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# from behind VPN if off-campus or on wireless ssh snumber@gc-prd-hpclogin1.rcs.griffith.edu.au source /usr/local/bin/s3proxy.sh #To gain internet access on the login node module load anaconda3/2021.11 conda create --name widg-env --channel conda-forge matplotlib jupyterlab ipywidgets ipympl source activate widg-env #To see the packages in your Conda environment, run this command conda list conda deactivate exit |
Learn more about ipywidgets and ipympl
Usage
Do Not Run Jupyter on the Login Nodes
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Internet is Not Available on Compute Nodes. Jupyter sessions will have to run on the compute nodes which do not have Internet access. This means that you will not be able to download files, clone a repo from GitHub, install packages, etc on the compute nodes. You will need to perform these operations on the login node node (e.g gc-prd-hpclogin1.rcs.griffith.edu.au) before starting the session. You can run commands which need Internet access on the login nodes (gc-prd-hpclogin1). Any files that you download while on the login node will be available on the compute nodes.
Running on a Compute Node via
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Interative pbs
First, from the login node (gc-prd-hpclogin1), request an interactive session on a compute node.
The command below requests 1 CPU-core with 4 GB of memory for 1 hour:
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http://127.0.0.1:8889/?token=61f8a2aa8ad5e469d14d6a1f59baac05a8d9577916bd7eb0 Another example: http://127.0.0.1:8890/?token=8df8a9a79c00f0813055d48dfc79785c8ff6597cc0b1c456 Choose "New" then "Python 3" to launch a new notebook. Note that Jupyter may use a port that is different than the one you specified. This is why it is important to copy and paste the URL. |
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When you are done, terminate the ssh tunnel on your local machine (desktop/laptop) by running lsof -i tcp: |
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8889 to get the PID and then kill -9 <PID> (e.g., kill -9 6010). |
Choose "New" then "Python 3" to launch a new notebook. Note that Jupyter may use a port that is different than the one you specified. This is why it is important to copy and paste the URL.
When you are done, terminate the ssh tunnel on your local machine (desktop/laptop) by running lsof -i tcp:8889 to get the PID and then kill -9 <PID> (e.g., kill -9 6010).
Running it as a PBS job
Aside on ssh
Looking at the man page for ssh, the relevant flags are:
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ssh -N -f -L localhost:8889:localhost:8889 snumber@n059.rcs.griffith.edu.au |
If the above procedure fails then try again using another port number as discussed above.
Lastly, open a web browser and copy and paste the URL from the previous output:
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