Mounted folders fail in Docker images after 2024-12-10 (failed to set working directory: chdir /path: no such file or directory)

[wieluk]

Hey, I’m not sure if this is a general bug or specific to our setup. What might have changed between 2024-12-10 and 2024-12-19? There are new Docker images but no release notes for those changes. It works fine until 2024-12-10, but all new images after that fail.

We have a /storage folder mounted in Docker. If we run:

ml freesurfer
cd /storage
freeview

or use the same with fmriprep, we get this error:

FATAL:   failed to set working directory: chdir /storage: no such file or directory

But the folder exists and is accessible by the user inside the container.

Any idea what changed or how to fix this?

[stebo85]

I can replicate the problem :)

Investigating now

[stebo85]

The problem is that due to a bug in Docker on MacOS on apple silicon we have to start the singularity containers with the -w flag. This flag results in directories not being created inside the container when they do not yet exist.

The workaround would be to change the /storage location to one of our supported locations - e.g. /data/ or /neurodesktop-storage

I also now added /storage as a new supported mount location