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."
Availability and Restrictions
Singularity is available on Ruby, Owens and Pitzer clusters. Only one version is available at any given time. To find out the current version:
Singularity is available to all OSC users.
Publisher/Vendor/Repository and License Type
SyLabs, Inc., 3-clause BSD License
No setup is required. You can use Singulairty directly on all clusters.
See HOWTO: Use Docker and Singularity Containers at OSC for information about using Singularity on Ruby, Owens and Pitzer clusters, including some site-specific caveats.
Example: Run a container from the Singularity hub
[owens-login01]$ singularity run library://godlovedc/funny/lolcow INFO: Downloading library image Progress |===================================| 100.0% _______________________________________ / You never have to change anything you \ | got up in the middle of the night to | | write. | | | \ -- Saul Bellow / --------------------------------------- \ ^__^ \ (oo)\_______ (__)\ )\/\ ||----w | || ||
- 2019-05-14 OSC Workshop: Containers for Research Computing. Please find the link in the workshop page for the tutorial material and slides.
Failed to pull a large Docker image
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 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 $TMPDIR for caches, squashfs temp files and download
[owens-login01]$ qsub -I -l nodes=1:ppn=1 [o0001]$ cd $TMPDIR [o0001]$ export SINGULARITY_CACHEDIR=$TMPDIR [o0001]$ export SINGULARITY_TMPDIR=$TMPDIR [o0001]$ singularity pull docker://qiime2/core:2019.1 [o0001]$ qiime2_core_2019.1.sif /where/to/keep/image/
Failed to run a container directly or pull an image from Singularity or Docker hub
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
$HOME/.singularity/cache. If the singularity version is prior to 3.0:
[owens-login01]$ cd $HOME/.singularity/cache [owens-login01 cache]$ rm -rf *
If the singularity version is 3.1 and above:
[owens-login01]$ singulariy cache clean -a
Alternatively, you can change the Singularity cache directory to different location by setting the variable
SINGULARITY_CACHEDIR. For example, in a batch job:
#PBS -N singularity_teset #PBS -l nodes=1:ppn=1 #PBS -j oe export SINGULARITY_CACHEDIR=$TMPDIR singularity run shub://vsoch/hello-world