Jupyter Lab or Notebook

Using Open OnDemand

Open OnDemand allows a Jupyter Lab or Notebook to be opened directly from a web browser.

Log on to OnDemand with your NIH credentials. Choose Jupyter under the InteractiveApps option or from the Pinned App icon.

Jupyter OnDemand Home

 
Choose the job submission parameters. The wall time selection is important as the job will be killed when the limit is reached. The maximum wall time for each partition is listed in the partition help text. You may select to have the first available GPU or can choose a specific type card. If you select using a GPU, the partition is then fixed as "gpu". Click Launch to submit the job request to FRCE.

Jupyter OnDemand Select

 
The next page shows the status of your job either as Queued or Starting or Running. Your job may sit in a queue for a few minutes depending on cluster load and resources requested.

Jupyter OnDemand Run

 
When the job is ready, please click on Connect to Jupyter. This will now launch a Jupyter App, presenting file listing on the left and a generic pane on the right  with choice of available kernels, consoles, etc.
 

Jupyter OnDemand Start

 
Selecting an existing app will open the app in the running window, allowing for normal execution.

Jupyter OnDemand App

From a command line

If running from a command line, it is necessary to run on a compute node. The first part will describe principles to run Jupyter and to ssh tunnel Juypter traffics. The second part will show an integrated process with a SLURM script.

Jupyter/7.1.3 is available with iKernels for bash, python 3.6-3.12 and R.

Part One(an automatic way): Setup ssh tunneling through sbatch:

There is a template sbatch script to help setup Jupyter notebook and the tunneling. As of 11/30/2023, the repository has been updated to reflect current OS migration on FRCE nodes.

  1. On FRCE head node, module load frce/1.0
  2. Run "sbatch_templates.sh". You will have directory ./FRCE_EXAMPLES/slurm/ created from the previous step.
  3. Run sbatch FRCE_EXAMPLES/slurm/jupyter_oel8.sh
  4. With that SLURM job running, you will get an email about a command line to setup ssh tunneling and the url used to access Jupyter notebook from your web browser.
  5. In some cases that suggested local port may have aready been used. In those cases, you will need to change the local port in the tunneling and url. In the ssh tunneling command, the first port number is for a local port that you are going to use in your browser.
  6. In rare cases, configuration in files under ~/.jupyter/ may interfere with the script. If you don't get Jupyter session email, try to move that directory to a different place, such as mv ~/.jupyter ~/.jupyter_bak.

Part Two(a manual way): Basic Steps

Step1, A user needs to have an interactive SLURM session. With the following command, user will be prompted to be on a compute node terminal.

  • srun --pty bash

Step2, Within the interactive session, setup environment necessary to run Jupyter.

  • module load jupyter

Step3, Within the session, a user can start a jupyter notebook server with the following command with a selected port above 32768.

  • jupyter-notebook --no-browser --ip $(hostname -i | sed "s/ /\n/g" | grep -v : ) --port 64000

Step4, take the hostname in the output line, such as fsitgl-hpc085 in the following example output. If the user defined port, for example 64000 above. If the port is not available, jupyter will assign another port number in the output.

  • http://fsitgl-hpc085p.ncifcrf.gov:64000/?token=ea8749e77c1045bf0b4a8272f2da6f505dab4d49069b2aa9

Step5, tunnel the tcp traffic from your desktop to jupyter though head node. We use 8888 of the local desktop in the following example.

  • From a Mac or Linux desktop:
    • ssh -L 8888:fsitgl-hpc085:64000 userid@fsitgl-head01p
  • From a Windows desktop using PuTTY:
    • Right-click on the title bar of the PuTTY window used to log into the cluster to bring up a menu. Select Change Settings.
    • In the resulting menu, select Connection ⇒ SSH ⇒ Tunnels. Add the ports from the jupyter output as shown here.
      http://localhost:8888/?token=ea8749e77c1045bf0b4a8272f2da6f505dab4d49069b2aa9
    • Click Add and then Apply.

Step6, on a web browser in your desktop, open the following url. Take the url in Step3, and replace fsitgl-hpc085p.ncifcrf.gov:64000 with localhost:8888 to have the following url to access from your web browser.

  • http://localhost:8888/?token=ea8749e77c1045bf0b4a8272f2da6f505dab4d49069b2aa9

Comments:

In the above example, we have two sets of tcp ports, such as 8888 and 64000 in the above example. Each set should be consistent. The 8888 in Step5 should match 8888 in Step4, and 64000 in Step3 should match the 64000 in Step4.