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.
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
--overlay option, or
--writable if you want to modify
the overlay embedded in SIF.
By default for security reasons the ext3 format is only supported in
unprivileged user namespace mode, so unless that default is changed a
-u/--userns option may be needed with a setuid-root installation.
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.
--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:
Filesystem image overlay
Apptainer provides a command
create to create persistent overlay images.
mkfs.ext3 must be installed on your system.
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 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
$ 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
$ apptainer overlay create --sparse --size 1024 /tmp/ext3_overlay.img
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
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
--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
$ 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.
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 sections of the admin guide). It is supported, however, and this section describes how to use it.
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
--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
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
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
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
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
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,
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:
datatypedetermines what kind of an object we attach, e.g. a definition file, environment variable, signature.
partfsshould be set according to the partition type, e.g. SquashFS, ext3, raw.
parttypedetermines the type of partition. In our case it is being set to overlay.
partarchmust be set to the architecture against which you’re building. In this case it’s
groupidis 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
apptainer sif add --help.
--overlay option, an overlay image inside a SIF is by
default mounted readonly.
To modify the overlay image, use the
--writable option (and likely
$ 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
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
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.