Using Gridware with Singularity

Much like how Gridware can be used within docker containers, Singularity can import those same containers into an image file. Providing an alternative to docker for distributing applications in a platform-agnostic manner.

To install singularity support, apply the feature profile (for more info on features see Feature Profiles:

alces customize apply feature/configure-singularity

Note

This feature compiles Singularity and installs it to /opt/apps on the system. Any client nodes that are to run Singularity containers will need to have the feature installed to do so

Once the feature has been installed, the Singularity binary can be added to the path by loading the module:

module load apps/singularity/2.4

Building Images

Singularity supports a range of build sources for its images, this documentation will focus primarily on using Singularity Hub for building container images.

To build the hello-world container from Singularity Hub:

singularity pull shub://vsoch/hello-world

This creates an image file in the current working directory called vsoch-hello-world-master.simg.

Running Containers

The image can either be executed as a binary or interactively logged into.

Executing Container

The container can be run using the predefined entrypoint (at /Singularity in the image):

[[email protected](scooby) ~]$ singularity run vsoch-hello-world-master.simg
RaawwWWWWWRRRR!!

Or it can have a single command passed through to it to run:

[[email protected](mycluster) ~]$ singularity exec vsoch-hello-world-master.simg cat /etc/os-release
NAME="Ubuntu"
VERSION="14.04.5 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.5 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"

Note

/home from the master system is automatically mounted within the container so scripts existing in the user’s home directory can be executed within the container

Logging into Container

To connect to an interactive shell on the image:

[[email protected](mycluster) ~]$ singularity shell vsoch-hello-world-master.simg
Singularity: Invoking an interactive shell within container...

Singularity vsoch-hello-world-master.simg:~>