 <p>So I found my problem. First of all, from the problem I undestand that it tries to close a window that's already closed, so I searched why and it looks like now the displays of pyplot are supposed to close directly after so when I add pl.show(block=True). Now I have a display but also a segmentation fault.</p> <p>After trying different backends it looks like TkAgg solves both problems. So no compatibility issues and I can see my plots.</p> <p>PS : for changing the backend from matplotlib go to <code>~/.matplotlib</code> and edit the file <code>matplotlibrc</code></p>