That paper I mentioned that explains OS noise really nicely (and other things to) is:

  • Petrini, F. , Kerbyson, D.J. and Pakin, S. (2003) The case of the missing supercomputer performance: Achieving optimal performance on the 8,192 processors of ASCI Q. In Proceedings of the 2003 ACM/IEEE conference on Supercomputing., page 55, . IEEE Computer Society. ((URL)) (BibTeX)

Since, there have been many papers that do similar analyses and offer solutions on a variety of machines and models. Google Scholar is your friend here.