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It is the gap between the computing performance predicted by Moore's law and the computing performance in reality.
This gap appears in multi core systems and is primary caused by physical factors. Multi core CPUs have in comparison to single core CPUs more pipelines, caches and control units which slow down the complete system.
Also software development which is lagging behind hardware development is added to Moore's gap because the software can't use the computing performance efficiently. There are high demands on software for the optimum usage of multi core systems. In a supercomputer are hundreds of CPUs with multiple cores which can do parallel complex calculations. To spread the different calculation tasks between the cores efficiently it needs to be supported by the software. It is comparable with 64-Bit- and multithread-software which was missing for the newest CPU generation for home computers at the beginning.