What is Singularity?

Containers are units of software that package up code and all dependencies, so that applications can run quickly and reliably in different computing environments. Singularity is a common container software package that has been designed for use on shared compute clusters. While it can also be installed on personal computers, we have found Docker to be easier for personal usage. If you are using a shared academic resource, there is a good chance that Singularity is already available. Singularity containers for SMOG2 are accessible through the Sylabs SMOG-SERVER page.

How to access SMOG 2 containers for Singularity

If singularity is installed on your computer, the following command will pull the container for the most recent released version of SMOG 2:

>$ singularity pull --arch amd64 library://smog-server/library/smog2:stable

If you want to use a different version, then change the tag "stable" to the desired version (e.g. gitversion, v2.4.4, v2.4.5-pre1, etc). The above command will download the container in the form of a Singularity Image Format file: smog2_<tag>.sif

The container can then be launched for interactive use with:

>$ singularity shell smog2_stable.sif

The only visible difference will be that the command prompt says "Singularity". However, SMOG 2 and all SMOG Tools will be available in your path. Just type "smog2" to get going. For detailed information on SMOG 2 usage, see the SMOG Tutorials page or SMOG 2 manual. In containers for SMOG v2.4.5, and later, you can use the command "smoginfo" to access more information about the container, including examples for how to use in non-interactive modes.

This resource is provided by the Center for Theoretical Biological Physics.
Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford