# How to use persistent storage in Singularity

#### Content

Singularity containers are immutable read-only by default. Overlays allow you to put on top of the container a writable file system.

Singularity automatically binds inside the image the \$HOME folder of the user and the folder where the .sif is, which means any changes made to that folder are permanent. You will not be able to write/execute/delete in all other paths inside a .sif container. This means that just by running bash inside the container you cannot make changes to the filesystem.

There are two ways to utilize persistence inside the container:

• overlay image
• writable sandbox directories

### Overlay image

#### Creating an overlay image

The overlay image is used as storage. Therefore we first need a file system image. Use the command below to create 500MB of storage.

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


Then we can start a container with any of the above commands described in the previous section and provide the overlay option to be used.

singularity shell --overlay overlay.img lent_latest.sif
singularity run -o overlay.img lent_latest.sif foamVersion
singularity exec -o overlay.img lent_latest.sif python ./hello_world.py


#### Managing the overlay image

This image later can be moved around and it contains only the changes made to the file system. That means that if we run the container without the overlay image then we will not see any changes we made before.

##### Copy the image to/from the Lichtenberg cluster
scp ip27fuzu@lcluster1.hrz.tu-darmstadt.de:/work/projects/project01204/overlay.img . # From cluster to CWD
scp overlay.sif  ip27fuzu@lcluster1.hrz.tu-darmstadt.de:/work/projects/project01204/ # From CWD to cluser


This image can be added (mounted) to the local file system and the changes only be viewed, which is useful for storing simulation results.

##### Expanding the storage size of the image
# Change overlay.img to 700MB from 500MB (previous example command)
e2fsck -f overlay.img && \
resize2fs my_overlay 700M


### 2. Creating writable sandbox directories

Here is a way to a container within a writable directory (called a sandbox). It’s possible to create a sandbox without root privileges, but to ensure proper file permissions it is recommended to do so as root. The resulting directory operates just like a container in a SIF file. To make changes within the container, use the --writable flag when you invoke your container. Note that the permissions for the user inside the container are the same as the ones outside of it (on the host system).

sudo singularity build --sandbox <NAME_OF_IMAGE> <DEF_FILE>/<LINK_TO_DOCKER_REPO>

sudo singularity build lent_immutable.sif lent_mutable/