By default, ATLAS automatically uses the architectural defaults anytime it has results for the given architecture and compiler. However, the compiler detection is based on the compiler name, not version, and so ATLAS's architectural defaults for gnu gcc4.7.0 might not be best for gcc3 or apple's gcc, etc, even though configure would use the architectural defaults in such cases.
So, there are times when you want to tell ATLAS to ignore any architectural defaults it might have. Common reasons include the fact that you have overridden the compiler flags ATLAS uses, or are using an earlier version of the supported compiler. In these cases, the best idea is often to install both with and without the architectural defaults, and compare timings. If both your installs (homegrown-compiler/flags+archdef, homegrown-compiler/flags+search) are slower than the architectural defaults using the default compiler, you should probably install the default compiler. However, if your results are largely the same, you know your changes haven't depressed performance and so it is OK to use the generated libraries (see Section for details on timing an ATLAS install). If your timing results are substantially better, and you haven't enabled IEEE-destroying flags, you should send your improved compiler and flags to the ATLAS team!
To force ATLAS to ignore the architectural defaults (and thus to perform a full ATLAS search), pass the following flags to configure:
-Si archdef 0
R. Clint Whaley 2016-07-28