I thought most of the scientific computation is written in Fortran. Anyways, I have used a big closed source scientific computation package several jobs ago to

I thought most of the scientific computation is written in Fortran. Anyways, I have used a big closed source scientific computation package several jobs ago to conduct experiments. The entire stack was running on windows at the time, but the operating system really did not (and does not) matter. I agree with you that MS compilers should support C99 but it has very little to do with how useful windows is for scientific computing. (Worst case scenario you can use an opensource compiler). I think the reason why the top 500 HPC clusters are using linux is the price of the operating system and not the functionality.