Sure, but if you are compiling without -mavx, why would you want the AVX intrinsics? You cannot use AVX intrinsics anyway, if AVX is not enabled.So I don't fully understand the problem this configure scripting is supposed to solve?
Think about run time check of available CPU features and then using this code for performance critical sections only. Allows to generate programs which are generic to all CPUs in the main code paths, and able to switch to high performance implementations of critical code paths depending on the feature of the CPU.
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