Page Comparison

The cl-submit-container is a new tool to submit requests for installing a Singularity container on the O2 cluster. An image source is used as an argument to generate an install request, which will build and deploy a Singularity container to an authorized container directory.

...

/n/cluster/container-scanning/bin/cl-submit-container --help

...

Basic cl-submit-container tool usage takes the following form:

$ /n/cluster/bin/cl-submit-container [image_source]

...

$ /n/cluster/container-scanning/bin/cl-submit-container --status
Job Name         Status          Log file
nginx.dockerfile FAILED          /n/app/singularity/userlogs/<HMSID>/nginx.dockerfile-2024-07-25T09:51:19.log

If a container fails to install, you can run the command /n/cluster/bin/cl-submit-container -r to see a detailed log of the process.

Please make sure to include the content of this log when submitting a ticket to rchelp@hms.harvard.edu about the failed container install.

Running Approved Containers

Once a container is submitted and successfully created, it will be available under a user-specific directory, i.e. /n/app/singularity/containers/<HMSID>. The user has read and execute permissions on this folder, but cannot modify any of its contents. For more information on running Singularity containers in o2, see Running Singularity Containers in O2.

Common Examples

1. Create a Singularity image called nginx with the nginx container pulled from Docker Hub URI:

   Code Block
   language bash
   $ /n/cluster/container-scanning/bin/cl-submit-container -n nginx docker://nginx:latest

2. Create a Singularity container container called genomics from a Dockerfile (note:-n genomics is used to name the image genomics instead of genomics_workflow)

   Code Block
   language bash
   $ /n/cluster/container-scanning/bin/cl-submit-container -n genomics ~/CONTAINERS/working_dir/genomics_workflow.dockerfile

3. Create a Singularity container from a Singularity definition file:

   Code Block
   language bash
   $ /n/cluster/container-scanning/bin/cl-submit-container ~/ollama.def