for which minimal communication between computer nodes is required. We considered one of the more accurate variants called Accelerated Weighted Ensemble Dynamics (AWE) and for which distributed computing can be made efficient. We implemented AWE using the Work Queue framework for task management and applied it to an all atom protein model (Fip35 WW domain). We can run with excellent scalability by simultaneously utilizing heterogeneous resources from multiple computing platforms such as clouds (Amazon EC2, Microsoft Azure), dedicated clusters, grids, on multiple architectures (CPU/GPU, 32/64bit), and in a dynamic environment in which processes are regularly added or removed from the pool. This has allowed us to achieve an aggregate sampling rate of over 500 ns/hour. As a comparison, a single process typically achieves 0.1 ns/hour.
authors.affiliation: University of Notre Dame, Notre Dame, IN 46656 ; Department of Computer Science & Engineering ; Interdisciplinary Center for Network Science and Applications.
authors.forename: Badi'
authors.initials: B
authors.lastname: Abdul-Wahid
authors.affiliation: University of Notre Dame, Notre Dame, IN 46656 ; Department of Computer Science & Engineering.
authors.forename: Li
authors.initials: L
authors.lastname: Yu
authors.affiliation: University of Notre Dame, Notre Dame, IN 46656 ; Department of Computer Science & Engineering.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Rajan
authors.affiliation: University of Notre Dame, Notre Dame, IN 46656 ; Department of Computer Science & Engineering ; Interdisciplinary Center for Network Science and Applications.
authors.forename: Haoyun
authors.initials: H
authors.lastname: Feng
authors.affiliation: Stanford University, 450 Serra Mall, Stanford, CA 94305 ; Department of Mechanical Engineering ; Institute for Computational and Mathematical Engineering.
authors.forename: Eric
authors.initials: E
authors.lastname: Darve
authors.affiliation: University of Notre Dame, Notre Dame, IN 46656 ; Department of Computer Science & Engineering.
authors.forename: Douglas
authors.initials: D
authors.lastname: Thain
authors.affiliation: University of Notre Dame, Notre Dame, IN 46656 ; Department of Computer Science & Engineering ; Interdisciplinary Center for Network Science and Applications.
authors.forename: Jesús A
authors.initials: JA
authors.lastname: Izaguirre