As mentioned, ATLAS typically gets its best performance when compiled with gcc using the flags that ATLAS automatically picks for your platform (this assumes you are installing on a system that ATLAS provides architectural defaults for). However, you can vary the interface (API) compilers without affecting ATLAS's performance. Since most compilers are interoperable with gcc this is what we recommend you do if you are using a non-default compiler. Note that almost all compilers can interoperate with gcc, though you may have to throw some special flags (eg., /iface:cref for MSVC++).
The configure flags to override the C interface compiler and flags are:
-C ic <C compiler> -F ic '<compiler flags>'
The configure flags to override the FORTRAN interface compiler and flags are:
-C if <FORTRAN compiler> -F if '<compiler flags>'
For example, assume you use the Sun Workshop compilers available
under Solaris. You can instruct configure to use them for building the
APIs rather than the gnu compilers with something like:
-C if f77 -F if '-dalign -native -xO5' \ -C ic cc -F ic '-dalign -fsingle -xO5 -native'
<985>>R. Clint Whaley 2016-07-28