NDLI: Computer Simulation of Polarizable Fluids: a Parallel Implementation Using Linda and Pvm

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Computer Simulation of Polarizable Fluids: a Parallel Implementation Using Linda and Pvm

Content Provider	Semantic Scholar
Author	Martino, Di Ruocco, Giancarlo M. Sampoli C. A. S. P. U. R.
Copyright Year	2007
Abstract	A parallel version of a molecular dynamic program has been implemented and tested on a cluster of alpha processors connected via gigaswitch. A replicated data method has been used to evaluate the long range dipolar forces and many-body polarization eeects. The proposed scheme is convenient for medium to large size sample. The actual code is able to perform molecular dynamic calculations over very large cell, exploiting the full memory capacity of the cluster. This is achieved partitioning the memory requested by the algorithms over the memory of the single processors. This approach is less expensive in terms of computational cost with respect to traditional vector supercomputers. Almost all the code (97%) has been par-allelized using pvm and linda parallel message passing primitives. The parallelization strategy will be discussed to evidentiate diiculties and adopted solutions during the porting of the code. A full report of speedup and results obtained on the alpha cluster will be presented. A comparison between fddi+gigaswitch comunication facility versus ethernet connection will be presented too. Performance data will be reported as function of the number of water molecules involved in the computation (4k,13.5k,32k) and for diierent cut-oo radii (0.8,1,1.2 nanometer). As result of the analisys the trade-oo between number of processes and speedup will be discussed. Performances data comparison between linda and pvm program implementation will be reported. Non optimal work condition of the cluster in non balanced processor load condition will be discussed also.
File Format	PDF HTM / HTML
Alternate Webpage(s)	http://www.netlib.org/pvm3/epvmug94/contrib/dimartino_a.ps
Language	English
Access Restriction	Open
Content Type	Text
Resource Type	Article

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