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. Follow the instructions given in Section 2.9.2, but additionally make sure you delete any prexisting directory that matches your ARCH definiton. Therefore, in the above example, in the ATLAS/CONFIG/ARCHS directory, you would additionally issue:
   rm -rf Core2Duo64SSE3
If such a subdirectory existed.

From your BLDdir directory, then issue:

   rm bin/INSTALL_LOG/*
   rm tune/blas/gemm/res/<pre>u*
   rm tune/blas/gemm/res/<pre>MMRES
   make build

Clint Whaley 2012-07-10