Urban Borštnik (2007) Parallel Computer Simulations on Clusters of Personal Computers. PhD thesis.
Parallel computer programs are used to speed up the calculation of computationally-demanding scientific problems such as molecular dynamics (MD) simulations. Parallel MD methods distribute calculations to the processors of a parallel computer but the efficiency of parallel computation decreases due to interprocessor communication. Calculating the interactions among all atoms of the simulated system is the most computationally demanding part of an MD simulation. Parallel methods differ in their distribution of these calculations among the processors, while the distribution dictates the method's communication requirements. I have developed a parallel method for MD simulation, the distributed-diagonal force decomposition method. Compared to other methods its communication requirements are lower and it features dynamic load balancing, which increase the parallel efficiency. I have designed a cluster of personal computers featuring a topology based on the new method. Its lower communication time in comparison to standard topologies enables an even greater parallel efficiency.
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