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'bring-your-own-Jupyter'

We also provide the capability for you to 'bring-your-own-Jupyter' so that all your code dependencies are dictated by you, and not by us. We recommend you do this by either building an apptainer image of your Jupyter environment or by building a conda environment on SDF storage.

If you wish for your jupyter environment to be more widely used (e.g. for others in your group), you can submit a pull-request to our slac-ood-jupyter repo to append your specific "Commands to initiate Jupyter" onto the list of preselectable Jupyter Images. Specifically, you will want to change form.yml.erb.

In a Conda environment

Once you have created your Conda environment on SDF (see Conda), ensure that you have jupyter installed in your conda environment:

conda install -c conda-forge jupyterlab

Then go to Jupyter portal, and select "Custom Conda Environment..." from the "Jupyter Instance" dropdown. You will need to customize the text that appears under "Commands to initiate Jupyter" to point to your custom conda environment:

export CONDA_PREFIX=<path-to-miniconda3>
export PATH=${CONDA_PREFIX}/bin/:$PATH
source ${CONDA_PREFIX}/etc/profile.d/conda.sh
conda env list
conda activate <your-environment-name>

Replace <path-to-miniconda3> and <your-environment-name> appropriately.

Fill the rest of the form as you would for any provided Jupyter Instance and click "Launch". If you run into any issues, please see Debugging your interactive session.

In a Container (such as Apptainer)

Once you have built or pulled an Apptainer or other OCI container image on SDF (see Apptainer page for more information on how to do that), ensuring that you have the jupyter[lab] binary in the image's PATH, go to the Jupyter portal, select "Custom Apptainer Image" from the "Jupyter Instance" dropown menu. Then modify the text in the "Commands to initiate Jupyter":

export APPTAINER_IMAGE_PATH=<path to apptainer image>
function jupyter() {
  apptainer \
    exec \
    --nv \
    -B /sdf,/fs,/sdf/scratch,/lscratch \
    ${APPTAINER_IMAGE_PATH} \
    jupyter $@;
}

Replace <path to apptainer image> with a path to your apptainer image:

  • The full path to an image you've already built on SDF: For example, if you ran apptainer build in your home directory, the image path may be /sdf/home/u/<username>/my-special-jupyter.sif

  • A tag available publicly on a remote registry (for example, docker://jupyter/datascience-notebook:lab-4.0.7) would download and use a specific version of Jupyter Lab already packaged into a container by Project Jupyter.

    • Note: If you use this method, the image will still need to be downloaded onto SDF and will (by default) take up disk space in your home directory under ~/.apptainer to store the resulting image.

Complete the rest of the form as you would for any provided Jupyter Instance and click "Launch". If you run into any issues, please see Debugging your interactive session.

Debugging your interactive session :id=debugging

If you get an error while using your Jupyter instance, go to the My Interactive sessions page, identify the session you want to debug and click on the Session ID link. You can then View the output.log file to troubleshoot.