Attach to neurodesktop docker container in VScode

[Proulx-S]

Hello Neurodesktopers! Thanks for the nice suite :-)

I am running neurodesktop in a docker container as in https://www.neurodesk.org/docs/getting-started/neurodesktop/linux/, Option 2. Point 1.

It works fine through browser interaction. But I'd like to interact with it through VScode, where VScode attaches to the container.

Attaching the container to VScode works easy with the Dev Container extension, but it makes neurodeskapps unusable:

Following neurodesk's instructions (https://www.neurodesk.org/docs/getting-started/neurocommand/visual-studio-code/), now something goes wrong as I attach the container:

See also full terminalOutput.txt.

Any suggestions?

Thanks a lot for your help :-)
Sebastien

Note: My ultimate goal is to interact with this neurodesktop container remotely using VScode, by first SSHing to my server with VScode extension Remote-SSH, then attaching the server-run container using VScode extension Dev-Containers. This is working but I'm getting the same issue described above for the simpler test case of using VScode directly on the server's desktop environment.

[stebo85]

@aswinnarayanan or @astewartau or @iishiishii - did you try this recently? Is this documentation outdated and need an update?

[aswinnarayanan]

@Proulx-S, the issue might be the root user. Can you try the following

su jovyan
ml fsl
ml
fsmlaths

[aswinnarayanan]

@aswinnarayanan or @astewartau or @iishiishii - did you try this recently? Is this documentation outdated and need an update?

Documentation is a bit outdated. The Remote-Containers has been replaced with devcontainers
If the issue was the user, we should document this https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user#_specifying-the-default-container-user

[Proulx-S]

[stebo85]

That looks like user namespaces and apparmor is not configured. Was this installed using the neurodeskapp?

[Proulx-S]

The Neurodesk App is installed but not used here. I use the following command to launch the Neurodesktop container:

docker volume create neurodesk-home &&
sudo docker run
--shm-size=1gb -it --security-opt apparmor=neurodeskapp --privileged --user=root --name neurodesktop
-v ~/neurodesktop-storage:/neurodesktop-storage
-v /local/users/sebp:/data/storage
-v /scratch/users/sebp:/data/scratch
--mount source=neurodesk-home,target=/home/jovyan
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)"
-p 8888:8888
-e NEURODESKTOP_VERSION=2025-03-14 vnmd/neurodesktop:2025-03-14

[iishiishii]

@Proulx-S What's your ubuntu version?
Can you run this command instead?

docker volume create neurodesk-home &&
sudo docker run
--shm-size=1gb -it --privileged --user=root --name neurodesktop
-v ~/neurodesktop-storage:/neurodesktop-storage
-v /local/users/sebp:/data/storage
-v /scratch/users/sebp:/data/scratch
--mount source=neurodesk-home,target=/home/jovyan
-e NB_UID="$(id -u)" -e NB_GID="$(id -g)"
-p 8888:8888
-e NEURODESKTOP_VERSION=2025-03-14 vnmd/neurodesktop:2025-03-14

It removes -security-opt apparmor=neurodeskapp which is supposed to be included only for ubuntu>=23.10

[Proulx-S]

Using ubuntu 24.04. Tried it anyway and get the same error.

[iishiishii]

@Proulx-S before module load step, could you set this variable neurodesk_singularity_opts to be empty and try again?

(base) root@neurodesktop-2025-03-12:~$ neurodesk_singularity_opts=
(base) root@neurodesktop-2025-03-12:~$ ml fsl
(base) root@neurodesktop-2025-03-12:~$ fslmaths

[Proulx-S]

Great! that worked, thanks! I further tried to include it in docker run -e, but for some reason it sets itself back. Any better way?

[Proulx-S]

Side quest:

From my host accessed through ssh within VScode, the follwing

sebp@takoyaki:$ echo $DISPLAY.
localhost:10.0.
sebp@takoyaki:$ gedit.
just works

From the container running on my host and attached to with VScode's dev-container extension, it does not (not the same is true with localhost:10.0):

(base) root@neurodesktop-2025-03-14:$ echo $DISPLAY
:10
(base) root@neurodesktop-2025-03-14:$ gedit

(gedit:10326): Gtk-WARNING **: 06:41:32.465: cannot open display: :10
(base) root@neurodesktop-2025-03-14:~$ itksnap
Launching ITK-SNAP
qt.qpa.xcb: could not connect to display :10
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: xcb.

/cvmfs/neurodesk.ardc.edu.au/containers/itksnap_4.0.2_20240117/itksnap: line 3: 10395 Aborted (core dumped) singularity --silent exec --cleanenv --env DISPLAY=$DISPLAY $neurodesk_singularity_opts --pwd "$PWD" /cvmfs/neurodesk.ardc.edu.au/containers/itksnap_4.0.2_20240117/itksnap_4.0.2_20240117.simg itksnap "$@"

[stebo85]

I will look at this when I am visiting.

Current Idea: this is XAUTHORITY and Wayland related, so maybe related to (neurodesk/neurocommand#328)