Jupyter Notebook - Lab

Jupyter notebook is available via the Open OnDemand graphical console. If you use Conda to manage your environments you may add each of them to the Jupyter web interface with the following commands.

Adding Conda environments to OOD Jupyter Notebooks.

Change into each environment from the terminal, install ipykernel and register the kernel. Note the unique names given that match the conda environment names.

(base) [login jupyter]$ conda env list

# conda environments:

base * /home/user/miniconda3

my-new-env /home/user/miniconda3/envs/my-new-env

conda activate base

conda install ipykernel

python -m ipykernel install --user --name base --display-name "Python (base)"

conda activate my-new-env

conda install ipykernel

python -m ipykernel install --user --name my-new-env --display-name "Python (my-new-env)"

Kill and relaunch your Jupyter via the Open OnDemand interface. Click "New" and you will be able to launch a new kernel based on the Conda environment of your choice.

Accessing group directories in Open OnDemand's Jupyter App.

By default, Jupyter's Open Ondemand app opens in $HOME which can not be overridden using Jupyter specific configuration files typically located in ~/.jupyter/jupyter_notebook_config.py. The following are two ways to overcome this existing limitation while using the OOD based Jupyter App.

1. Launch Jupyter via OOD and manually change directory.

Launch and connect to the Jupyter App, launch any kernel, in the command line use Jupyter specific commands to change the directory. %cd /resnick/groups/<groupname>/<target directory> . You may run the %pwd command to verify.

2. A more efficient way to access group directories is to create a simple symlink from a home directory to the target group directory. Once complete, you would launch Jupyter and simply click on the symlink located in your home directory to access the intended group directory.

cd ~/

mkdir -p /resnick/groups/<your group dir>/<your username>/my-jupyter-notebooks

ln -s /resnick/groups/<your group dir>/<your username>/my-jupyter-notebooks ./

Adding Julia language environments to OOD Jupyter Notebooks.

First load the Julia module and install the Julia Kernel

module load julia/1.4.2

julia> using Pkg

julia> Pkg.add("IJulia")

Then navigate to the OOD portal (VPN if off campus) > login > click Interactive Apps > Jupyter Notebook > select cores/time/gpus > Launch > Connect to Jupyter.

Once launched you should be able to select the Jupyter 1.4.2 kernel by clicking New > Julia 1.4.2

Secondary method

|Pkg.instantiate()|the project. |julia --project -e 'using IJulia;
installkernel("Julia VizClima", "--project=$(pwd())")'|

Changing default startup folder

You can change the default Jupyter startup folder by adding the following to the Jupyter config ~/.jupyter/jupyter_notebook_config.json

c.NotebookApp.notebook_dir="<directory>"

Another simple method that both retains the existing ~/ startup directory while allowing one to switch to directories outside of home is to create a symlink in ~/ that points to the group dir. At this point you will be able to click on the symlinked directory in Jupyter to navigate to the desired group location.

For example:

mkdir -p /resnick/groups/<group>/<username>/my-jupyter-notebooks

ln -s /resnick/groups/<group>/<username>/my-jupyter-notebooks ~/my-jupyter-notebooks-in-group-dir

Troubleshooting OpenOndemand's Jupyter Application

If you receive a Proxy or 502 Bad Gateway errors while launching/connecting to the Jupyter Apps try the following.

Fully log out of Open Ondemand, clear the browse cache/cookies then log back into the Open OnDemand console.
Move ~/.jupyter to ~/.jupyter.bak , attempt to login to OOD and start a new Jupyter session.
Edit your ~/.bashrc and comment out all conda related lines.

comment out the conda init items in bashrc:

from: __conda_setup

to: unset __conda_setup