Automating-GIS-processes / csc-notebook-dockerfile

How to build the image for CSC notebooks

CSC Notebooks dockerfile

This is to keep track of changes to the dockerfile used to instantiate containers in which CSC Notebooks are run.

When creating the CSC Notebooks workspace and application, this repository can be directly referenced, see detailed instructions below.

Steps to create docker image, a workspace and application for AutoGIS

1. Create a docker image

• Check out this repository

• Adjust environment variables in Dockerfile

  • Specifically, make sure that AUTOGIS_SITE_COMMIT is referencing a commit of Automating-GIS-processes/site in which the ci/environment.yml has been updated to list packages pinned to up-to-date versions (see the README there)

• Build the docker image:

docker build --network=host --tag autogis2022 ./

2. Upload the docker image to CSC’s rahti repository

• Follow the instructions in CSC’s user manual to upload the image to their docker registry.
  • I used autogis as <yourrahtiproject>, autogis2022 as <yourimagename>, and v2022.1 (and v2022.2 ...) as the version tag. Note that you have to create a Rahti project beforehand.

3. Create a workspace

Log into https://notebooks.csc.fi/, navigate to ’Manage workspaces’, and choose ’Create new workspace’. Fill in the necessary details, and choose ’Create’.

As an example, for the 2022 iteration of the course, I entered the following information:

workspace name	workspace description
Automating GIS processes 2, 2022	‘Automating GIS processes 2’ is a Masters’ level course at the Department of Geosciences and Geography, University of Helsinki. https://studies.helsinki.fi/courses/?searchText=GEOG-329-2

Note: CSC Notebook workspaces have a default lifetime of only 180 days. Be sure to create the workspace late enough so it lasts for the entire course.

4. Create an application

Navigate to ‘Manage workspaces’, then choose the newly created workspace in the left pane.

• On the right side, open the ’Applications’ tab and click ’+ Application’.
• Choose any of the available templates (we are using our custom image, anyways)
• Enter the resulting container image path and tag from step 2 (it should look something like docker-registry.rahti.csc.fi/autogis/autogis2022:v2022.1)
• Enter a name and description (in 2022, I used the same values as for the workspace, see table above). Fiddle with the tags if you feel like it.
• Then, select ’Lab’ as the jupyter interface, a session lifetime appropriate for the course, and as much memory as you can per student (this can be increased upon request, if, e.g., accessibility calculations or other RAM-intensive analyses are carried out)
• Choose ‘Git clone from repository’ as a Download method, and add the URL of the Automating-GIS-processes/notebooks as a Source (URL): https://github.com/Automating-GIS-processes/notebooks.git
• Enable Shared folders and User work folders.