ssh -Y -l <username> <system name>.sdsc.edu
cdinto one you have already created
git clone https://github.com/sdsc-hpc-training-org/notebook-examples.git
Run the jupyter command. Be sure to set the –ip to use the hostname, which will appear in your URL :
[mthomas@comet-14-01:~] jupyter notebook --no-browser --ip='/bin/hostname'
You will see output similar to below:
[I 08:06:32.961 NotebookApp] JupyterLab extension loaded from /home/mthomas/miniconda3/lib/python3.7/site-packages/jupyterlab [I 08:06:32.961 NotebookApp] JupyterLab application directory is /home/mthomas/miniconda3/share/jupyter/lab [I 08:06:33.486 NotebookApp] Serving notebooks from local directory: /home/mthomas [I 08:06:33.487 NotebookApp] The Jupyter Notebook is running at: [I 08:06:33.487 NotebookApp] http://comet-14-01.sdsc.edu:8888/?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b [I 08:06:33.487 NotebookApp] or http://127.0.0.1:8888/?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b [I 08:06:33.487 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 08:06:33.494 NotebookApp] To access the notebook, open this file in a browser: file:///home/mthomas/.local/share/jupyter/runtime/nbserver-6614-open.html Or copy and paste one of these URLs: http://comet-14-01.sdsc.edu:8888/?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b or http://127.0.0.1:8888/?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b [I 08:06:45.773 NotebookApp] 302 GET /?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b (126.96.36.199) 0.74ms [E 08:06:45.925 NotebookApp] Could not open static file '' [W 08:06:46.033 NotebookApp] 404 GET /static/components/react/react-dom.production.min.js (188.8.131.52) 7.39ms referer=http://comet-14-01.sdsc.edu:8888/tree?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b [W 08:06:46.131 NotebookApp] 404 GET /static/components/react/react-dom.production.min.js (184.108.40.206) 1.02ms referer=http://comet-14-01.sdsc.edu:8888/tree?token=6d7a48dda7cc1635d6d08f63aa1a696008fa89d8aa84ad2b
Notice that the notebook URL is using HTTP, and when you connect the browser on your local sysetm to this URL, the connection will not be secure. Note: it is against SDSC Comet policy to run applications on the login nodes, and any applications being run will be killed by the system admins. A better way is to run the jobs on an interactive node or on a compute node using the batch queue (see the Comet User Guide), or on a compute node, which is described in the next sections.
Jobs can be run on the cluster in
batch mode or in
interactive mode. Batch jobs are performed remotely and without manual intervention. Interactive mode enable you to run/compile your program and environment setup on a compute node dedicated to you. To obtain an interactive node, type:
srun --pty --nodes=1 --ntasks-per-node=24 -p compute -t 02:00:00 --wait 0 /bin/bash You will have to wait for your node to be allocated - which can take a few or many minutes. You will see pending messages like the ones below:
srun: job 24000544 queued and waiting for resources srun: job 24000544 has been allocated resources [mthomas@comet-18-29:~/hpctrain/python/PythonSeries]
You can also check the status of jobs in the queue system to get an idea of how long you may need to wait.
Launch the Jupyter Notebook application. Note: this application will be running on a compute node, and you must keep track of the given URL:
jupyter notebook --no-browser --ip='/bin/hostname'
This will give you an address which has localhost in it and a token. Something like:
http://comet-14-0-4:8888/?token=xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx You can then paste it into your browser. You will see a running Jupyter notebook and a listing of the notebooks in your directory. From there everything should be working as a regular notebook. Note: This token is your auth so don't email/send it around. It will go away when you stop the notebook.
To learn about Python, run the
Python basics.ipynb notebook. To see an example of remote visualization, run the
Copy the the URL above into the browser running on your laptop.
Enjoy. Note that your notebook is unsecured.