FFTW auto-build and advice is no longer generally applicable
Recent testing on Haswell suggests both that use of hyperthreads and FFTW compiled with AVX can be beneficial, so we need to try to update our build-own-fftw and build-system advice to be a bit more applicable. (Rossen should have some of our own performance results here, but I haven't seen them yet.)
In particular, Cray's modified FFTW might have properties different from standard FFTW, and it would be nice to have a hint in the install guide about which is best to use, and the best way to configure and run on Crays.
Updated FFTW recommendations in install-guide.
Both SSE2 and AVX should be used, and there is now
info about the upcoming FFTW-3.3.5 with more SIMD support,
as well as a link to an unofficial prerelease on the gmx site.