Yes it is correct that for amd64 SSE is enabled by default in the
compiler. But (if I'm not wrong) the FFTW --enable-sse flag does not
(only) set compiler flags. Instead it activates the specially written
SSE optimized kernels are compiled. Because the --enable-sse flag is not
passed, those kernels are not compiled even though all amd64 processors
have SSE/SSE2. Thus SSE is activated in the compiler but not for FFTW.

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https://bugs.launchpad.net/bugs/602586

Title:
  SSE is not enabled for amd64

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