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Singularity on Caviness
Build a Singularity container
There are several ways to get a Singularity container onto Caviness, but here are the two to consider using if reproducibility is important.
- You can build a Singularity container from a Docker or Singularity Hub on Caviness.
- You can build a container on your local system and copy it to Caviness.
Build a Singularity container from Docker or Singularity Hub Registry
Caviness does not support Docker, but you can build a Singularity container from an existing Docker container or from a Singularity Hub container regsitry. Starting on the head node, load the Singularity software into your environment using VALET, and build your container.
Docker Hub example
$ vpkg_require singularity $ singularity build tensorflow.simg docker://tensorflow/tensorflow
Singularity Hub example
$ vpkg_require singularity $ singularity build hello-world.simg shub://vsoch/hello-worldw
More details on this can be found in the Singularity User Guide.
One example of a container registry is https://biocontainers.pro/registry/#/.
Build a container on your local system
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.
Execute your Singularity container through SLURM
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.
Inside your interactive session or your batch job you must first issue the command
vpkg_require singularity
Then you can use the singularity commands to execute your container, like the example below.
[traine@login01 ~]$ workgroup -g it_css
[(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:~>
Common Singularity commands
Some common commands are listed here. For more information about Singularity, see the Singularity web site.
shell | Start a shell within your container using the operating system you have set up your container to use. |
exec | Run a single command within your container. |
run | Run a recipe script you have set up within your container. Using a recipe script forces users of your container to use a pre-established workflow. |
help | Provides help on Singularity. |