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Robust and effective implementations for large-scale realistic application programs are analyzed under the assumption that they are executed on the next-generation supercomputer system. In order to estimate performance of all-electron calculations of a ribosome, a discrete-event simulation for the parallel program is introduced, in which execution of program components and communications between them is emulated. Through the analysis, it is realized that middleware developed for Grids is still valid and useful even for massively-parallel supercomputer systems since they have a huge number of cores and full stability over weeks is not guaranteed.
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