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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 use 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 singularity.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

To use a persistent overlay, you must first have a container.

$ sudo singularity build ubuntu.sif library://ubuntu

Filesystem image overlay

Since 3.8, {Singularity} provides a command singularity 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:

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

singularity 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:

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

Note

Filesystem image overlays are only supported when {singularity} is installed in setuid mode. An unprivileged installation of {Singularity} can create these kinds of overlays, but cannot mount them to the container at runtime.

Sparse overlay images

Since 3.11, {Singularity} 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.

$ singularity 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 dtrudg-sylabs dtrudg-sylabs 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.

To create an overlay image file with 500MBs of empty space:

$ dd if=/dev/zero of=overlay.img bs=1M count=500 && \
    mkfs.ext3 overlay.img

Now you can use this overlay with your container, though filesystem permissions still control where you can write, so sudo is needed to run the container as root if you need to write to / inside the container.

$ sudo singularity shell --overlay overlay.img ubuntu.sif

To manage permissions in the overlay, so the container is writable by unprivileged users you can create a directory structure on your host, set permissions on it as needed, and include it in the overlay with the -d option to mkfs.ext3:

$ mkdir -p overlay/upper overlay/work
$ dd if=/dev/zero of=overlay.img bs=1M count=500 && \
     mkfs.ext3 -d overlay overlay.img

Now the container will be writable as the unprivileged user who created the overlay/upper and overlay/work directories that were placed into overlay.img.

$ singularity shell --overlay overlay.img ubuntu.sif
Singularity> echo $USER
dtrudg
Singularity> echo "Hello" > /hello

Note

The -d option to mkfs.ext3 does not support uid or gid values >65535. To allow writes from users with larger uids you can create the directories for your overlay with open permissions, e.g. mkdir -p -m 777 overlay/upper overlay/work. At runtime files and directories created in the overlay will have the correct uid and gid, but it is not possible to lock down permissions so that the overlay is only writable by certain users.

Directory overlay

A directory overlay is simpler to use than a filesystem image overlay, but a directory of modifications to a base container image cannot be transported or shared as easily as a single overlay file.

Note

For security reasons, if {Singularity} 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.

Non-root users can use directory overlays if {Singularity} is installed in non-setuid mode, and the kernel (>=5.11) of the system supports this.

Create a directory as usual:

$ mkdir my_overlay

The example below shows the directory overlay in action.

$ sudo singularity shell --overlay my_overlay/ ubuntu.sif

{Singularity} ubuntu.sif:~> mkdir /data

{Singularity} ubuntu.sif:~> chown user /data

{Singularity} ubuntu.sif:~> apt-get update && apt-get install -y vim

{Singularity} ubuntu.sif:~> which vim
/usr/bin/vim

{Singularity} ubuntu.sif:~> exit

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:

$ singularity 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.

singularity 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:

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

Note

SIF embedded overlays are only supported when {singularity} is installed in setuid mode. An unprivileged installation of {Singularity} can create these kinds of overlays, but cannot mount them to the container at runtime.

Embed an overlay image in SIF

To embed an existing overlay in a SIF image, or to create an empty overlay when using {Singularity} <3.8, use the sif add subcommand.

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

$ dd if=/dev/zero of=overlay.img bs=1M count=500 && \
    mkfs.ext3 overlay.img

Then, you can add the overlay to the SIF image using the sif functionality of {Singularity}.

$ singularity sif add --datatype 4 --partfs 2 --parttype 4 --partarch 2 --groupid 1 ubuntu_latest.sif overlay.img

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 singularity sif add --help.

After you've completed the steps above, you can shell into your container with the --writable option.

$ sudo singularity shell --writable ubuntu_latest.sif

Final note

You will find that when using the --overlay option, your changes persist across sessions as though you were using a writable container.

$ singularity shell --overlay my_overlay/ ubuntu.sif

{Singularity} ubuntu.sif:~> ls -lasd /data
4 drwxr-xr-x 2 user root 4096 Apr  9 10:21 /data

{Singularity} ubuntu.sif:~> which vim
/usr/bin/vim

{Singularity} ubuntu.sif:~> exit

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

$ singularity shell ubuntu.sif

{Singularity} ubuntu.sif:~> ls /data
ls: cannot access 'data': No such file or directory

{Singularity} ubuntu.sif:~> which vim

{Singularity} ubuntu.sif:~> exit

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 my_overlay && \
    resize2fs my_overlay 700M

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