Standalone Jupyter Notebook¶

Caution: manual approach, requires command line use

This is a manual mechanism to start a Jupyter notebook within a SLURM job on HiPerGator and connect to it from the web browser running on your local computer.

Interactive Session¶

If you're in a dev SLURM session then
- Note the host name, which you'll need to create an SSH tunnel to your notebook. - Load jupyter module. - Start a jupyter notebook with launch_jupyter_lab or launch_jupyter_notebook. Note the information printed to the console. - Create an SSH tunnel from your local computer to the notebook using SSH forwarding (see below).

SLURM Job¶

If you would like a notebook to live for longer than the 12-hour time limit for dev sessions start it inside a SLURM job.
- If you don't want to go through copying/pasting the initial authentication token for every jupyter job set a default password for your notebooks with the following commands
module load jupyter jupyter-notebook password
- Create a job script similar to the example below. Adjust options as necessary.

#SBATCH --job-name=jupyter
#SBATCH --output=jupyter_notebook_%j.log
#SBATCH --ntasks=1
#SBATCH --mem=2gb
#SBATCH --time=04:00:00
date;hostname;pwd    
module add jupyter    
launch_jupyter_notebook

- Note: The jupyter environment includes all R and python packages/modules we installed on request.

Connection Information¶

Once the job starts look at the jupyter_notebook_$SLURM_JOBID.log SLURM output file to learn the hostname and the port jupyter notebook was started on. The ssh tunnel and local URI paths should already be there. For example,

$ cat jupyter_6595668.log
Fri Apr 14 16:22:02 EDT 2017
c10b-s14.ufhpc
/home/jdoe    
Starting Jupyter Notebook on port 23312 on the c10b-s14.ufhpc server.    
SSH tunnel command:
        ssh -NL 23312:c10b-s14.ufhpc:23312 jdoe@hpg.rc.ufl.edu    
Local browser URI:
        http://localhost:23312

If you have not set a default personal password with 'jupyter-notebook password' you will need to find and use the automatically generated authentication token, which is written to the job log once the notebook server starts. For example,

  [W 15:38:37.568 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended
  ...
      Copy/paste this URL into your browser when you connect for the first time,
      to login with a token:
          http://(c100b-s1.ufhpc or 127.0.0.1):29926/?token=06b1c3f73bb847234c198a22bd62b7f20101b04d1bc2b64a
  ...
  [I 15:40:13.516 NotebookApp] Adapting to protocol v5.0 for kernel b5d6cea6-d214-4b37-b01e-4250ae6179c9    
    Copy the token to use it as the password the first time you connect to
    the notebook. In this example the token is
    `06b1c3f73bb847234c198a22bd62b7f20101b04d1bc2b64a`.

Create Tunnel From Local Machine¶

Copy paste the tunnel command from the job script or write your own based on how you manually started a notebook. ssh -NL 23312:c10b-s14.ufhpc:23312 <jdoe@hpg.rc.ufl.edu>

Browse To Notebook¶

In a web browser on the local machine open http://localhost:23312

Provide the personal password or the token from the job log as the password to authenticate. Enjoy using the rich python programming and visualization environment provided by Jupyter running on UFRC computing resources. Again, note that the default Jupyter Notebook setup you see should have at least four kernels - two default kernels (python and R) that come with Jupyter and two additional kernels that provide access to environments provided by RC-specific environment modules e.g. 'RC R-3.5.1' and 'RC Py3-3.6.5', which match the same environment modules you use in batch jobs.

Filesystem Access¶

See Jupyter Filesystem Access for details on how to set up convenient filesystem access from the jupyterlab interface.