CSC Computing Environment

Apptainer tutorial

💬 In this tutorial, we will get familiar with the basic usage of Apptainer (previously Singularity) containers.

  1. To run these exercises on Puhti, use sinteractive or open a compute node shell in the Puhti web interface.
sinteractive --account <project>   # replace <project> with your CSC project, e.g. project_2001234

Getting started

  1. Download a test container image from Allas:
wget  https://a3s.fi/saren-2001659-pub/tutorial.sif
ls -lh tutorial.sif
  1. The file we downloaded is a container image. It contains all the software and data of the container in a single file. In this case, the container is very bare-bones and thus quite small, about 50 MB.
    • Actual application containers are typically larger since they also contain the software installation and may in some cases include reference data, etc.

Basic usage

💬 There are three basic ways to run software in an Apptainer container:

Apptainer exec

  1. To execute a command inside the container, use apptainer exec:
apptainer exec tutorial.sif hello_world
  1. Compare the outputs of the following commands:
grep "^NAME" /etc/os-release
apptainer exec tutorial.sif grep "^NAME" /etc/os-release

💭 The tutorial container is based on Ubuntu 18.04. The host and the container use the same kernel, but the rest of the system can vary.

Apptainer exec in batch jobs

💡 apptainer exec is the run method you will typically use in batch job scripts.

  1. Create a file called test.sh:
module load nano    # The compute nodes do not have nano available by default
nano test.sh
  1. Copy the following contents into the file and replace <project> with your actual CSC project, e.g. project_2001234:
#!/bin/bash
#SBATCH --job-name=test           # Name of the job visible in the queue.
#SBATCH --account=<project>       # Choose the billing project. Has to be defined!
#SBATCH --partition=test          # Job queues: test, interactive, small, large, longrun, hugemem, hugemem_longrun
#SBATCH --time=00:01:00           # Maximum duration of the job. Max: depends of the partition. 
#SBATCH --mem=1G                  # How much RAM is reserved for job per node.
#SBATCH --ntasks=1                # Number of tasks. Max: depends on partition.
#SBATCH --cpus-per-task=1         # How many processors work on one task. Max: Number of CPUs per node.

apptainer exec tutorial.sif hello_world
  1. Submit the job to the queue with:
sbatch test.sh

💡 For more information on batch jobs, see Docs CSC.

Apptainer run

💬 When containers are created, a standard action called the runscript is defined. Depending on the container, it may simply print out a message, or it may launch a program or service inside the container.

💭 If you are using a container created by someone else, you will need to check the documentation provided by the creator for details.

  1. In our test container the runscript prints out a simple message:
apptainer run tutorial.sif
  1. Give the container image execute rights so that you can run it directly:
chmod u+x tutorial.sif
./tutorial.sif
  1. You can see the actual script with the command:
apptainer inspect --runscript tutorial.sif

Apptainer shell

  1. Open a shell inside the container:
apptainer shell tutorial.sif
  1. Notice that the command prompt changed. You can now run any software inside the container interactively:
hello_world
  1. Exit the container with:
exit

More information

💬 This tutorial is meant as a brief introduction to get you started.

☝🏻 When searching online for instructions, pay attention that the instructions are for the same version of Apptainer as you are using. There has been some command syntax changes etc. between versions so older instructions may not work as copy/paste. Also note that Apptainer is formerly known as Singularity.

💡 For more detailed instructions, see the Apptainer documentation.

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