In recent times, even in downturn Intel has done some smart purchases. I feel this deal is win-win for both the Intel and Cray. I feel this deal is more in favour of Cray because they still keep the IP rights which means they can build on those IP's.
I am not sure what is Cray's advantages are in their interconnects are... at the base band, for a given signaling frequency (& wire gauge in case of Copper), the latencies are comparable between IB and Cat6A. The hardware-dependent latencies are a small fraction of the overall latency figures.
On the mother boards, it is a different story -perhaps this is where Cray brings in some advantages? It is not clear from the article...
"Bolding, however, was adamant that the “strong partnership” with Intel would not affect Cray’s relationship with either AMD or Nvidia..", this is like telling your girlfriends that marriage will not affect their relationship.
I'm sure that Intel did not enjoy that the X6 was filled with AMD cpus. This could be looked at similar to sponsoring a cycling team (which can sometimes cost in the neighborhood of 50 million). Plus you get technology and IP on top of it! Cray doesn't really lose much, presumably, since they can still use the technology...
In the long term, I can see Intel extending its on chip ring bus and QPI processor bus with hooks into the system clustering interconnect to provide performance advantages and extend its reach into systems (i.e. platform) technologies. Such hooks could make its processors and networking chips preferred solutions in HPC systems. Look out Mellanox!
This is a very great business technique Cray is getting benefited two ways getting more money and simultaneously not reducing the overhead without completely loosing them, its really a great work done by Cray.