Scientific Computing and Data

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Singularity

In Minerva we support Singularity. It is in the Chimera compute partition as a module.

To pull a singularity image:

# pull with default name, vsoch-hello-world-master.simg

$ singularity pull shub://vsoch/hello-world

# pull with custom name

$ singularity pull –name hello.simg shub://vsoch/hello-world

# To create a container within a writable directory (called a sandbox)

$ singularity build –sandbox lolcow/ shub://GodloveD/lolcow

 

More details on how to create container within a writable directory.

To pull a docker image:

        $ singularity pull docker://ubuntu:latest

To run a simg:

$ singularity run hello-world.simg

$ ./hello-world.simg

 

Note that /tmp and user home directory is automatically mounted into the singularity image but not orga. If you would like to get a shell with orga mounted in the image, use command:

$ singularity shell -B /sc/orga/project/xxx hello.simg

 

Singularity build is not supported for normal users due to the sudo privileges. If you would like to build a new image or convert a docker image, you can use Sylabs Build. After signing in using Google,  you can pull or upload your recipe, trigger the singularity build, and download the image afterwards.

For full documentation of singularity, please refer to Singularity website.