The performance of different communication mechanisms and algorithms used for parallelization of molecular dynamics code
R Metkowski and P Bala and T Clark, PARALLEL PROCESSING APPLIED MATHEMATICS, 2328, 154-161 (2002).
Communication performance appears to have the most important influence on parallelization efficiency of large scientific applications. Different communication algorithms and communication mechanisms were used in parallelization of molecular dynamics code. In is shown that in the case of fast communication hardware well scaling algorithm must be used. Presented data shows that MD code can be also run efficiently on the pentium cluster but low latency communication mechanism must be used.
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