To shut down Jupyter and any notebooks that are running, you have to go to the command prompt (Terminal on OS X or Anaconda Prompt in Windows) where you started Jupyter. Press Control-c, and quickly type 'y' and press enter. You have to type 'y' and press enter within 5 seconds, or the message 'No answer for 5s: resuming operation..." will appear. If that happens, press Control-c again.