T.W. Clark, J.A. McCammon, L.R. Scott, and S. Wlodek. I/O limitations in parallel molecular dynamics. In Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego, CA, December 1995. IEEE Computer Society Press. Frank Baker and Janus Wehmer, production editors. Available on CD-ROM and at http://www.supercomp.org/sc95/proceedings. Home/Search Document Not in Database Summary Related Articles Check |
This paper is cited in the following contexts:
Applications of Parallel I/O - Kotz (1996) (Correct)
....files, one containing three three dimensional matrices X, Y, and Z, 1 http: www.cs.dartmouth.edu reports abstracts TR96 297.html. and the other containing the four dimensional matrix Q. The matrices are spread over all the nodes, and each file is written in parallel by the processors. ffl [CSWM95] They discuss data production rates and their impact on the performance of scientific applications using parallel computers. They present performance data for a biomolecular simulation of the enzyme, acetylcholinesterase, which uses the parallel molecular dynamics program EulerGROMOS. The ....
Terry W. Clark, L. Ridgway Scott, Stanislaw Wlodek, and J. Andrew McCammon. I/O limitations in parallel molecular dynamics. In Proceedings of Supercomputing '95, 1995.
Attributes of Molecular Dynamics Calculations: Accounting for CPU.. - Clark (1997) Self-citation (Clark) (Correct)
....the system. One point consists of the the Cartesian coordinates for position and velocity. The frequency these data are output depends on the simulation goals. Were it not for periodic and abbreviated outputting and calculation of properties on the fly, output alone could dominate the calculation [9]. Shake is a method used to constrain bonds to a fixed length thereby permitting a time step up to five times greater than that used without constraints [27] Shake is expensive to parallelize for distributed algorithms due to the interprocess dependencies arising from bonds crossing domains. ....
....simulation details can be difficult to interpret and reproduce. Similarly, the picture one sees in evaluating a computing system with molecular dynamics may depend significantly on diversity in the simulation. In addition, because of variability in simulation parameters and algorithmic approaches [5, 9, 23, 29], one may benefit by considering attendant caveats when comparing different molecular dynamics algorithms, sequential and parallel alike. In the next section we look at features that are less dependent on the simulation input parameters, but, rather, are indicative of the molecular dynamics ....
T.W. Clark, J.A. McCammon, L.R. Scott, and S. Wlodek. I/O limitations in parallel molecular dynamics. In Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego, CA, December 1995. IEEE Computer Society Press. Frank Baker and Janus Wehmer, production editors. Available on CD-ROM and at http://www.supercomp.org/sc95/proceedings.
Molecular Dynamics of Acetylcholinesterase Dimer.. - Wlodek, Clark.. (1997) (1 citation) Self-citation (Clark Scott Wlodek Mccammon) (Correct)
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Clark, T. W.; Scott, L. R.; Wlodek, S.; and McCammon, J. A. I/O limitations in parallel molecular dynamics. In Baker, F. and Wehmer, J., editors, Proceedings of the 1995 ACM/IEEE Supercomputing Conference. IEEE Computer Society Press, 1995. Available on CD-ROM and at http://www.supercomp.org/sc95/proceedings.
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