I have installed numpy with my own ATLAS, but trying to install PyMC, it can't find the ATLAS libs. I also have an older package that formerly installed but no longer does. I'm being a bit lazy, but am I missing something? Briefly checking, it looks like the conventions/assumptions for site.cfg in an installation as per site.cfg.example are different from those expected of numpy.distutils.system_info. I have the directories specified under [DEFAULT] as per the installation instructions. If I don't have the libraries installed in one of the default folders, it looks like they're not found. [~/] [1]: from numpy.distutils import system_info [~/] [2]: np.show_config() atlas_threads_info: libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/home/skipper/built/atlas_files/lib'] define_macros = [('ATLAS_INFO', '"\\"3.9.32\\""')] language = f77 include_dirs = ['/home/skipper/built/atlas_files/include'] blas_opt_info: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/home/skipper/built/atlas_files/lib'] define_macros = [('ATLAS_INFO', '"\\"3.9.32\\""')] language = c include_dirs = ['/home/skipper/built/atlas_files/include'] atlas_blas_threads_info: libraries = ['ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/home/skipper/built/atlas_files/lib'] define_macros = [('ATLAS_INFO', '"\\"3.9.32\\""')] language = c include_dirs = ['/home/skipper/built/atlas_files/include'] lapack_opt_info: libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas'] library_dirs = ['/home/skipper/built/atlas_files/lib'] define_macros = [('ATLAS_INFO', '"\\"3.9.32\\""')] language = f77 include_dirs = ['/home/skipper/built/atlas_files/include'] lapack_mkl_info: NOT AVAILABLE blas_mkl_info: NOT AVAILABLE mkl_info: NOT AVAILABLE [~/] [3]: system_info.get_info('atlas',1) /usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:462: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(self.notfounderror.__doc__) [3]: {}