Mount hook function failure

Oct 13, 2025 by wbrum.org 100 views

Introduction

Apptainer, a popular containerization tool, has been a valuable asset for researchers and developers working on Google Colab. However, recent changes by the Google Colab team have caused Apptainer to stop working, leaving many users frustrated and seeking solutions. In this article, we will delve into the issue, explore possible causes, and provide a step-by-step guide to get Apptainer up and running again in Google Colab.

Background

Apptainer, formerly known as Singularity, is an open-source containerization platform that allows users to create and manage containers for various applications. Google Colab, a free online platform for data science and machine learning, has been a popular choice for users to run Apptainer containers. However, recent changes by the Google Colab team have caused Apptainer to stop working, resulting in a series of errors and permission denied issues.

Reproducing the Problem

To reproduce the problem, we can use the following minimal example:

### Step 1: Install Apptainer
```bash
%%bash 
sudo apt update
sudo apt install -y software-properties-common
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer-suid

Step 2: Download a Sample Container

curl -X GET https://neurocontainers.neurodesk.org/itksnap_3.8.0_20201208.simg -O

Step 3: Execute the Container

!apptainer exec itksnap_3.8.0_20201208.simg itksnap

Error Message

The error message we receive is:

INFO:    Try appending ':ro' to your overlay image or using '--fakeroot'
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

Possible Causes

Based on the error message, it appears that the issue is related to permission denied errors when trying to mount the container. There are several possible causes for this issue:

Permission issues: The Google Colab team may have made changes to the permission settings, causing Apptainer to fail when trying to mount the container.
Mount hook function failure: The mount hook function may be failing due to a bug or incompatibility issue.
Overlay image issues: The overlay image may be corrupted or not properly configured, causing Apptainer to fail when trying to mount the container.

Troubleshooting Steps

To troubleshoot the issue, we can try the following steps:

Step 1: Check Permission Settings

We can check the permission settings by running the following command:

!ls -l /var/lib/apptainer/mnt/session/

This will show us the permission settings for the mount directory.

Step 2: Check Mount Hook Function

We can check the mount hook function by running the following command:

!apptainer mount --debug itksnap_3.8.0_20201208.simg

This will show us the output of the mount hook function.

Step 3: Check Overlay Image

We can check the overlay image by running the following command:

!apptainer inspect itksnap_3.8.0_20201208.simg

This will show us the details of the overlay image.

Step 4: Try Appending ':ro' to Overlay Image

We can try appending ':ro' to the overlay image by running the following command:

!apptainer exec itksnap_3.8.0_20201208.simg itksnap --overlay itksnap_3.8.0_20201208.simg:ro

This will try to mount the container with read-only permissions.

Step 5: Try Using '--fakeroot'

We can try using '--fakeroot' by running the following command:

!apptainer exec itksnap_3.8.0_20201208.simg itksnap --fakeroot

This will try to mount the container with a fake root directory.

Conclusion

In conclusion, the issue with Apptainer stopping working in Google Colab is likely due to permission denied errors when trying to mount the container. We can troubleshoot the issue by checking the permission settings, mount hook function, and overlay image. By trying to append ':ro' to the overlay image and using '--fakeroot', we can try to resolve the issue. If none of these steps work, we may need to reach out to the Google Colab team for further assistance.

Future Work

In the future, we can explore the following options to resolve the issue:

Update Apptainer: We can try updating Apptainer to the latest version to see if the issue is resolved.
Contact Google Colab Team: We can reach out to the Google Colab team to report the issue and ask for further assistance.
Explore Alternative Solutions: We can explore alternative solutions, such as using a different containerization platform or modifying the Apptainer configuration.

References

Apptainer Documentation
Google Colab Documentation
Stack Overflow: Apptainer not working in Google Colab
Apptainer Stopped Working in Google Colab: A Q&A Guide ================================================================================

Introduction

Apptainer, a popular containerization tool, has been a valuable asset for researchers and developers working on Google Colab. However, recent changes by the Google Colab team have caused Apptainer to stop working, leaving many users frustrated and seeking solutions. In this article, we will provide a Q&A guide to help users troubleshoot and resolve the issue.

Q: What is the issue with Apptainer in Google Colab?

A: The issue is related to permission denied errors when trying to mount the container. This is likely due to changes made by the Google Colab team to the permission settings.

Q: How can I reproduce the problem?

A: You can reproduce the problem by running the following minimal example:

### Step 1: Install Apptainer
```bash
%%bash 
sudo apt update
sudo apt install -y software-properties-common
sudo add-apt-repository -y ppa:apptainer/ppa
sudo apt update
sudo apt install -y apptainer-suid

Step 2: Download a Sample Container

curl -X GET https://neurocontainers.neurodesk.org/itksnap_3.8.0_20201208.simg -O

Step 3: Execute the Container

!apptainer exec itksnap_3.8.0_20201208.simg itksnap

Q: What is the error message I receive?

A: The error message you receive is:

INFO:    Try appending ':ro' to your overlay image or using '--fakeroot'
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

Q: What are the possible causes of the issue?

A: The possible causes of the issue are:

Permission issues: The Google Colab team may have made changes to the permission settings, causing Apptainer to fail when trying to mount the container.
Mount hook function failure: The mount hook function may be failing due to a bug or incompatibility issue.
Overlay image issues: The overlay image may be corrupted or not properly configured, causing Apptainer to fail when trying to mount the container.

Q: How can I troubleshoot the issue?

A: You can troubleshoot the issue by trying the following steps:

Step 1: Check Permission Settings

You can check the permission settings by running the following command:

!ls -l /var/lib/apptainer/mnt/session/

This will show you the permission settings for the mount directory.

Step 2: Check Mount Hook Function

You can check the mount hook function by running the following command:

!apptainer mount --debug itksnap_3.8.0_20201208.simg

This will show you the output of the mount hook function.

Step 3: Check Overlay Image

You can check the overlay image by running the following command:

!apptainer inspect itksnap_3.8.0_20201208.simg

This will show you the details of the overlay image.

Step 4: Try Appending ':ro' to Overlay Image

You can try appending ':ro' to the overlay image by running the following command:

!apptainer exec itksnap_3.8.0_20201208.simg itksnap --overlay itksnap_3.8.0_20201208.simg:ro

This will try to mount the container with read-only permissions.

Step 5: Try Using '--fakeroot'

You can try using '--fakeroot' by running the following command:

!apptainer exec itksnap_3.8.0_20201208.simg itksnap --fakeroot

This will try to mount the container with a fake root directory.

Q: What are the next steps if none of the troubleshooting steps work?

A: If none of the troubleshooting steps work, you may need to reach out to the Google Colab team for further assistance. You can also try updating Apptainer to the latest version or exploring alternative solutions.

Q: What are the future work options to resolve the issue?

A: The future work options to resolve the issue are:

Update Apptainer: You can try updating Apptainer to the latest version to see if the issue is resolved.
Contact Google Colab Team: You can reach out to the Google Colab team to report the issue and ask for further assistance.
Explore Alternative Solutions: You can explore alternative solutions, such as using a different containerization platform or modifying the Apptainer configuration.

Q: Where can I find more information about Apptainer and Google Colab?

A: You can find more information about Apptainer and Google Colab on the following websites: