Description

From the JupyterLab website: JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data. JupyterLab is flexible: configure and arrange the user interface to support a wide range of workflows in data science, scientific computing, and machine learning. JupyterLab is extensible and modular: write plugins that add new components and integrate with existing ones.

JupyterNotebook is one of the tools available for use in the JupyterLab suite.

PLEASE NOTE: Do not run JupyterLab on a login node, as it can be resource intensive. Instead, please ensure that you only run it inside of an SRUN Interactive session.

Using JupyterLab/JupyterNotebook on CIRCE/SC via X2Go

Installing JupyterLab

To install JupyterLab, you'll first need to log-in to CIRCE/SC, open a terminal inside of X2Go, and install Miniconda3 using the directions below:

Instructions on installing Miniconda3

1. [user@itn0 ~]$ cd $HOME

2. [user@itn0 ~]$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

3. [user@itn0 ~]$ chmod +x Miniconda3-latest-Linux-x86_64.sh

4. [user@itn0 ~]$ ./Miniconda3-latest-Linux-x86_64.sh

   • answer "yes" to adding Miniconda3 install location to PATH in your ~/.bashrc
5. log-out of CIRCE/SC, then log back in

6. [user@itn0 ~]$ which conda pip

   • make sure it returns with both lines below:
     • ~/miniconda3/bin/conda
     • ~/miniconda3/bin/pip

7. [user@itn0 ~]$ pip install --upgrade pip

8. [user@itn0 ~]$ conda update --all -y

9. [user@itn0 ~]$ conda install -y anaconda

Once Miniconda3 is installed, you can proceed with installing JupyterLab.

Instructions on installing JupyterLab via Miniconda3

To create a dedicated JupyterLab Miniconda virtual environment, you can do so by running the commands below:

1. [user@itn0 ~]$ cd $HOME

2. [user@itn0 ~]$ conda create --name jupyter -c conda-forge jupyterlab

Running JupyterLab inside of an SRUN Interactive Session

Each time you wish to run JupyterLab/JupyterNotebook, you can do so by running the commands below:

1. Connect to CIRCE/SC via X2Go
2. Export your DISPLAY variable
3. Request an SRUN Interactive Session:

   • [user@itn0 ~]$ srun --time=00:30:00 --ntasks=1 --pty /bin/bash

4. Once the SRUN Interactive Session has been dispatched, load your JupyterLab conda environment:

   • [user@mdc-1057-29-41 ~]$ conda activate jupyter

5. Start Firefox in the background on the compute node:

   • [user@mdc-1057-29-41 ~]$ firefox &

6. Start JupyterLab:

   • [user@mdc-1057-29-41 ~]$ jupyter lab

Terminating JupyterLab

When you are finished using JupyterLab, you can terminate the processes using the steps below:

1. Close the Firefox window
2. CTRL-C in the terminal window, and enter "y" to confirm terminating the JupyterLab server process

3. [user@mdc-1057-29-41 ~]$ conda deactivate jupyter

Documentation

Home Page, User Guides, and Manuals

• Jupyter Home Page:
  • https://jupyter.org/
• JupyterLab Documentation:
  • https://jupyter.org/documentation

Reporting Bugs

Report bugs with JupyterLab to the IT Help Desk: rc-help@usf.edu