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JASMIN Notebooks Service

 

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Jupyter Notebooks service on JASMIN

The JASMIN Notebooks Service provides access to Jupyter Notebooks  in a web browser.

What is a Jupyter Notebook?  

A Jupyter Notebook is an interactive document containing live code and visualisations that can be viewed and modified in a web browser. These documents can be shared, often using GitHub, and many projects distribute example code as Jupyter notebooks. Users interact with their notebooks using the open-source Jupyter Notebook server application.

Jupyter has support for many languages including Python, R, Scala and Julia, which are implemented by plugins known as “kernels”. The JASMIN Notebook Service provides kernels with the latest Jaspy software environment and JasR (R) environment installed by default. The /apps/jasmin/jaspy directory is mounted directly into the notebook service, providing access to all Jaspy and JasR versions available on the scientific analysis servers. These environments are active by default, so there is no need for the module commands described in the linked article. You can also install and use your own environments as explained below.

The JASMIN Notebook Service uses JupyterHub  to manage multiple Jupyter Notebook servers. After authenticating with a JASMIN account (with the correct access), a user gets access to their own notebook server. The notebook server runs as the authenticated user, and the user can access their home directory, Group Workspaces and CEDA Archive data as they would from a scientific analysis server.

Getting access to the JASMIN Notebook Service  

In order to access the JASMIN Notebook service, first, follow the steps in Getting started with JASMIN to get a JASMIN account and the jasmin-login service.

Using the JASMIN Notebook Service  

To use the JASMIN Notebook Service, navigate to https://notebooks.jasmin.ac.uk  . This will redirect you to the JASMIN Accounts Portal, where you should sign in with your JASMIN Account. If you have previously accessed the notebook service from the computer you are using, this may happen automatically.

The first time you access the JASMIN Notebook Service from a new computer or browser, you will be asked to verify your email address after signing in. To do this, make sure the “Email” method is selected and click “Send me a code”:

Sign in with 2-factor authentication
Sign in with 2-factor authentication

This will result in an email being sent to your registered email address containing a six-digit verification code. Enter this code and press “Verify code”. Each code lasts between 15 and 30 minutes.

Upon successfully signing in and verifying your email if required, you will be redirected back to the JASMIN Notebook Service. The service will then create a notebook server for you to use, and you will see a loading page:

Loading page
Loading page

After a few seconds, or in some rare cases a minute or two, you will be taken to the JupyterLab interface:

JupyterLab interface
JupyterLab interface

The folder shown in the left-hand panel will be your home directory on JASMIN, exactly as if you had logged in to a scientific analysis server. Any changes made in JupyterLab will be immediately reflected on the scientific analysis servers and LOTUS, and vice-versa. You can then launch, edit and run Python notebooks using the JupyterLab interface. Notebooks can access files from the CEDA Archive, and also have read-only access to group workspaces. For example, this notebook reads a file belonging to the CCI project from the CEDA Archive and plots the data on a map:

Example notebook
Example notebook

A full discussion of the power of the JupyterLab interface is beyond the scope of this documentation, but the JupyterLab documentation  is excellent, and there are many tutorials available on the internet.

Profile Selection  

When starting your notebook server, you will be presented with a profile picker that offers three modes:

Normal Mode (Default) This is the standard notebook environment with access to the latest Jaspy (Python) and JasR (R) kernels. Use this mode for regular notebook work.

Safe Mode This mode removes user and will not load Python packages from your home directory configuration, which can be useful if you have accidentally installed a broken version of Jupyter or other packages in your home directory that prevent your notebook server from starting correctly. While safe mode bypasses these issues for testing, you may want to clean up the broken installation (see troubleshooting section below).

GPU Mode This mode provides your notebook server with access to a MIG GPU partition, useful for machine learning and other GPU-accelerated workflows. Access requires the ORCHID access role. See the JASMIN Notebooks with GPUs page for more details.

Using Different Kernels  

Old Jaspy and JasR Versions  

While the notebook service provides the latest Jaspy and JasR versions as default kernels, all older versions are also available. To use an older version:

  1. Open a terminal in JupyterLab (File → New → Terminal)
  2. Run conda env list to see all available Jaspy and JasR environments
  3. Activate the environment you want: conda activate <environment-name>
  4. Install it as a kernel: python -m ipykernel install --user --name <kernel-name>

The kernel will then appear in your list of available kernels and persist across sessions. These older versions are maintained for the same period as they are available on the scientific analysis servers.

Using Julia  

The notebook service has juliaup installed, which can be used to provision Julia and create Julia kernels. To set up Julia:

  1. Open a terminal in JupyterLab
  2. Use juliaup to install your desired Julia version (e.g., juliaup add release)
  3. Launch Julia and install the IJulia package: 
    using Pkg
Pkg.add("IJulia")
  4. The Julia kernel will then be available in your notebook interface

Intended usage and limitations  

The JupyterLab environment provided by the JASMIN Notebooks Service is powerful, but it has some limitations that reflect the type of usage that we want to encourage.

