Running Singularity Containers in O2


The csubmitter tool is no longer available.

if you need to install your container, please contact and provide all relevant information about your container, and we will install it for you.


We are running a pilot project to support Singularity containers in O2; Singularity allows users to execute software containers within regular O2 jobs, and it is fully compatible with existing Docker images. 

Common Install Formats

Typically requests will contain one of the following:

  • Docker or singularity image file (.img, .sif, etc)

  • Definition file(s) for installing containers (<spec>), or a link to container repository. These can be built using the commands:

    singularity build <container-name>.sif docker://path/to/containername #or singularity build <container-name>.sif <spec>
  • nf-core modules: a path to the directory containing nf-core images created from a command like:

    nf-core download -x none --container-system singularity --parallel-downloads 8 nf-core/<package-name>

How to run Singularity containers in O2

Once a container has been approved and moved under the path /n/app/singularity/containers it can be used in O2 within any Slurm Interactive srun or sbatch  job.

The singularity executable is not available on login nodes, to execute your container you must be running an interactive or batch slurm job

The most common utilization of singularity containers is to start a shell within the container using the command  singularity shell /path/to/container_file  as in the example below:

compute-a-17-80:~ singularity shell /n/app/singularity/containers/debian10.sif Singularity> cat /etc/os-release |head -1 PRETTY_NAME="Debian GNU/Linux 10 (buster)" Singularity>

or to execute a specific command inside the container  with singularity exec /path/to/container_file command_to_run  followed by any required flag or inputs, for example:

In the above example the cat  command is executed inside the ubuntu container. 

Singularity containers can also be executed within standard O2 batch job by calling the desired singularity command inside the sbatch script, for example

Note 1:

By default only /tmp and /home/$USER are available inside the singularity container. 

Any other filesystems available in O2 compute nodes can be mounted inside the Singularity container using the flag -B, for example 

Access permissions for those filesystem is preserved inside the container.

Note 2:

By default not all env variables might be ported inside the singularity container. If a variable defined outside Singularity needs to be ported inside the container and it is not available by default, it can be pre-set  outside the container with the prefix SINGULARITYENV_.  For example the variable FOO can be ported inside the singularity container by presetting it as SINGULARITYENV_FOO

Note 3:

If you plan to use one or more GPU cards inside the container you need to submit the O2 job to a partition that supports GPU computing and add the flag --nv to your singularity command, for example:

singularity exec --nv -B /n/scratch /n/app/singularity/containers/$USER/your_container.sif



Additional documentation about the singularity command can be found on the official Singularity webpage.