Are you aware of Dan J. Bernstein's library?: http://cr.yp.to/djbfft.html

According to his benchmarks (from 1999?) it is faster than FFTW. I don't
know whether that's still the case, a quick search did turn up
http://projects.scipy.org/pipermail/scipy-dev/2002-August/001107.html
which suggests that this was still the case in 2002. Support for djbfft
seems to have been integrated into scipy.

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