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How to configure Linux to run benchmarks as stable as possible?

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http://unix.stackexchange.com – I have several long running benchmarks (SPEC CPU 2006 benchmarks) to run on a Linux server. The server is running Gentoo Linux with a Linux Kernel 3.6.11. I saw some big differences between different runs and I'm thinking that it could be some problem with my configuration. I'm the only user of the server. I have already disabled the CPU frequency scaling feature of the kernel. Is there some others things I should configure/disable/enable in the kernel or on the installation ? I do not need to make the server faster, but I want to make sure that the benchmarks are not encountering pe (HowTos)