NOTE: Building Singularity containers are currently not supported on the OSGConnect access point. The guide assumes that you have your own Linux machine where you can install Singularity and execute commands via sudo.

This guide is meant to accompany the instructions for using containers
in the Open Science Pool. You can use your own custom container to run
jobs in the Open Science Pool. This guide describes how to create your
own Singularity container "image" (the blueprint for the container).

For an overview and how to execute images on OSG, please see Use Containers on the OSG

Install Singularity

Install Singularity to your computer using the appropriate version for your operating system. Note that OSG does not provide any container build hosts. sudo is required to build the images.

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. We strongly recommend using one of the OSG's published containers as your starting point. 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 \
            libbz2-dev \
            libcurl4-gnutls-dev
    wget https://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz
    tar -xzf R-3.6.0.tar.gz
    cd R-3.6.0
    ./configure
    make
    make install

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

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 \
            libbz2-dev \
            libcurl4-gnutls-dev
    wget https://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz
    tar -xzf R-3.6.0.tar.gz
    cd R-3.6.0
    ./configure
    make
    make install

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

$ sudo singularity build my-container.sif image.def

Note that sudo here is currently required.

Once the image is built, you can upload it to Stash, test it on OSGConenct, and use it in your HTCondor jobs. This is all described in the container guide.

 

This page was updated on May 20, 2022 at 18:10 from start/software/containers-singularity.md.