IPython/Jupyter notebook setup on SDSC Comet


September 17, 2015


This tutorial explains the setup to run an IPython Notebook on a computing node on the supercomputer Comet at the San Diego Supercomputer Center and forward the port encrypted with SSH to the browser on a local laptop.

Quick reference

  • Add module load python scipy to .bashrc
  • Make sure you can ssh passwordless within comet, i.e. ssh comet.sdsc.edu from comet login node works without password
  • Get submit_slurm_comet.sh from https://gist.github.com/zonca/5f8b5ccb826a774d3f89
  • Change the port number and customize options (duration)
  • sbatch submit_slurm_comet.sh
  • Remember the login node you are using
  • From laptop, use bash tunnel_notebook_comet.sh N where N is the Comet login number (e.g. 2) from https://gist.github.com/zonca/5f8b5ccb826a774d3f89
  • From laptop, open browser and connect to http://localhost:YOURPORT

Detailed walkthrough

One time setup on Comet

Login into a Comet login node, edit the .bashrc file in your home folder (with nano .bashrc for example) and add module load python scipy at the bottom. This makes sure you always have the Python environment loaded in all your jobs. Logout, log back in, make sure that module list shows python and scipy.

You need to be able to SSH from a node to another node on comet with no need of a password. Create a new SSH certificate with ssh-keygen, hit enter to keep all default options, DO NOT ENTER A PASSWORD. Then use ssh-copy-id comet.sdsc.edu, enter your password to make sure the key is copied in the authorized hosts. Now you can check it works by executing:

ssh comet.sdsc.edu

from the login node and make sure you are NOT asked for your password.

Configure the script for SLURM and submit the job

Copy submit_slurm_comet.sh from https://gist.github.com/zonca/5f8b5ccb826a774d3f89 on your home on Comet.

Change the port number in the script to a port of your choosing between 8000 and 9999, referenced as YOURPORT in the rest of the tutorial. Two users on the same login node on the same port would not be allowed to forward, so try to avoid common port numbers as 8000, 9000, 8080 or 8888. Tho

Choose whether you prefer to use a full node to have access to all 24 cores and 128GB of RAM or if you only need 1 core and 5GB of RAM and change the top of the script accordingly.

Choose a duration of your job, for initial testing better keep 30 minutes so your job starts straight away.

Submit the job to the scheduler:

sbatch submit_slurm_comet.sh

Wait for the job to start running, you should see R in:

squeue -u $USER

The script launches an IPython notebook on a computing node and tunnels its port to the login node.

You can check that everything worked by checking that no errors show up in the notebook.log file, and that you can access the notebook page with wget:

wget localhost:YOURPORT

should download a index.html file in the current folder, and NOT give an error like “Connection refused”.

Check what login node you were using on comet, i.e. the hostname on your terminal on comet, for example comet-ln2.

Tunnel the port to your laptop

Linux / MAC

Download the tunnel_notebook_comet.sh script from https://gist.github.com/zonca/5f8b5ccb826a774d3f89.

Customize the script with your port number.

Lauch bash tunnel_notebook_comet.sh N where N is the comet login node number. So if you were on comet-ln2, use bash tunnel_notebook_comet.sh 2.

The script forwards the port from the login node of comet to your laptop.


Install putty.

Follow tutorial for local port forwarding on https://www.akadia.com/services/ssh_putty.html/

  • set comet-ln2.sdsc.edu as remote host, 22 as SSH port
  • set YOURPORT as tunnel port, replace both 8080 and 80 in the tutorial with your port number.

Connect to the Notebook

Open a browser and type http://localhost:YOURPORT in the address bar.