Apptainer/Singularity

Apptainer/Singularity is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.

From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."

On June 21th, 2022, Singularity is replaced with Apptainer, which is just a renamed open-source project to avoid conflicts with SingularityCE so it can be accepted into the Linux Foundation. Apptainer 1.0 has the same code as Singularity after versions 3.8.x, and still provides the command singularity (apptainer is the official command). Thus, user should continue running containers on OSC systems without any issue: 

1. Containers built with Apptainer will continue to work with installations of Singularity.
2. User will see warnings about SINGULARITY_ and SINGULARITYENV_ environment variables.
    A future version of Apptainer may stop supporting environment variable compatibility so we recommned
    users to add respective APPTAINER_ and APPTAINERENV_ counterparts in their job environments.

For more detail, pleae visit the Singularity Compatibility page.

If you experience issues using Singularity after downtime, please contact OSC help.

Availability and Restrictions

Versions

Apptainer/Singularity is available on Owens and Pitzer clusters. Only one version is available at any given time. To find out the current version:

singularity version

Check the release page for the changelog: https://github.com/apptainer/apptainer/releases

Access

Apptainer/Singularity is available to all OSC users.

Publisher/Vendor/Repository and License Type

Apptainer project, established as Apptainer a Series of LF Projects LLC; 3-clause BSD License

Usage

Set-up

No setup is required. You can use Apptainer/Singularity directly on all clusters.

Using Singularity

See HOWTO: Use Docker and Singularity Containers at OSC for information about using Apptainer/Singularity on Owens and Pitzer clusters, including some site-specific caveats.  

Example:  Run a container from the Singularity hub

[owens-login01]$ singularity run shub://singularityhub/hello-world
INFO:    Downloading library image
Tacotacotaco
If unsure about the amount of memory that a singularity process will require, then be sure to request an entire node for the job. It is common for singularity jobs to be killed by the OOM killer because of using too much RAM.


Known Issues

Reached your pull rate limit

Update: 06/16/2021 
Version: all

You might encounter an error while pulling a large Docker image:

ERROR: toomanyrequests: Too Many Requests.

or

You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limits.

On November 20, 2020, Docker Hub puts rate limits on anonymous and free authenticated pull requests. The rate limits for anonymous and authenticated pulls are 100 per 6 hours and 200 per 6 hours, respectively. Anonymous users have limits enforced via IP. Since all computing nodes at OSC share the same IP, anonymous pull rate limit is shared by all OSC users if you are not authenticated. 

If you encounter this error and want to get rid of it, please consider setting up authenticated access to  Docker Hub: https://apptainer.org/docs/user/main/endpoint.html?highlight=endpoint#ma....

 

Failed to pull a large Docker image

Update: 05/21/2019 
Version: all

You might encounter an error while pulling a large Docker image:

[owens-login01]$ singularity pull docker://qimme2/core
FATAL: Unable to pull docker://qiime2/core While running mksquashfs: signal: killed

The process could be killed because the image is cached in the home directory which is a slower file system or the image size might exceed a single file size limit.

The solution is to use other file systems like /fs/scratch and $TMPDIR for caches and temp files to build the squashfs filesystem:

[owens-login01]$ sinteractive -n 1 -A PAS1234 
bash-4.2$ export APPTAINER_CACHEDIR=$TMPDIR
bash-4.2$ export APPTAINER_TMPDIR=$TMPDIR 
bash-4.2$ singularity pull docker://qiime2/core:2019.1
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
...
INFO:    Creating SIF file...
bash-4.2$ exit

Failed to run a container directly or pull an image from Singularity or Docker hub

Update: 03/08/2019 
Version: all

You might encounter an error while run a container directly from a hub:

[owens-login01]$ singularity run shub://vsoch/hello-world
Progress |===================================| 100.0%
FATAL: container creation failed: mount error: can't mount image /proc/self/fd/13: failed to find loop device: could not attach image file too loop device: No loop devices available

One solution is to remove the Singularity cached images from local cache directory $HOME/.apptainer/cache.

singulariy cache clean

Alternatively, you can change the Singularity cache directory to different location by setting the variable APPTAINER_CACHEDIR. For example, in a batch job:

#/bin/bash
#SBATCH --job-name="singularity_test"
#SBSTCH --ntasks=1

export APPTAINER_CACHEDIR=$TMPDIR
singularity run shub://vsoch/hello-world

Workshop

Further Reading

Supercomputer: