This is the NOMAD Oasis distribution of Sathya-S3. 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.
In this README you will find instructions for:
- Deploying the distribution
- Adding a plugin
- Using the jupyter image
- Updating the distribution from the template
- Solving common issues
Below are instructions for how to deploy this NOMAD Oasis distribution for a new Oasis and for an existing Oasis
-
Make sure you have docker installed. Docker nowadays comes with
docker compose
built in. Prior, you needed to install the stand-alone docker-compose. -
Clone the repository or download the repository as a zip file.
git clone https://github.com/Sathya-S3/nomad-oasis-test.git cd nomad-oasis-test
or
curl-L -o nomad-oasis-test.zip "https://github.com/Sathya-S3/nomad-oasis-test/archive/main.zip" unzip nomad-oasis-test.zip cd nomad-oasis-test
-
On Linux only, recursively change the owner of the
.volumes
directory to the nomad user (1000)sudo chown -R 1000 .volumes
-
Pull the images specified in the
docker-compose.yaml
Note that the image needs to be public or you need to provide a PAT (see "Important" note above).
docker compose pull
-
And run it with docker compose in detached (--detach or -d) mode
docker compose up -d
-
Optionally you can now test that NOMAD is running with
curl localhost/nomad-oasis/alive
-
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 4. and 5. above.
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.
Please see the Jupyter image section below for more information on the jupyter NORTH image being generated in this repository.
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
If you already have an Oasis running you only need to change the image being pulled in
your docker-compose.yaml
with ghcr.io/sathya-s3/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.
To add a new plugin to the docker image you should add it to the plugins table in the pyproject.toml
file.
Here you can put either plugins distributed to PyPI, e.g.
[project.optional-dependencies]
plugins = [
"nomad-material-processing>=1.0.0",
]
or plugins in a git repository with either the commit hash
[project.optional-dependencies]
plugins = [
"nomad-measurements @ git+https://github.com/FAIRmat-NFDI/nomad-measurements.git@71b7e8c9bb376ce9e8610aba9a20be0b5bce6775",
]
or with a tag
[project.optional-dependencies]
plugins = [
"nomad-measurements @ 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.
[project.optional-dependencies]
plugins = [
"ikz_pld_plugin @ git+https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas.git@30fc90843428d1b36a1d222874803abae8b1cb42#subdirectory=PVD/PLD/jeremy_ikz/ikz_pld_plugin"
]
Once the changes have been committed to the main branch, the new image will automatically be generated.
In addition to the Docker image for running the oasis, this repository also builds a custom NORTH image for running a jupyter hub with the installed plugins.
This image has been added to the configs/nomad.yaml
during the initialization of this repository and should therefore already be available in your Oasis under "Analyze / NOMAD Remote Tools Hub / jupyter"
The image is quite large and might cause a timeout the first time it is run. In order to avoid this you can pre pull the image with:
docker pull ghcr.io/sathya-s3/nomad-oasis-test/jupyter:main
If you want additional python packages to be available to all users in the jupyter hub you can add those to the jupyter table in the pyproject.toml
:
[project.optional-dependencies]
jupyter = [
"voila",
"ipyaggrid",
"ipysheet",
"ipydatagrid",
"jupyter-flex",
]
In order to update an existing distribution with any potential changes in the template you can add a new git remote
for the template and merge with that one while allowing for unrelated histories:
git remote add template https://github.com/FAIRmat-NFDI/nomad-distribution-template
git fetch template
git merge template/main --allow-unrelated-histories
Most likely this will result in some merge conflicts which will need to be resolved. At the very least the Dockerfile
and GitHub workflows should be taken from "theirs":
git checkout --theirs Dockerfile
git checkout --theirs .github/workflows/docker-publish.yml
For detailed instructions on how to resolve the merge conflicts between different version we refer you to the latest template release notes
Once the merge conflicts are resolved you should add the changes and commit them
git add -A
git commit -m "Updated to new distribution version"
Ideally all workflows should be triggered automatically but you might need to run the initialization one manually by navigating to the "Actions" tab at the top, clicking "Template Repository Initialization" on the left side, and triggering it by clicking "Run workflow" under the "Run workflow" button on the right.
I get an Error response from daemon: Head "https://ghcr.io/v2/Sathya-S3/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.