Persistent Overlays

Persistent overlay directories allow you to overlay a writable file system on an immutable read-only container for the illusion of read-write access. You can run a container and make changes, and these changes are kept separately from the base container image.

Overview

A persistent overlay is a directory or file system image that “sits on top” of your immutable SIF container. When you install new software or create and modify files the overlay will store the changes.

If you want to use a SIF container as though it were writable, you can create a directory, an ext3 file system image, or embed an ext3 file system image in SIF to use as a persistent overlay. Then you can specify that you want to use the directory or image as an overlay at runtime with the --overlay option, or --writable if you want to modify the overlay embedded in SIF.

If you want to make changes to the image, but do not want them to persist, use the --writable-tmpfs option. This stores all changes in an in-memory temporary filesystem which is discarded as soon as the container finishes executing.

Note

The --writable-tmpfs size is controlled by sessiondir max size in apptainer.conf. This defaults to 64MiB, and may need to be increased if your workflows create larger temporary files.

You can use persistent overlays with the following commands:

• run

• exec

• shell

• instance start

Usage

Filesystem image overlay

Apptainer provides a command apptainer overlay create to create persistent overlay images.

Note

dd and mkfs.ext3 must be installed on your system. Additionally mkfs.ext3 must support -d option in order to create an overlay directory tree usable by a regular user.

For example, to create a 1 GiB overlay image:

$ apptainer overlay create --size 1024 /tmp/ext3_overlay.img

apptainer overlay create also provides an option --create-dir to create additional directories owned by the calling user. This option can be specified multiple times to create several such directories. This is particularly useful when you need to make a directory that is writable by your user.

For example:

$ apptainer build /tmp/nginx.sif docker://nginx
...
$ apptainer overlay create --size 1024 --create-dir /var/cache/nginx /tmp/nginx_overlay.img
$ echo "test" | apptainer exec --overlay /tmp/nginx_overlay.img /tmp/nginx.sif sh -c "cat > /var/cache/nginx/test"

Sparse overlay images

Apptainer allows the creation of overlay images as sparse files. A sparse overlay image only takes up space on disk as data is written to it. A standard overlay image will use an amount of disk space equal to its size, from the time that it is created.

To create a sparse overlay image, use the --sparse flag.

$ apptainer overlay create --sparse --size 1024 /tmp/ext3_overlay.img

Note that ls will show the full size of the file, while du will show the space on disk that the file is currently using:

$ ls -lah /tmp/ext3_overlay.img
-rw-------. 1 user user 1.0G Jan 27 11:47 /tmp/ext3_overlay.img

$ du -h /tmp/ext3_overlay.img
33M     /tmp/ext3_overlay.img

If you copy or move the sparse image you should ensure that the tool you use to do so supports sparse files, which may require enabling an option. Failure to copy or move the file with sparse file support will lead to it taking its full size on disk in the new location.

Create an overlay image manually

You can use tools like dd and mkfs.ext3 to create and format an empty ext3 file system image that will be used as an overlay.

Fakeroot with overlay

If you want to be able to modify the container with an overlay (including with --writable-tmpfs) you will generally want to run it either as root or with --fakeroot because usually containers are modifiable only by root.

If that is the way you plan to use the image, then when creating the filesystem image with overlay create also give it a --fakeroot option.

For example:

$ apptainer build ubuntu.sif docker://ubuntu
...
$ apptainer overlay create --fakeroot --size 1024 overlay.img
$ apptainer shell --fakeroot --overlay overlay.img ubuntu.sif
Apptainer> which vim
Apptainer> apt-get update && apt-get install -y vim
...
Apptainer> which vim
/usr/bin/vim

An exception is if you are using the 4th fakeroot mode with a setuid installation and no unprivileged user namespaces available. In that case the --fakeroot option to overlay create makes the overlay image unwritable, so leave it out. This case also has other restrictions in that it only works when the underlying image is a sandbox directory, and yet the overlay itself must not be a directory.

Directory overlay

A directory overlay is simpler to use than a filesystem image overlay. On the other hand, a directory of modifications to a base container image cannot be transported or shared as easily as a single overlay file, and it generally does not work well on network file servers (see the NFS and Lustre / GPFS / PanFS sections of the admin guide). It is supported, however, and this section describes how to use it.

