Apptainer/Singularity Container Images

This guide is meant to accompany the instructions for using containers under the PATh Facility. You can use your own custom container to run jobs. This guide describes how to create your own Apptainer/Singularity container "image" (the blueprint for the container).

For an overview and how to execute images on the PATh Facility, please see Containers - Overview

Identify Components

What software do you want to install? Make sure that you have either the source code or a command that can be used to install it through Linux (like apt-get or yum).

You'll also need to choose a "base" container, on which to add your particular software or tools. See the available containers on Docker Hub here: OSG Docker Containers The best candidates for you will be containers that have "osgvo" in the name.

Editing the Build Spec

Create a folder on your computer and inside it, create a blank text file called image.def.

The first lines of this file should include where to get the base image from. If using the OSG's Ubuntu 20.04 image that would look like this:

Bootstrap: docker
From: opensciencegrid/osgvo-ubuntu-20.04:latest

Then there is a section called %post where you put the additional commands to make the image just like you need it. For example:

%post
    apt-get update -y
    apt-get install -y \
            build-essential \
            cmake \
            g++ \
            r-base-dev

    R -e "install.packages('cowsay', dependencies=TRUE, repos='http://cran.rstudio.com/')"

See the Apptainer documentation for a full reference on how to specify build specs. Note that the %runscript section is ignored when the container is executed under the PATh Facility.

The final image.def looks like:

Bootstrap: docker
From: opensciencegrid/osgvo-ubuntu-20.04:latest

%post
    apt-get update -y
    apt-get install -y \
            build-essential \
            cmake \
            g++ \
            r-base-dev

    R -e "install.packages('cowsay', dependencies=TRUE, repos='http://cran.rstudio.com/')"

Once your build spec is ready, you can "build" the container image by running this command:

$ apptainer build my-container.sif image.def

Once the image is built, you can copy it to a data directory, test it on the Access Point, and use it in your HTCondor jobs. This is all described in Containers - Overview.