Jupyter Notebook

Jupyter Notebook is accessible through the Open OnDemand web interface.

Launching Jupyter

1. Go to interactive.hpc.caltech.edu

2. Select Interactive Apps → Jupyter Notebook

3. Choose resources and launch

Adding Conda Environments as Kernels

Register your Conda environments with Jupyter:

conda activate myenv
conda install ipykernel
python -m ipykernel install --user --name myenv --display-name "Python (myenv)"

After registration, restart Jupyter to see new kernels in the New menu.

Accessing Group Directories

Option 1: Manual Navigation

In a notebook cell:

%cd /resnick/groups/<groupname>/<target>

Option 2: Symlinks

Create links from your home directory:

ln -s /resnick/groups/<group>/<user>/data ~/data-link

Then access via the symlink in Jupyter.

Julia Support

module load julia/1.4.2
julia

In Julia REPL:

using Pkg
Pkg.add("IJulia")

Then select Julia 1.4.2 kernel in Jupyter.

Configuration

Set default startup folder in ~/.jupyter/jupyter_notebook_config.py:

c.NotebookApp.notebook_dir = "/resnick/groups/mygroup/notebooks"

Troubleshooting

Jupyter Won’t Start

1. Log out completely

2. Clear browser cache and cookies

3. Log back in

Kernel Issues

Rename the Jupyter config directory and restart:

mv ~/.jupyter ~/.jupyter.bak

Conda Conflicts

Comment out conda initialization in ~/.bashrc if experiencing issues:

# >>> conda initialize >>>
# (comment out this section)
# <<< conda initialize <<<