Note

For security reasons, if Apptainer is installed in setuid mode, you must be root to use a bare directory as an overlay. ext3 file system images can be used as overlays without root privileges. If unprivileged user namespaces are also available, however, the --userns or --fakeroot options should make it work.

Create a directory as usual:

$ mkdir my_overlay

The example below shows the directory overlay in action.

$ apptainer shell --fakeroot --overlay my_overlay ubuntu.sif
Apptainer> mkdir /data
Apptainer> apt-get update && apt-get install -y vim
...
Apptainer> which vim
/usr/bin/vim

You will find that your changes persist across sessions as though you were using a writable container.

$ apptainer shell --userns --overlay my_overlay ubuntu.sif
Apptainer> ls -ld /data
drwxr-xr-x 2 user group 4096 Apr  9 10:21 /data
Apptainer> which vim
/usr/bin/vim

If you mount your container without the --overlay directory, your changes will be gone.

$ apptainer shell ubuntu.sif
Apptainer> ls /data
ls: cannot access 'data': No such file or directory
Apptainer> which vim

Readonly overlay

After all modifications to an overlay (either ext3 image or directory) have been completed, it can be mounted read-only by appending a :ro to the overlay path and no longer needs to use --fakeroot.

Continuing the above example:

$ apptainer shell --userns --overlay my_overlay:ro ubuntu.sif
Apptainer> which vim
/usr/bin/vim
Apptainer> touch /usr/bin/myfile
touch: cannot touch '/usr/bin/more': Read-only file system

Overlay embedded in SIF

It is possible to embed an overlay image into the SIF file that holds a container. This allows the read-only container image and your modifications to it to be managed as a single file.

To add a 1 GiB writable overlay partition to an existing SIF image:

$ apptainer overlay create --size 1024 ubuntu.sif

Warning

It is not possible to add a writable overlay partition to a signed, encrypted SIF image or if the SIF image already contains a writable overlay partition.

apptainer overlay create also provides an option --create-dir to create additional directories owned by the calling user, it can be specified multiple times to create many directories. This is particularly useful when you need to make a directory writable by your user.

So for example:

$ apptainer build /tmp/nginx.sif docker://nginx
$ apptainer overlay create --size 1024 --create-dir /var/cache/nginx /tmp/nginx.sif
$ echo "test" | apptainer exec /tmp/nginx.sif sh -c "cat > /var/cache/nginx/test"

Embed an overlay image in SIF

To embed an existing overlay in a SIF image, or to create an empty overlay, use the sif add subcommand.

In order to do this, you must first create a file system image:

$ apptainer sif add --datatype 4 --partfs 2 --parttype 4 --partarch 2 --groupid 1 ubuntu.sif overlay.img
$ apptainer sif list ubuntu.sif | grep -i ext3
5    |1       |NONE    |29810688-1103552512       |FS (Ext3/Overlay/amd64)

Below is the explanation what each parameter means, and how it can possibly affect the operation:

• datatype determines what kind of an object we attach, e.g. a definition file, environment variable, signature.

• partfs should be set according to the partition type, e.g. SquashFS, ext3, raw.

• parttype determines the type of partition. In our case it is being set to overlay.

• partarch must be set to the architecture against which you’re building. In this case it’s amd64.

• groupid is the ID of the container image group. In most cases there’s no more than one group, therefore we can assume it is 1.

All of these options are documented within the CLI help. Access it by running apptainer sif add --help.

Unlike the --overlay option, an overlay image inside a SIF is by default mounted readonly. To modify the overlay image, use the --writable option (and likely also the --fakeroot option):

$ apptainer shell --writable --fakeroot ubuntu.sif
Apptainer> apt-get update && apt-get install -y vim
...
Apptainer> exit
$ apptainer exec ubuntu.sif which vim
/usr/bin/vim

Final note

To resize an overlay, standard Linux tools which manipulate ext3 images can be used. For instance, to resize the 500MB file created above to 700MB one could use the e2fsck and resize2fs utilities as follows:

$ e2fsck -f overlay.img && \
    resize2fs overlay.img 700M

More information on creating and manipulating ext3 images on various Linux distribution are available where documentation for those respective distributions is found.