Singularity

Singularity (opens new window) provides application containers for Linux that is also compatible with Docker.

• Install with Conda
• Common practices and commands
  • Pull Docker image
  • Run Docker image
  • Listing running containers
  • Stop running container
  • Where are the images stored ?
  • Temporary file storage

Install with Conda

Requirements

• Conda (miniconda), see our Conda tutorial for more details.
• Conda channels: conda-forge, bioconda

Add the conda-forge channel

You will need the conda-forge channel to install Singularity. If you have not set channels yet make sure to add it:

conda config --add channels conda-forge

Install singularity in conda environment

Create environment and install Singularity:

conda create -n singularity -c conda-forge "singularity>=3.0.0"

Activate your singularity environment and try running Singularity:

conda activate singularity

singularity --help

Common practices and commands

All information is collected from official Singularity documentation (link above).

Pull Docker image

You can use the pull (opens new window) and build (opens new window) commands to download pre-built images from an external resource like the Container Library (opens new window) or Docker Hub (opens new window).

#-- Example
singularity pull library://library/default/alpine

#-- Example
singularity build  -B $TMPDIR lolcow.sif docker://godlovedc/lolcow

Run Docker image

For demonstration, let’s use an easy (though somewhat useless) example of alpine_latest.sif (opens new window) image from the container library (opens new window):

singularity pull library://alpine
#-- The above command will save the alpine image from the Container Library as alpine_latest.sif.

To start an instance, you should follow below pattern:

singularity instance start -B $TMPDIR      <image>    <instance-name>

singularity instance start -B $TMPDIR alpine_latest.sif instance1

This command causes Singularity to create an isolated environment for the container services to live inside.

Listing running containers

One can confirm that an instance is running by using the instance list command like so:

singularity instance list

INSTANCE NAME    PID      IMAGE
instance1        12715    /home/ysub/alpine_latest.sif

Stop running container

When you are finished with your instance you can clean it up with the instance stop command as follows:

singularity instance stop instance1

Where are the images stored ?

By default, Singularity will create a set of folders in your $SINGULARITY_CACHEDIR directory for docker layers, Cloud library images, and metadata, respectively:

$SINGULARITY_CACHEDIR/cache/library
$SINGULARITY_CACHEDIR/cache/oci
$SINGULARITY_CACHEDIR/cache/oci-tmp

Temporary file storage

By default, Singularity won't recognize lab tmp storage. You can apply lab tmp storage location /mnt/scratch/tmp to a container using -B $TMPDIR variable

#-- Example
singularity shell -B $TMPDIR docker://ubuntu