Cray and AMD announced today that they will continue making Cray supercomputers with AMD Opteron processors. They already had an existing relationship but this deal extends it until the end of the decade.
I imagine using off the shelf components like the AMD processors will help them lower development and hardware costs. Of course when you're building a 2048 processor super-computer, cost usually isn't an issue.
It seems to me that super computers have been getting kind of phased out over recent years in favor of clusters of machines instead. Clusters can be built much cheaper, by expanded easily, and are built from off the shelf components. Most clustered systems these days are running linux or something similar (it is free, and the tools needed for clustering are widely available, such as Beowulf). Microsoft also has some parallel computing software, but I imagine it would get quite costly as the size of your cluster grew.
I'm not sure what kind of operating system Cray is using for these systems. They used to have their own OS, which may have changed.
The Cray and AMD partnership is to create a new supercomputer for the government, which they will use to crack encryption and all sorts of other things that people without an unlimited budget could never imagine being capable of.
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