With a fresh install

First, run config as usual. Then, tail the created Make.inc file, and see if the macro INSTFLAGS includes -a 1. If so, ATLAS has some architectural defaults for your architecture (though perhaps not for your compiler, if you have forced the use of a non-default compiler), which won't include your shiny new kernel. So, you will need to remove the files indicating the default gemmK kernel for your precision. To do this, scope your ARCH setting in your Make.inc. For the purposes of this discussion, let us say it set to Core2Duo64SSE3 (i.e., in the below example, substitute the definition of ARCH for Core2Duo64SSE3). Go to ATLAS/CONFIG/ARCHS, and issue the following commands:

   gunzip -c Core2Duo64SSE3.tgz | tar xvf -
   rm Core2Duo64SSE3/gemm/gcc/<pre>u* 
   rm Core2Duo64SSE3/gemm/gcc/<pre>MMRES
   rm Core2Duo64SSE3.tgz
   tar cvf Core2Duo64SSE3.tar Core2Duo64SSE3
   gzip Core2Duo64SSE3.tar
   mv Core2Duo64SSE3.tar.gz Core2Duo64SSE3.tgz

Now, continue install as normal, and your kernel should be used if it beats what ATLAS is presently using. Note that this assumes you are using gcc as the gemmK compiler, which is the default on most systems. If you are using a different compiler, you would substitute its name instead of gcc in the above lines. If there is no subdirectory with the name of your compiler in the tarfile, ATLAS has no architectural defaults for that compiler, and thus you need to make no changes to the tarfile.