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Alot of research is done by universities on computing clusters of this scale. It isn’t just the spooks.

Case in point is the Texas Advanced Computing Center http://www.tacc.utexas.edu/

I'm curious, are you a Longhorn, or are you familiar with TACC for some other reason? (Not that TACC is a secret or anything, just curious since I work with TACC almost daily.)

Also, as you pointed out, these types of machines are used all the time for science and engineering, both open science and classified work (I don't do classified work but I've been at various national labs for brief periods. The fact that the machines exist for classified work is not a secret, you just can't use them if you don't have a security clearance).

Three other responses to things that have come up on this thread. First, the benchmarks actually do require that the computer works together on the same problem, you can't just shove 100,000 processors together and all have them run a separate problem and then claim you are the fastest. There is no need for conspiracy theories here, the Chinese are much more advanced than we might like. However, just putting the computer together and running a benchmark doesn't ultimately prove that much if they don't have useful applications that require this much processing power.

Second, there is no reason to believe that the NSA has significantly more powerful computers than this. If you want to believe that because it makes you happy, go ahead, I don't have evidence against it, but there is no reason to believe that they would have access to more computing power than the national labs, when an important goal of the labs is to increase computer simulation capabilities for use in national defense related research. Obviously it is possible that the NSA has computers that are 10 times more powerful or 100 times more powerful, but it is unlikely, since that would put them years ahead of the forefront of computer research everywhere else. It is possible that the NSA is hiding the existence of a Stargate and are currently preparing us for an alien invasion, but I don't just assume that the NSA is doing everything I see in movies.

Finally, as you pointed out, alot of the reason for this is not technology, it is funding. We could build larger computers than this, but building and maintaining them is expensive. Few if any private companies have the need for computers like this, so if the US wants to stay ahead in this field, the US government is going to have to step up and pay for it. Obviously this is government spending, but new weapons and defense technologies don't invent themselves.