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This will check for the presence of ssh keys and it will create and add it to authorized_keys file if needed. | This will check for the presence of ssh keys and it will create and add it to authorized_keys file if needed. | ||
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====To use Jupyter notebook on sapelo2 with an interactive job==== | ====To use Jupyter notebook on sapelo2 with an interactive job==== | ||
Revision as of 11:03, 5 November 2020
Category
Programming
Program On
Sapelo2
Version
5.0.0, 5.6.0, 6.0.3
Author / Distributor
Description
"The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text" Jupyter
Running Program
Versions
Please also refer to Running Jobs on Sapelo2.
- Jupyter 5.0.0 is installed as part of Anaconda3 5.0.1 with python 3.6.3. This version is installed at /apps/eb/Anaconda3/5.0.1
- Jupyter 5.6.0 is installed as part of Anaconda2 5.3.0 with python 2.7.15. This version is installed at /apps/eb/Anaconda2/5.3.0
- Jupyter 6.0.3 is installed as part of Anaconda3 2020.02 with python 3.7.6. This version is installed at /apps/eb/Anaconda3/2020.02
Please note: You do not have to install jupyter notebook on your local machine.
To use Jupyter 5.0.0, please load the module:
module load Anaconda3/5.0.1
To use Jupyter 5.6.0, please load the module:
module load Anaconda2/5.3.0
To use Jupyter 6.0.3, please load the module:
module load Anaconda3/2020.02
To use Jupyter notebook on sapelo2 with an interactive job
The port number for the jupyter notebook server should be some random value between 8000 and 10000. Assign this value to the variable 'NOTEBOOKPORT' in the submission script below replacing 8888. Please do not use 8888. If more than one person uses that same value you cannot establish the ssh tunnel
Sample steps to use jupyter 6.0.3, once you connect to sapelo2:
qlogin NOTEBOOKPORT=8888 IPUSED=$(hostname -i) echo "NOTEBOOKPORT is " $NOTEBOOKPORT echo "IPUSED is " $IPUSED module load Anaconda3/2020.02 jupyter-notebook --port $NOTEBOOKPORT --ip=$IPUSED --no-browser
After running the steps above, establish a another ssh tunnel from your desktop or laptop to sapelo2 login node at port NOTEBOOKPORT.
If you are using a Linux or Apple machine for your desktop or laptop you can use the following command to establish the ssh tunnel
Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using (see the output of the echo commands above)
ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@sapelo2.gacrc.uga.edu
Unless you have ssh key configured, you will be prompted for your MyID password and for Archpass Duo authentication. Once authentication is established, this session prompt will hang and you are ready to go to the next step.
If you are using a Windows machine for your desktop or laptop download the plink program to use in place of the ssh client. The command for windows would be as follows: Assuming the plink.exe is in the current directory where you have a command window open.
Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using (see the output of the echo commands above)
plink -ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@sapelo2.gacrc.uga.edu
Once you establish the ssh tunnel by running the command above you can access the Jupyter notebook by going to http://localhost:NOTEBOOKPORT using the browser on your desktop or laptop (make sure you replace NOTEBOOKPORT with the port number you used in the qlogin session). If the page displayed on the browser asks for a token or password, you can check the token shown in your qlogin session and copy and paste it into the token field in the page displayed in your browser. For example, the qlogin terminal might show something like this:
[I 15:02:58.309 NotebookApp] JupyterLab alpha preview extension loaded from /usr/local/apps/eb/Anaconda3/5.0.1/lib/python3.6/site-packages/jupyterlab
JupyterLab v0.27.0
Known labextensions:
[I 15:02:58.312 NotebookApp] Running the core application with no additional extensions or settings
[I 15:02:58.348 NotebookApp] Serving notebooks from local directory: /home/shtsai/sapelo2/tests/jupyter
[I 15:02:58.349 NotebookApp] 0 active kernels
[I 15:02:58.349 NotebookApp] The Jupyter Notebook is running at: http://10.56.13.168:8812/?token=e53a8f93b9506136dcdb8632f078ed64896dafee66032f16
[I 15:02:58.349 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 15:02:58.351 NotebookApp]
Copy/paste this URL into your browser when you connect for the first time,
to login with a token:
http://10.56.13.168:8812/?token=e53a8f93b9506136dcdb8632f078ed64896dafee66032f16
Copy and paste the token, which in the example above is e53a8f93b9506136dcdb8632f078ed64896dafee66032f16, into the proper field in the page displayed in your browser.
Documentation
Details at https://jupyter.readthedocs.io/en/latest/index.html
System
64-bit Linux