Re:The arrangement (Score 2, Interesting)

A torus shape gives you the easiest way to get a short point to point communications path. It's better than a fat tree or a straight mesh type topology.

The Cray XT3 and Xt4 systems us a X Y Z physical connection. So, X is along the rows and modules within a cabinet (width), Y is vertical within a Cabinet (height), and Z is between the rows (depth).

This works fairly well from a maintenance AND a performance view. You can get some other more esoteric structures built, but they have trade offs in performance vs maintainability. This one works pretty well for these systems