With an old install, but using full install command

When rebuilding an old install, the main trap is to avoid having architectural defaults make it so you don't time your new kernel. Tail your Make.<arch> file, and see if the macro ARCHDEF is set. If so, cd to the directory pointed at by ARCHDEF, and then issue

   rm <pre>u* 
   rm <pre>MMRES

From your ATLAS directory, then issue:

   rm bin/<arch>/INSTALL_LOG/*
   rm tune/blas/gemm/<arch>/res/<pre>u*
   rm tune/blas/gemm/<arch>/res/<pre>MMRES
   make install arch=<arch>