| Table of Contents |
|---|
| Warning |
|---|
The csubmitter tool is no longer available. if you need to install your container, please contact rchelp@hms.harvard.edu and provide all relevant information about your container, and we will install it for you. |
Overview
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.
...
| Code Block |
|---|
#!/bin/bash #SBATCH -p short #SBATCH -t 2:00:00 #SBATCH -c 1 #SBATCH --mem=4G singularity exec /n/app/singularity/containers/$USER/your_container.sif tool_to_run |
Note 1:
By default only /tmp and /home/$USER are available inside the singularity container.
...
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
| Code Block |
|---|
compute-a-16-21:~ FOO="something" compute-a-16-21:~ export SINGULARITYENV_FOO=$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:
...