Software Exercise 3.1: Use Singularity from OSG Connect¶

Background¶

Containers are another way to manage software installations. We don't have the time to go fully into the details of building and using containers, but can use pre-existing containers to run jobs.

One caveat for using containers: not all systems will support them. HTCondor has built-in features for using Docker and many Open Science Grid resources have Singularity installed, but they are not always available everywhere.

Setup¶

Make sure you are logged into login04.osgconnect.net (the OSG Connect submit server for this workshop). For this exercise we will be using Singularity containers that are hosted by OSG Connect, in a very similar way to the software modules.

To get an idea on what container images are available on the OSG, take a look at the directory path /cvmfs/singularity.opensciencegrid.org/opensciencegrid.

Job Submission¶

For this job, we will use the OSG Connect Ubuntu "Xenial" image. Copy a submit file you used for a previous exercise on OSG Connect and add the following lines:

requirements = HAS_SINGULARITY == true
+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-ubuntu-xenial:latest"

If you had other requirements in the submit file, remove them. These options will do two things:

• require that your job runs on servers that have Singularity installed and can access the OSG Connect repository of Singularity containers
• tells the job which Singularity container to use

To test and see if our job is really running in Ubuntu, use this script for the job's executable:

#!/bin/bash

hostname
lsb_release -a

Submit the job and look at the output file.