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There are three primary limits to performance at the supercomputer level: individual processor speed, the overhead involved in making large numbers of processors work together on a single task, and the input/output speed between processors and between processors and memory. Input/output speed between the data-storage medium and memory is also a problem, but no more so than in any other kind of computer, and, since supercomputers all have amazingly high RAM capacities, this problem can be largely solved with the liberal application of large amounts of money.
The speed of individual processors is increasing all the time, but at a great cost in research and development, and the reality is that we are beginning to reach the limits of silicon based processors. Seymour Cray showed that gallium arsenide technology could be made to work, but it is very difficult to work with and very few companies know enough to make usable processors based on it. It was such a problem that Cray Computer was forced to acquire their own GaAs foundry so that they could do the work themselves.