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."
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 all OSC 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 all OSC 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
Known Issues
Reached your pull rate limit
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
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/ess/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
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
- 2019-05-14 OSC Workshop: Containers for Research Computing. Please find the link in the workshop page for the tutorial material and slides.
