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Overview
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Containers available from other repositories or webpages must be first downloaded on O2 and then submitted with the --image-path flag.
Note: The testing process can take from several minutes to a few hours, depending on the type of container tested.
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More details about the csubmitter tool are available here
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The csubmitter tool is still in a pilot-test stage and might not work properly all the times. If you notice that after a day your container has not been processed, please let us know at rchelp@hms.harvard.edu |
How to prepare your Docker container to pass the csubmitter scan
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#!/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.
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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
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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:
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