Tips, tricks and frequently asked questions

I’m having problems when building a container (e.g. `fakeroot`-errors)

Sometimes when the host system and the guest container have operating systems from different eras (e.g. Ubuntu 16.04 is really old), you might want to use the pre-built Apptainer binaries. These can be installed without any privileges.

The reason for this errors is that a critical piece of software called GLIBC might be too new in the host system. For more info, see the third point in Apptainer’s fakeroot documentation.

Where should I install my software?

Quite often in Docker images software is installed under root-user’s home folder (/root). This is the wrong approach. Installing software there with the assumption that the container will be run by root-user can cause permission headaches.

Folders under /home are also bad as that is commonly mounted by Apptainer and thus the bind mount hides software installed there.

You should install manual installations of software to, for example, /opt or /usr/local. See Filesystem Hierarchy Standard for explanation on how different folders are organized.

I have sensitive code that I would need to have in the container

Instead of installing your sensitive application to the image you can instead mount the application directory inside the container.

If your program requires compilations or installations, you can install dependencies into the container image and then install software in a bound folder or on a persistent overlay.

If you still decide to put sensitive code in your image, remember that it is visible to everyone who has access to the image.

I have an existing container, but I would want to do small modifications to the code

If you want to do you’re own modifications to the code you can either use persistent overlays or you can use the following trick:

Copy the code that you want to modify from the container to a folder outside of the container:
```
$ apptainer exec my_container.sif cp -r /path/to/code/src src
```
Modify the code outside of the container
Bind mount modified code from outside of the container back into the container
```
$ apptainer run --bind src:/path/to/code/src my_container.sif
```

My container starts to become huge

Remember to clean up any unnecessary source code or software in your %post-block. If your program does not need e.g. development headers once it has been installed, you can remove them.

You can also try multi-stage builds where one container is used to build a software, which is then copied to another container that has only those packages required to run the software.

I would want to install my conda environment in a container

See this repository for an example definition file that can be used to bootstrap conda environment into a Apptainer container image.