Singularity Overlays¶

Efficient handling of large input and output (I/O) volumes is crucial for scientific workflows, particularly those involving tasks like image processing. However, when dealing with a multitude of files (e.g., Python packages comprising numerous small files), this can effect workflow speed and even impact the overall filesystem performance for other users.

To address these challenges, a persistent overlay serves as an empty writable filesystem that gets mounted within the Singularity container during runtime. It preserves any modifications made to its filesystem while the container is active. While the overlay appears as just another directory from the container’s perspective, the HPC filesystem treats it as a single file, enabling all I/O operations to be applied to this consolidated file. This key aspect of overlays reduces the burden on the HPC filesystem by managing metadata solely for the overlay file instead of individual files within the overlay.

An Overlay is simply a directory or a filesystem image which sits on top of a Singularity container.

The user can make benefit of the overlays in any of the following ways:

You have too many conda environments eating up your number of files limit
You have a data set consisting of a large number of small files
You would like to share your environments (R,conda,etc) with your collaborators with no installation required.

Creating an Overlay¶

To create an overlay, use the create-overlay command. This command takes the size of the overlay in megabytes and the number of files as arguments. The usage is as follows:

create-overlay -s <size-in-Megabytes> -n <number-of-files-in-1000's> [ -o <name-of-overlay> ]

# Example:
create-overlay -s 500 -n 700

The above example will create an overlay by the name overlay-500M-700K.ext3 of 500MB capacity with a number of file limit of 700K. The overlay will be named overlay-<size>M-<numfiles>K.ext3 by default. It can be customized by specifying the name with -o argument.

A sample output of the create-overlay command is shown below:

(3-4.11.0)[wz22@login2 overlay_testing]$ create-overlay -s 500 -n 700
======================
# Overlay Info       #
======================
Overlay Size: 500M
No. of Files limit: 700K
Name of Overlay: overlay-500M-700K.ext3
======================
# Creating overlay   #
======================
463483904 bytes (463 MB, 442 MiB) copied, 8 s, 57.9 MB/s
500000+0 records in
500000+0 records out
512000000 bytes (512 MB, 488 MiB) copied, 8.73192 s, 58.6 MB/s
mke2fs 1.45.4 (23-Sep-2019)
Creating filesystem with 125000 4k blocks and 700480 inodes
Filesystem UUID: b51f9007-3ad2-418e-8a41-f51b0f3361bd
Superblock backups stored on blocks:
        5896, 17688, 29480, 41272, 53064

Allocating group tables: done
Writing inode tables: done
Creating journal (4096 blocks): done
Copying files into the device: done
Writing superblocks and filesystem accounting information: done

====================
#      Done      #
====================
Finished creating overlay. It is located in /scratch/wz22/overlay_testing/overlay-500M-700K.ext3

Mounting an Overlay¶

To mount an overlay, use the mount-overlay command. This command takes the name of the overlay file as an argument. You can specify multiple overlays by using the -o option multiple times. The usage is as follows:

mount-overlay -o <name-of-overlay> [-o <name-of-overlay>] [-c <path-to-container>]...

# Example:
mount-overlay -o overlay1.ext3 -o overlay2.ext3

The above example will mount the overlays overlay1.ext3 and overlay2.ext3 simultaneously.

Note

Please note that when mounting or running multiple overlays, it is important to be aware that only the first overlay specified will be mounted as writable, while the remaining overlays will be mounted as read-only. This means that any changes made to the first overlay will be retained, but modifications to the subsequent overlays will not be allowed.

Running with an Overlay¶

To run a command with the overlay mounted, use the run-overlay command. This command takes the name of the overlay file and a command file as arguments. You can specify multiple overlays by using the -o option multiple times. The usage is as follows:

run-overlay -o <name-of-overlay> [-o <name-of-overlay> ...] [-c <path-to-container>] -f <command-file>

# Example:
run-overlay -o overlay1.ext3 -o overlay2.ext3 -f file1.txt

The above example will run the commands present in file1.txt with the overlays overlay1.ext3 and overlay2.ext3 mounted simultaneously.

Hint

Custom Container You can also use your own base containers with mount-overlay and run-overlay commands with -c option to override the default container.

Note

If you need finer control over the overlay, you can directly use the underlying Singularity commands such as singularity shell, singularity exec, etc. For example, you can mount multiple overlays using the singularity shell command as follows:

singularity shell --overlay overlay1.ext3 --overlay overlay2.ext3 /share/apps/admin/singularity-images/centos-8.2.2004.sif

This will start an interactive shell within the container with both overlays mounted. From there, you can manually perform operations and run commands within the overlay filesystem.

Similarly, you can use the singularity exec command to run a specific command with multiple overlays. For example:

singularity exec --overlay overlay1.ext3 --overlay overlay2.ext3 /share/apps/admin/singularity-images/centos-8.2.2004.sif command

Using these commands directly gives you more control and flexibility over the overlays, but it requires manual setup and execution. The mount-overlay and run-overlay commands provided earlier are simplified wrappers that handle the common tasks automatically for you.

Analogy: Understanding Overlays¶

To help understand overlays, let’s consider an analogy. Think of the Singularity container as your personal workspace, and the overlays as additional layers on your workspace.

The base container is your initial workspace, containing all the tools and resources you need.
Each overlay represents a specific task or project, with its own set of files and modifications.
Mounting an overlay is like placing a transparent sheet on top of your workspace. It adds new files and modifications without altering the original workspace.
Running a command with an overlay is like working on your workspace with the transparent sheet in place. The changes made by the command are temporary and isolated within the overlay, leaving your original workspace intact.

You can also think of the Singularity container as your personal computer (PC), and the overlay as an external hard disk or a pendrive.

When you run a Singularity container with an overlay with the mount-overlay or run-overlay command, it’s like logging into your container PC and plugging in the overlay pendrive. Just like you can navigate your files in /scratch and /home, you can also access files in the overlay by navigating to the desired folders.

You can write files and create directories in the overlay (for example /data , /env , /conda etc). Any files/directories created outside /scratch and /home will reside inside the overlay filesystem. This allows you to store environments, datasets, and other files specific to your needs.

mkdir /data

By using overlays, you can keep your base container clean and separate different tasks or projects, making it easier to manage and share your work with others.

Job Submission¶

To submit a job that uses the overlay, you can include the necessary commands in a job script. Here’s an example:

#!/bin/bash
#SBATCH --mem=8GB
#SBATCH --time=1:00:00

run-overlay -o overlay1.ext3 -o overlay2.ext3 -f file.txt

This script will run the commands present in file.txt with the overlays overlay1.ext3 and overlay2.ext3 mounted simultaneously.

An example file.txt is given below:

source ~/.bashrc
conda activate /opt/conda-envs/myenv
python abc.py

If you need finer control over the overlay or want to use the underlying Singularity commands directly, you can modify the job script as follows:

#!/bin/bash
#SBATCH --mem=8GB
#SBATCH --time=1:00:00

#Specify location of the overlay.ext3 file
overlay_ext3=/scratch/$USER/<project_dir>/<chosen-file>.ext3

singularity \
    exec --overlay $overlay_ext3:ro \
    /share/apps/jubail/singularity-images/centos-8.2.2004.sif  \
    /bin/bash -c "source ~/.bashrc; \
                conda activate /opt/conda-envs/myenv; \
                python <path_to_python_script_file>.py "

Note that in this case, you will need to manually mount the overlays and use the singularity exec command to run the desired command. This provides finer control over the overlay setup and execution.

Remember to adjust the resource requirements (e.g., memory and time) in the job script according to your specific needs.