Singularity on Caviness

There are several ways to get a Singularity container onto Caviness.

• You can build a Singularity container from a Docker container.
• You can copy a container from a container registry to Caviness.
• You can build a container on your local system and copy it to Caviness

Caviness does not support Docker, but you can build a Singularity container from an existing Docker container. Starting on the head node, load the Singularity software into your environment using VALET, and build your container.

$ vpkg_require singularity
$ singularity build tensorflow.simg docker://tensorflow/tensorflow

Another option is to copy an existing Singularity container from a registry. Use the singularity pull command on Caviness to copy a pre-existing container from a container registry. If you use the singularity pull command to copy a Docker container, it will be converted to Singularity during the pull process.

To copy a container from a registry:

1. Log in to Caviness
2. Load singularity via VALET

vpkg_require singularity

1. Copy the container you want with the singularity pull command.

More details on this can be found in the Singularity User Guide.

One example of a container registry is https://biocontainers.pro/registry/#/.

You can build your Singularity container on your local system, installing the singularity program if you need to. For more information on how to do this, see the Singularity web site. Copy your container to Caviness using the usual file transfer methods. See the Transferring files to/from Caviness for more information.

Once your container is on Caviness you can run it. Containers must run on Caviness' compute nodes, not on the head node. Remember you must specify a workgroup before running any jobs on Caviness, then use either the salloc or sbatch command to get access to a compute node. See the Running Jobs on Caviness for more information on SLURM and using Caviness' compute nodes.

vpkg_require singularity

Then you can use the singularity commands to execute your container, like the example below.

    [(it_css:traine)@login01 ~]$ salloc --ntasks=1 --cpus-per-task=4
    salloc: Granted job allocation 844
    salloc: Waiting for resource configuration
    salloc: Nodes r00n45 are ready for job
    [traine@r00n45 ~]$ vpkg_require singularity
    Adding package `singularity/2.5.1` to your environment
    [traine@r00n45 ~]$ singularity shell tensorflow.simg 
    Singularity: Invoking an interactive shell within container...

    Singularity tensorflow.simg:~> tensorboard --help

           USAGE: /usr/local/bin/tensorboard [flags]

    Try --helpfull to get a list of all flags.

    Singularity tensorflow.simg:~> grep Cpus_allowed_list /proc/$$/status
    Cpus_allowed_list:	0-3
    Singularity tensorflow.simg:~>

Some common commands are listed here. For more information about Singularity, see the Singularity web site.