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Distributed Molecular Modeling over Very-Low-Bandwidth Computer Networks

Will Ware*

14 Washington Ave.
Arlington MA 02174
email: wware@world.std.com

This is an abstract for a poster to be presented at the Fifth Foresight Conference on Molecular Nanotechnology. A draft of the full article is available at the author's Web site. The full paper is also available here.

The Internet offers the possibility of distributing a molecular modeling task over a number of geographically diverse computers. If these computations can be arranged not to intrude on the extant workloads of home and office desktop computers, vast resources may become available. This scenario offers extremely limited communication bandwidth, so the problem of partitioning molecular modeling (normally a fairly communication-intensive task) in a reasonably efficient manner becomes interesting. This paper presents a partitioning approach that will allow individual processors to simulate thousands of time steps before requiring communication with other processors.

Communication bandwidth is replaced by duplicated computations, exploiting the spatially localizable influence of each atom upon its neighbors. Processors are assigned to model overlapping cubical regions of space. Duplicate modeling results for overlap regions gradually diverge, due to differences in the boundary information available to neighboring processors. By characterizing these divergences and keeping track of them, processors can update one another locally, each processor acting as the expert on a small cubical region of space in the center of its own initially assigned area.

Each processor is ignorant of the world beyond its own initially assigned region. The unknown effects of that outer world propogate inward from the known border over time. The velocity of propogation is characterizable. A processor may continue computing without communicating with its neighbors until noticeable external effects reach its area of expertise. With periodic updates from its neighbors, a processor should be able to simulate for long periods of time.

The trade-off of communication bandwidth with duplicated computations is acceptable in the envisioned scenario. This approach might also be useful in more traditional computing environments of networked workstations, in cases where communication bandwidth may be significantly expensive compared to computation.


*Corresponding Address:
Will Ware,14 Washington Avenue, Arlington MA 02174, email: wware@world.std.com, http://world.std.com/~wware/
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