Jupyter

The Jupyter Notebook is an open source web application for interactive data science and scientific computing across over 40 programming languages. It allows you to create and share documents that contain live code, equations, visualizations and explanatory text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, machine learning and much more. 

1. Install your own version of python.

   login001: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
   login001: chmod u+x Miniconda3-latest-Linux-x86_64.sh
   login001: ./Miniconda3-latest-Linux-x86_64.sh

2. Install jupyter within anaconda

   login001: miniconda3/bin/conda install jupyter

3. Start up jupyter
   

   1. Request a default # of cores and memory as a test.

      Get an allocation on a compute node. Write down the name of the assigned compute node

      login001: srun -c 4 --pty -p interactive bash
      alpha001: 

      NOTE: This gives you four cores, for future runs of jupyter you can ask for more, up to 40. Be sure to select the matching # of threads in the top right corner of the jupyter interface.

   2. Start jupyter on the compute node. It will display the port # the software is running on, usually 8888

      alpha001: miniconda3/bin/jupyter notebook --no-browser
      [NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
      [NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

      NOTE: Be aware of the port number 8888 above. Your port may be different, Adjust the instructions below accordingly.
      NOTE: Jupyter may output a start up token at this point which may be required when logging in via the web interface. You can cut and paste it.

4. Access jupyter
   1. Now setup forwarding from your workstation thru the headnode to the assigned compute node, in this example it is alpha001

      Your Workstation: ssh username@login.cluster.tufts.edu -L 8888:localhost:8888 ssh alpha001 -L 8888:localhost:8888

   2. Point the browser on your workstation to http://localhost:8888/    and the jupyter web interface should come up.

   3. NOTE: If jupyter asks for a token, this can be found when you started it up. Cut and paste the correct value.
      
   4. Do computation, do science!
5. Exit jupyter
   1. Don't forget to exit jupyter so it isn't taking up resources

      The Jupyter Notebook is running at: http://localhost:8888/
      Shutdown this notebook server (y/[n])? y
      [C 14:19:54.199 NotebookApp] Shutdown confirmed
      [I 14:19:54.199 NotebookApp] Shutting down kernels

Project Home Page

http://jupyter.org/