Google Colab Setup Script Broken

[neilashm]

Hello,

Some time in the past few days, running NeuroDesk in a Colab environment seems to have stopped working. The setup script finishes execution without any issues. However, when running any fsl command (bet or fslinfo), I receive the following error:

FATAL: container creation failed: mount hook function failure: hook function for tag sessiondir returns error: while mounting /var/lib/apptainer/mnt/session/mountinfo to /proc/self/mountinfo: permission denied

This has broken several of our scripts which we were using for teaching a course. Please advise how we may resolve this issue asap.

Thanks,
Neil

[stebo85]

Dear @neilashm - we are looking into it now

[stebo85]

Dear @neilashm - we can reproduce the problem and it seems to be related to an update in google colab. We try to workaround the issues caused by this.

[SteffenBollmann]

Dear @neilashm - there is currently no workaround for this because Colab disabled a crucial feature that's needed to run containers. Would it be possible for you to use our Neurodesk Play cloud (https://play.neurodesk.org) instead of google colab?

[neilashm]

Hi @stebo85, just tested one of our notebooks on the European play.neurodesk server and that seems to work for our purposes. Thanks for the help, and I hope you get an answer back soon about mounting to /proc in the colab environment.

[stebo85]

Ok, great to hear. Here is the google colab issue I opened: googlecolab/colabtools#5173

But the absence of an answer suggests that this is not a bug but a new security feature in google colab.

[stebo85]

Dear @neilashm - it indeed seems that google is mitigating an undisclosed kernel vulnerability. They might remove this mitigation in the future, but it would definetely help if you can also comment on the issue: googlecolab/colabtools#5173

[neilashm]

@stebo85 Just commented. Hope they revisit the decision. Thanks!