Interaction via ssh

[m13slash9]

Is it possible to interact with Neurodesk via ssh? If yes, how can the connection be enabled?

It would be nice to have a possibility to use some tools in Neurodesk by providing commands over ssh and data transfer over scp.
This could work both with Neurodesk installed locally and remotely, but at the moment I'm more interested in connecting to a local installation.

[stebo85]

Yes, this is possible. You can install Neurocommand locally (or remotely) and then connect to this setup via ssh. You can follow these instructions: https://www.neurodesk.org/docs/getting-started/neurocommand/

On the local setup you wouldn't even need SSH - you can call the containers directly once setup with neurocommand.

Another way would be to setup only the CVMFS container section of Neurodesk: https://www.neurodesk.org/docs/getting-started/neurocontainers/cvmfs/ (this can also be done remotely).

Let us know if this works for you. If not can you describe your setup in more detail (e.g. which operating systems are involved) and we can give more detailed guidance.

[stebo85]

That could be possible, too. Can you try if this works for you: https://www.neurodesk.org/docs/getting-started/neurocommand/visual-studio-code/

it sounds very close to what you want to achieve

[m13slash9]

Thank you, but that seems to employ some tools very particular to VS.

I'm wondering something more general like ssh can be used.
I guess, this would only require opening a particular port, when running the neurodesktop container, and setting up the sshd service in the neurodesktop image. Though I'm not sure if I can change these settings when starting up the NeurodeskApp.

[stebo85]

@m13slash9 - VS code just makes this very easy, but if you do not want to use VS code you can also connect to a running container using the following (you don't need SSH for that!):

docker ps
# note the name of the running container, e.g. neurodeskapp-49977

# now connect to this container
docker exec -ti neurodeskapp-49977 bash

# then switch to the jovyan user
su jovyan

Is this what you mean? Does this work for you? This would also work via SSH, where you run the neurodesktop container on a remote system.

[m13slash9]

Thank you! This is very close, and it seems to be the way I'd need to work with.

[stebo85]

cool - great to hear this works for you :)

[m13slash9]

Finally found a solution to enable proper SSH connection to neurodesktop.
If anyone interested, it is possible like this:

You first need to start neurodesktop manually with an additional port open for ssh (e.g., port 22222).

To do this follow the instructions according to your system (e.g., Windows).

Use the Option 2 (Advanced): Using Terminal set of commands, but add an additional port open in the docker run line, e.g.,

docker run --shm-size=1gb -it --privileged --user=root --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage --mount source=neurodesk-home,target=/home/jovyan -p 8888:8888 -p 22222:22222 -e NEURODESKTOP_VERSION=2024-05-25 vnmd/neurodesktop:2024-05-25

Then you need to set up the sshd service inside the neurodesk container. To do this, connect to the running container via
docker exec -it -u root neurodesktop bash

Then, open the /etc/ssh/sshd_config and change the default setting of #Port 22 to your selected port e.g., Port 22222

Add your public authorization keys to /home/jovyan/.ssh/authorized_keys

Start the sshd service with service ssh restart

Now you should be able to SSH into neurodesktop with ssh -p 22222 jovyan@localhost

Note, that after stopping the container you'd be able to start it with just docker start -ai neurodesktop, but you will still need to restart the ssh service, e.g., with docker exec -it -u root neurodesktop service ssh restart

[stebo85]

Great to hear this is working :) have you tried using the default port 22? Does this work as well?

[m13slash9]

As far as I got it, starting Windows 10, there is a native sshd service in Windows that monitors port 22, then there is sshd service in WSL that monitors port 2222, so you'd need to either disable them and the associated routing, or just choose a different port.

Another possibility is to run docker with -p 22222:22 port routing, so that the ssh -p 22222 jovyan@localhost would be directed to port 22 inside the container, but I have not checked that. It should remove the need to edit /etc/ssh/sshd_config but you'll still need to start the ssh service

[stebo85]

Cool - doing the port mapping during the docker call sounds like the best solution and I can't see why this wouldn't work :)

[m13slash9]

Just checked - it indeed works with -p 22222:22 forwarding, so no need to edit /etc/ssh/sshd_config

[stebo85]

Great - thank you for testing and sharing the solution