JupyterNotebooksAFS

Install Jupyter Notebook

Download and install Miniconda as described in Miniconda. To create a new environment and install Jupyter Notebook, use

login-1-105 ~ >: conda create --name jupyter python=3.7

Activate the new 'jupyter' environment

login-1-106 ~ >: conda activate jupyter
(jupyter) login-1-107 ~ >:

Next, install Jupyter Notebook

(jupyter) login-1-107 ~ >: conda install jupyter notebook

Create the following script (jupyter.sh)

#!/bin/bash -l

conda activate jupyter

port=$(shuf -i 6000-9999 -n 1)

cat<<EOF

Jupyter server is running on: $(hostname)
Job starts at: $(date)

Step 1: Create SSH tunnel

Open new terminal window, and run:
(If you are off campus you will need VPN running)

ssh -L $port:localhost:$port $USER@$HOSTNAME
Step 2: Connect to Jupyter

Keep the terminal in the previouse step open. Now open browser, find the line with

 Or copy and paste one of these URLs:

the URL will be something like:

http://localhost:${port}/?token=XXXXXXXX

EOF

jupyter notebook --no-browser --port $port --notebook-dir=$(pwd)

Next, create a script which will execute krenew (krenew.sh). krenew is required as the AFS tokens expire at eight-hour intervals so that tokens can be renewed automatically to run the Jupyter Notebook process without any interruption. For details, see Krenew

krenew -t -b -K 60 -- bash -c "$PWD/jupyter.sh >> $PWD/output.log 2>&1"

To make the file krenew.sh executable, use

chmod +x krenew.sh

Then execute the krenew.sh

./krenew.sh

This will generate an output file output.log. Now open the log file and copy the URL. The URL will be in the following format

http://localhost:${port}/?token=XXXXXXXX

To kill the Jupyter Notebook process, you need to use the following command first to see the currently running processes.

login-1-106 ~ >: top -u guest

Replace guest with NJIT UCID. Once you execute the command, you will see the output something like the following

 PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
20653 guest    20   0   33132   1440   1072 S   0.0  0.0   0:00.04 krenew
20654 guest    20   0  113284   1216   1040 S   0.0  0.0   0:00.00 bash
20655 guest    20   0  113288   1624   1368 S   0.0  0.0   0:00.00 jupyter.sh
20693 guest    20   0  482688  89112  13024 S   0.0  0.0   1:23.88 jupyter-noteboo
21752 guest    20   0  862064  56588   9084 S   0.0  0.0   0:33.90 python
21772 guest    20   0  126384   2164   1684 S   0.0  0.0   0:00.00 bash
26251 guest    20   0  184632   2504   1116 S   0.0  0.0   0:00.00 sshd
26252 guest    20   0  126252   2100   1636 S   0.0  0.0   0:00.00 bash
26294 guest    20   0  172940   2524   1648 R   0.0  0.0   0:00.14 top

Identify the process ID (PID) responsible for running Jupyter Notebook. In this above output, the PID is 20693. To kill the process, use

login-1-106 ~ >: kill -9 20693