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 | || || [owens-login01]$
Failed to run a local image from $HOME that have restricted access permissions
You might encounter a sittuation like
[owens-login01]$ cd $HOME [owens-login01]$ singularity pull shub://vsoch/hello-world WARNING: Authentication token file not found : Only pulls of public images will succeed Progress |===================================| 100.0% [owens-login01]$ singularity run hello-world_latest.sif FATAL: container creation failed: mount error: can't mount image /proc/self/fd/9: failed to find loop device: could not attach image file too loop device: No loop devices available
Check if your home directory has the restricted permissions
drwx------ or drwxr-x---
[owens-login01]$ ll -d $HOME drwx------ 29 tester PXX0000 4096 Mar 8 10:50 /users/PXX0000/tester
Due to root squash of home directory file system, you are not able to run an image from home directory with restricted permissions. It is recommended to place your container images in project or scratch directories which have faster image loading speed.
If you would like to place Singularity images in home directory, you may consider to change the permission:
[owens-login01]$ chmod 711 $HOME [owens-login01]$ ll -d $HOME drwx--x--x 29 tester PXX0000 4096 Mar 8 10:50 /users/PXX0000/tester
Failed to run a container directly or pull an image from Singularity or Docker hub
You might encounter an error while run a container directly from a hub:
[owens-login01]$ 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