The JASMIN Notebooks Service is primarily intended for interactively producing visualisations of existing data, not for processing vast amounts of data. As such, the resources made available to each notebook server are limited.

For larger processing tasks with Notebooks, users should consider using the JASMIN Dask Gateway service  , which provides an easy way for processing managed from within a Jupyter Notebook to be scaled out to multiple LOTUS jobs in parallel.

Alternatively, use the LOTUS batch processing cluster separately, before using the notebooks service to visualise the output.

Doing this means that the bulk of the resource usage will be shared by the LOTUS cluster rather than the Notebooks service itself.

Using the GPU-enabled Notebook Service  

Please see the JASMIN Notebooks with GPUs enabled page to learn about using Notebooks with GPU access.

Common issues and questions  

I get “403 forbidden” when I try to access the JASMIN Notebook Service  

This error occurs when you do not have the correct permissions to access the JASMIN Notebook service. Please ensure you have been granted the jasmin-login and allow some time for the changes to propagate through the system.

Which software environment is used by the Notebook Service?  

The JASMIN Notebook Service provides the latest Jaspy and JasR environments as default kernels. See the Jaspy page for details about the packages included. Older versions can be installed as additional kernels as described above.

Can I install additional packages?  

The recommended way to do this is to create your own Python virtual environment and install additional packages into that. You can make that virtual environment persist as a kernel to use again next time you use the Notebooks service. Environments created correctly will also work on the scientific analysis servers.

If you believe that the package is more widely applicable, you can request an update to Jaspy.

Can I use a different software environment?  

Yes, you can create Python virtual environments or Conda environments for custom software stacks.

I get “503 service unavailable” when I try to access the JASMIN Notebook Service  

This error occurs when your notebook server is unable to start. By far the most common cause of this error is when you are over your quota in your home directory. As part of starting up, Jupyter needs to create some small files in your home directory in order to track state. When it is unable to do this because you are over your quota, you will see the “503 service unavailable” error.

If you see this error, try connecting to JASMIN using SSH and checking your home directory usage. After clearing some space in your home directory, your notebook server should be able to start again.

I get the following message when my notebook is queued for spawning  

Error message
Error message

The message above indicates that the Notebook service is oversubscribed -busy- and there are no resources available to start your Notebook server. Please try again later!

Please use the scientific analysis server and LOTUS for processing and Jupyter Notebook for lighter visualisation.

I get “403 forbidden” or other errors when trying to save my notebook  

This error commonly occurs when your home directory is full or over quota. The JASMIN filesystem does not expose quotas in a standard way, so Jupyter cannot provide a clear error message.

To check your home directory usage:

  1. Open a terminal in JupyterLab (File → New → Terminal)
  2. Run du -sh ~ to see your total home directory usage
  3. Compare this to the home directory quota (see Storage)

If you are over quota, you will need to delete or move files to free up space. Common culprits include old conda environments, cached package downloads, and large data files that should be stored in group workspaces.

My notebook server won’t start or I have Jupyter errors  

If your notebook server fails to start or you experience strange Jupyter-related errors, this may be caused by a broken Jupyter installation in your home directory (typically in ~/.local/lib/python*/site-packages/).

Quick fix: Use Safe Mode

Start your notebook server in Safe Mode using the profile picker. This bypasses your user-installed packages and should allow you to access your notebooks.

Permanent fix: Clean up the broken installation

  1. Connect to JASMIN via SSH or open a terminal in JupyterLab (in Safe Mode)
  2. Rename your local Python packages directory: 
    mv ~/.local ~/.local.old
  3. Restart your notebook server in Normal Mode

This will remove all user-installed Python packages. If you had custom packages you need, reinstall them in a proper virtual environment instead of your home directory.

Example Notebooks  

In support of the JASMIN Notebook Service, we have developed a GitHub repository with a collection of Notebooks that demonstrate some of the important features of the service. The following provides a general introduction:

https://github.com/cedadev/ceda-notebooks/blob/master/notebooks/training/intro/notebook-tour.ipynb 

Other Notebooks can be found within the repository, under:

https://github.com/cedadev/ceda-notebooks/tree/master/notebooks 

Webinar / video tutorial  

A CEDA webinar on 16th June 2020  demonstrated how to use the service. A recording of the event is available:

Further info  

Here are a set of links to learn more about Jupyter Notebooks and the JASMIN Notebook Service:

• Last updated on 2026-01-14 as part of:  Update screenshots in notebooks pages (d48abe06d)
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