Jupyter Notebooks

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Software Modules

Conda Environments

Jupyter Notebooks

0. Connect to Bigelow's VPN
1. Start an interactive session
For c1 or c3:
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qsub -I -q route -l walltime=8:00:00 -l ncpus=2,mem=16G -N jupyter-interactive
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Use an additional -l model=<model> option if the user wants to specifically use c1 or c3.
For c2:
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qsub -I -V -q scgc-route -l walltime=8:00:00 -l ncpus=2,mem=32G -N jupyter-interactive
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2. Navigate to your notebooks directory, set up environment:
Run:
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module load anaconda3
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​
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unset XDG_RUNTIME_DIR
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3. Determine the IP address of the compute nodes
Run:
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cat /etc/hostname
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The hostname should be displayed. Then, using the table below, find out the IP address of the machine:
Hostname
IP address
c1
10.10.1.1
c2
10.2.1.61
c3-0
10.2.13.0
c3-1
10.2.13.1
c3-2
10.2.13.2
c3-3
10.2.13.3
c3-4
10.2.13.4
c3-5
10.2.13.5
c3-6
10.2.13.6
c3-7
10.2.13.7
c3-8
10.2.13.8
c3-9
10.2.13.9
c3-10
10.2.13.10
c3-11
10.2.13.11
c3-12
10.2.13.12
c3-13
10.2.13.13
c3-14
10.2.13.14
Alternatively, use the ifconfig command to find out the IP address.
4. Start a jupyter notebook session
Run:
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jupyter notebook --no-browser --port=<port> --ip=<ip address>
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The port can be in the range of 8888-8898. The ip address is the IP found in the previous step. For example, if you are in c1, to start a session, run:
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jupyter notebook --no-browser --port=8888 --ip=10.10.1.1
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You should get ouput that looks like this:
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Copy/paste this URL into your browser when you connect for the first time,
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    to login with a token:
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        http://10.10.1.1:8888/?token=3258d683aae77486e9880349b0c61b2412f32ae787a9463b
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Note the 'port' value in the URL. Above it is '8888', but this could vary if others are also running notebooks on the server you're working on.
5. Copy and paste the URL from your notebook session into a browser on your local machine.
In the above example you would copy "http://10.10.1.1:8888/?token=3258d683aae77486e9880349b0c61b2412f32ae787a9463b", open your browser of choice, and paste it into the navigation bar.

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Data Science

RStudio

Last modified 1yr ago

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Contents

0. Connect to Bigelow's VPN

1. Start an interactive session

2. Navigate to your notebooks directory, set up environment:

3. Determine the IP address of the compute nodes

4. Start a jupyter notebook session

5. Copy and paste the URL from your notebook session into a browser on your local machine.