Persistent overlay images are new to version 2.4! This feature allows you to overlay a writable file system on an immutable read-only container for the illusion of read-write access.
A persistent overlay is an image that “sits on top” of your compressed, immutable squashfs container. When you install new software or create and modify files the overlay image stores the changes.
In Singularity versions 2.4 and later an overlay file system is automatically added to your squashfs or sandbox container when it is mounted. This means you can install new software and create and modify files even though your container is read-only. But your changes will disappear as soon as you exit the container.
If you want your changes to persist in your container across uses, you
can create a writable image to use as a persistent overlay. Then you
can specify that you want to use the image as an overlay at runtime
You can use a persistent overlays with the following commands:
To use a persistent overlay, you must first have a container.
$ singularity build ubuntu.simg shub://GodloveD/ubuntu
Then you must create a writable, ext3 image. We can do so with the
$ singularity image.create my-overlay.img
Now you can use this overlay image with your container. Note that it is not necessary to be root to use an overlay partition, but this will ensure that we have write privileges where we want them.
$ sudo singularity shell --overlay my-overlay.img ubuntu.simg Singularity ubuntu.simg:~> touch /foo Singularity ubuntu.simg:~> apt-get install -y vim Singularity ubuntu.simg:~> which vim /usr/bin/vim Singularity ubuntu.simg:~> exit
You will find that your changes persist across sessions as though you were using a writable container.
$ sudo singularity shell --overlay my-overlay.img ubuntu.simg Singularity ubuntu.simg:~> ls /foo /foo Singularity ubuntu.simg:~> which vim /usr/bin/vim Singularity ubuntu.simg:~> exit
If you mount your container without the
--overlay option, your changes will be
$ sudo singularity shell ubuntu.simg Singularity ubuntu.simg:~> ls /foo ls: cannot access 'foo': No such file or directory Singularity ubuntu.simg:~> which vim Singularity ubuntu.simg:~> exit