Run neurodesktop docker container from the littlest jupyterhub? #395
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Hello, I can run neurodesktop as a docker container on the linux server and connect using the web browser and the neurodeskapp, but it's the part of starting it from jupyterhub that is failing. I get no error, it just seems to start some basic notebook. This is my config.py located in /opt/tljh/config/jupyterhub_config.d/. The other notebooks launch OK.
First of all, I don't know if this is even possible. If it is, can you point me in the right direction? Or do you know of any tutorial or guide on how to accomplish this? Thanks! |
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Replies: 4 comments 9 replies
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Dear @UppsalaBrainBehaviorLab, that could work but we haven't tried this particular setup yet. What we have tried and many people got to work well is to use Kubernetes to run Jupyterlab (https://z2jh.jupyter.org/en/stable/) and then run the Neurodesk image in there. Would that be an option for you? It seems that tljh seems like a great approach for a single node setup (https://tljh.jupyter.org/en/latest/topic/whentouse.html) and I am not sure why what you tried doesn't work yet. Can you share more details what you exactly tried and what happens? Is the change in the jupyterhub_config.d/config.py the only one you made? What you do you mean with "it just seems to start some basic notebook" - how does this notebook look like? Is this inside the neurodesk docker container? One other problem I anticipate is that you might not be able to run cvmfs inside the container (except when running as privileged). So I would recommend to install CVMFS on the host: https://www.neurodesk.org/docs/getting-started/neurocontainers/cvmfs/ - our image recognizes on startup if this directory is there, but you will need to provide a mount command to the docker spawner. Kind regards |
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Hello @stebo85, Thanks for your reply. I first tried tljh since we are only using one node and I thought Kubernetes would be too much hassle without any gains. I installed tljh as according to their instructions at https://tljh.jupyter.org/en/latest/install/custom-server.html I then added a config.py to the jupyterhub_config.d directory. I tried some different versions without success, this is the simplest:
I don't have much experience with jupyterhub or lab, but to me it looks like it starts some sort of default notebook. There is no mentionof neurodesktop in the logfiles from journalctl -u jupyterhub or journalctl -u jupyter-USER. I see this: Any thoughts appreciated. Cheers, |
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Thanks so much for the work @stebo85! I will test it and report back. |
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Dear @stebo85, I tried the install script and got it to work with a minor edit. Thanks a lot! First, I received this error when running the install command:
I identified this as originating from the docker-compose command in the tljh_neurodesk.py, line 15. I am not sure this is the best way, but it was solved by changing docker-compose to docker compose: |
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Dear @UppsalaBrainBehaviorLab - it took a while, but we finally got neurodesk to work with a TLJH plugin. Can you test this out here https://github.com/NeuroDesk/tljh-neurodesk and let us know how far you get?
It's not as nice of a setup as using Kubernetes, but it might work well enough for your usecase :)