Alternative to Docker in Google Colab: Apptainer

instruction.md

There have been many discussions under this gist about installing docker in Google Colab: https://gist.github.com/mwufi/6718b30761cd109f9aff04c5144eb885

As a possible alternative, Apptainer works on Google Colab.

You can follow the instruction in the document to install it: https://apptainer.org/docs/admin/latest/installation.html#install-ubuntu-packages

It is possible to convert a docker image to .sif file for Apptainer:

!apptainer build hello.sif docker://hello-world

However, it is worth noting that Google Colab has some restrictions on root user's capabilities, so you must gain full capabilities in a new user namespace created by unshare -r before running Apptainer as root:

!unshare -r apptainer run hello.sif

or just run as a regular user:

# The user in the container will be somebottle
!sudo -u somebottle apptainer run hello.sif

# The user in the container will be root
!sudo -u somebottle apptainer run --fakeroot hello.sif

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Additionally, if you want to run a CUDA application inside a container, you need to use flag --nv in the command line, according to https://apptainer.org/docs/user/1.3/gpu.html#requirements

# execute 'nvidia-smi' inside a newly created container
!unshare -r apptainer exec --nv pytorch-gpu.sif nvidia-smi

You may run into a problem like this:

That's because Apptainer depends on ldconfig -p to find shared libraries, but NVIDIA libraries haven't been added to it on Google Colab.

Follow these steps to fix it:

1. Check the LD_LIBRARY_PATH to find nvidia library path:

   !unshare -r env | grep LD_
   # >> LD_LIBRARY_PATH=/usr/lib64-nvidia

2. Write the nvidia library path into /etc/ld.so.conf.d/:

   !echo "/usr/lib64-nvidia" >> /etc/ld.so.conf.d/nvidia.conf

3. Refresh library cache:

   !ldconfig

Now you'll be able to find nvidia library files in ldconfig -p, and can execute nvidia-smi command normally:

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I hope this helps!

Original post: https://github.com/cat-note/bottleofcat/blob/main/Containerization/GPUApptainerOnGoogleColab.md