Installing Jupyter lab

Installing Jupyter lab

1. If you haven’t already, install anaconda/miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

2. Create a new environment

conda create -n CNN

3. Activate the environment and install Jupyter lab

bash to restart the shell

conda activate CNN
pip install jupyterlab

Connecting to Jupyter Lab through an SSH tunnel

4. Start an interactive session

srun -p gpu --pty -t 8:00:00 --mem=30GB --gres=gpu /bin/bash

Make a note of the node you’re connected to, e.g. erc-hpc-comp001

5. Within this session, start Jupyter lab without the display on a specific port (here this is port 9998)

conda activate CNN
jupyter lab --no-browser --port=9998 --ip="*"
python -m notebook --no-browser --port=9998 --ip="*" # if the above line does not work

6. Open a separate connection to CREATE that connects to the node where Jupyter Lab is running using the port you specified earlier. (Problems known with VScode terminal)

ssh -m hmac-sha2-512 -o ProxyCommand="ssh -m hmac-sha2-512 -W %h:%p k21116947@bastion.er.kcl.ac.uk" -L 9998:erc-hpc-comp031:9998 k21116947@hpc.create.kcl.ac.uk

Note:

• k12345678 should be replaced with your username.
• erc-hpc-comp001 should be replaced with the name of node where Jupyter lab is running
• 9998 should be replaced with the port you specified when running Jupyter lab (using e.g. --port=9998)
• authorize via https://portal.er.kcl.ac.uk/mfa/

7. Go to http://localhost:9998/lab (assuming you had specified port 9998 earlier, if not replace this with the port you used)