Using Atlas from scipy

You don't have to copy anything anywhere.

You should add the atlas libraries to the list of locations ld will search.

In directory /etc/ld.so.conf.d you can add the file atlas-lib.conf. This file should contain the directory of libatlas.so.3gf, which is /usr/lib/atlas-base.

You can do this by running

echo "/usr/lib/atlas-base" | sudo tee /etc/ld.so.conf.d/atlas-lib.conf

Finally run

sudo ldconfig

to update ld so that it knows about this new file.

Alternatively you can set LD_LIBRARY_PATH to include the path to the library when you run and it should be available within SciPy.