nicholson boom-lab Woods Hole Oceanographic Institution

Running Jupyter Notebooks on Poseidon

Running Jupyter Notebooks Remotely on Poseidon

Based on this blog post from the Alexander Lab.

1: Connect to Poseidon

Open a Terminal window on your local machine and type:

colette$ ssh <whoi.ID>@poseidon.whoi.edu

2. Module load Anaconda

To use conda or any other software on Poseidon, you need to load the associated module first. The anaconda3/2021.11 module contains a recent version of conda. The anaconda/5.1 module contains a much older version of conda, which will make solving environments and adding packages extremely slow.

[colette.kelly@poseidon-l2 ~]$ module load anaconda3/2021.11

3. Activate conda environment

[colette.kelly@poseidon-l2 ~]$ source activate <env-name>

4. Start interactive session on a compute node

You need at least 1 GB memory to work with data from one float; more (2 GB+) for working with a region’s worth. The session will time out if you go over the requested memory.

(conda-env) srun -N 1 -n 1 --mem=1000 --time=00:30:00 --pty bash

5. run “export XDG_RUNTIME_DIR=”

You should only need to do this once:

[colette.kelly@pn026 ~]$ export XDG_RUNTIME_DIR=""

6. Launch Jupyter Notebook without a browser window

[colette.kelly@pn026 ~]$ jupyter notebook --no-browser --port=8888

7. Create an SSH tunnel

Open a new Terminal window on your local machine and type the following. Replace “pn026” with whatever node the interactive session is running on.

colette$ ssh -t -t <whoi.ID>@poseidon.whoi.edu -L 8888:localhost:8888 ssh pn026 -L 8888:localhost:8888

8. Open Jupyter Notebook in a browser window

Copy-past the url that begins with “http://localhost:8888/tree?token=” into a browser window. Or, if Jupyter passwork is configured, just enter “localhost:8888” in a browser window.

You can set configure a Jupyter password by entering the following in a terminal:

jupyter notebook password

You’ll need to restart your Jupyter Notebook session to be able to use the new password.

9. Shut down Jupyter Notebook

Make sure you shut down the Jupyter Notebook (either control-C in Terminal or with the Jupyter GUI), otherwise you might run into issues re-opening a port.

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