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Shawn Doughty (Deactivated)

Shawn Doughty (Deactivated)

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Excerpt

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 moreSageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.

 

  1. Code Block
    languagebash
    titleInstall 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. Code Block
    titleInstall jupyter within anaconda
    login001: miniconda3/bin/conda install jupyter
  3. Start up jupyter

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

      Code Block
      languagebash
      titleGet 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. Code Block
      titleStart 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. Code Block
      languagebash
      titleNow 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. Code Block
      titleDon'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

...