schumannj's NOMAD Oasis Distribution

This is the NOMAD Oasis distribution of schumannj. Below are instructions for how to deploy this distribution and how to customize it through adding plugins.

Important

Depending on the settings of the owner of this repository, the distributed image might be private and require authentication to pull. If you want to keep the image private you need to configure and use a personal access token (PAT) according to the instructions in the GitHub docs here. If you want to make the image public (recommended), you should make sure that your organization settings allow public packages and make this package public after building it. You can read more about this in the GitHub docs here.

Tip

In order for others to find and learn from your distribution we in FAIRmat would greatly appreciate it if you would add the topic nomad-distribution by clicking the ⚙️ next to "About" on the main GitHub page for this repository.

Deploying the distribution

Below are instructions for how to deploy this NOMAD Oasis distribution for a new Oasis and for an existing Oasis

For a new Oasis

1. Make sure you have docker installed. Docker nowadays comes with docker compose built in. Prior, you needed to install the stand-alone docker-compose.
2. Get the nomad-oasis.zip archive from your distribution repository using for example curl

curl -L -o nomad-oasis.zip "https://github.com/schumannj/NOMAD_Oasis_test/raw/main/nomad-oasis.zip"

3. Unzip the nomad-oasis.zip file and enter the extracted directory

unzip nomad-oasis.zip
cd nomad-oasis

4. On Linux only, recursively change the owner of the .volumes directory to the nomad user (1000)

sudo chown -R 1000 .volumes

5. Pull the images specified in the docker-compose.yaml (retrieved from the nomad-oasis.zip). Note that the image needs to be public or you need to provide a PAT (see "Important" note above).

docker compose pull

6. And run it with docker compose in detached (--detach or -d) mode

docker compose up -d

7. Optionally you can now test that NOMAD is running with

curl localhost/nomad-oasis/alive

8. Finally, open http://localhost/nomad-oasis in your browser to start using your new NOMAD Oasis.

Whenever you update your image you need to shut down NOMAD using

docker compose down

and then repeat steps 5. and 6. above.

NOMAD Remote Tools Hub (NORTH)

To run NORTH (the NOMAD Remote Tools Hub), the hub container needs to run docker and the container has to be run under the docker group. You need to replace the default group id 991 in the docker-compose.yaml's hub section with your systems docker group id. Run id if you are a docker user, or getent group | grep docker to find your systems docker gid. The user id 1000 is used as the nomad user inside all containers.

You can find more details on setting up and maintaining an Oasis in the NOMAD docs here: nomad-lab.eu/prod/v1/docs/oasis/install.html

For an existing Oasis

If you already have an Oasis running you only need to change the image being pulled in your docker-compose.yaml with ghcr.io/schumannj/NOMAD_Oasis_test:main for the services worker, app, north, and logtransfer.

If you want to use the nomad.yaml from this repository you also need to comment out the inclusion of the nomad.yaml under the volumes key of those services in the docker-compose.yaml.

    volumes:
      # - ./configs/nomad.yaml:/app/nomad.yaml

To run the new image you can follow steps 5. and 6. above.

Adding a plugin

To add a new plugin to the docker image you should add it to the plugins.txt file.

Here you can put either plugins distributed to PyPI, e.g.

nomad-material-processing

or plugins in a git repository with either the commit hash

git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@71b7e8c9bb376ce9e8610aba9a20be0b5bce6775

or with a tag

git+https://github.com/FAIRmat-NFDI/[email protected]

To add a plugin in a subdirectory of a git repository you can use the subdirectory option, e.g.

git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@30fc90843428d1b36a1d222874803abae8b1cb42#subdirectory=PVD/PLD/jeremy_ikz/ikz_pld_plugin

If the plugin is new, you also need to add it under plugins in the nomad.yaml config file that will be included in the image. For example, if you have added a schema plugin nomad_material_processing you should add the following:

plugins:
  options:
    schemas/nomad_material_processing:
      python_package: nomad_material_processing

Once the changes have been committed to the main branch, the new image will automatically be generated.

FAQ/Trouble shooting

I get an Error response from daemon: Head "https://ghcr.io/v2/schumannj/NOMAD_Oasis_test/manifests/main": unauthorized when trying to pull my docker image.

Most likely you have not made the package public or provided a personal access token (PAT). You can read how to make your package public in the GitHub docs here or how to configure a PAT (if you want to keep the distribution private) in the GitHub docs here.