As Jay Lyman, an analyst at The 451 Group points out, Linux is only growing stronger in supercomputing. "When considered as the primary OS or part of a mixed-OS supersystem, Linux is now present in 469 of the supercomputer sites, 93.8% of the Top500 list. This represents about 10 more sites than in November 2007, when Linux had presence in 91.8% of the systems. In fact, Linux is the only operating system that managed gains in the November 2008 list. A year ago, Linux was the OS for 84.6% of the top supercomputers. In November 2008, the open source OS was used in 87.8% of the systems. Compare this to Unix, which dropped from 6% to 4.6%, mixed-OS use which dropped from 7.2% to 6.2% and other operating systems, including BSD, Mac OS X and Windows, which were all down this year from the November 2007 list."
Microsoft is proud that a system running Windows HPC Server 2008 took 10th place... behind nine supercomputers running Linux. Even then, this was really more of a stunt than a demonstration that the HPC Server system is ready to compete with the big boys.
You see, there are no Microsoft programming tools to write supercomputer compatible applications. That will come years from now with Visual Studio 2010 and when Microsoft's F# is more than a research project language. In short, Windows HPC isn't ready for prime-time.
In the meantime, the real work is being done on the Linux computers. The number one supercomputer? Once more it's IBM's Linux-powered Roadrunner That's the same supercomputer, which this summer broke supercomputing's sound barrier: a sustained run of more than one petaflop per second or 1.026 quadrillion calculations per second. Beat that Microsoft!
The Roadrunner does have competition now though. The Cray XT Jaguar also recently busted the petaflop wall. The Cray also, of course, runs Linux. In the XT's case, it's running CNL (Compute Node Linux). CNL is based on SUSE Linux.
Needless to say, all the Linux systems do have working parallel-processing languages, like GCC, PGI and PathScale. For now, and the foreseeable future, Linux will not only stay the fastest computers, they'll also be the most useful fast computers.