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Apptainer (Singularity)​

What is Apptainer?​

Apptainer (formerly known as Singularity) is a container technology that allows you to run complex scientific applications. It is an alternative to Docker, but built and optimised for running on a HPC cluster.

Why should I use Apptainer?​

Apptainer provides several advantages over Docker and other container technologies:

  • It provides verifiable reproducibility of your scientific applications. In many HPC conferences such as Supercomputing Conference (SC), users are required to provide reproducible results. This can be achieved by using Apptainer.
  • It readily integrates with HPC infrastructure, such as SLURM, GPUs, high speed Mellanox IB, parallel file system Lustre, etc.
  • The container image format SIF is designed to be portable across different HPC systems.

I have scripts written for singularity. Can I use them with apptainer?​

Yes, you can use the same scripts written for singularity with apptainer. However, we recommend you to slowly migrate to apptainer.

How do I pull an Apptainer image?​

To pull an Apptainer image, you can use the apptainer pull command. For example, to pull the latest version of Alpine Linux, type:

$ apptainer pull docker://alpine

You should see output like this:

INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 2408cc74d12b done  
Copying config a366738a18 done  
Writing manifest to image destination
Storing signatures
2022/05/24 14:20:38  info unpack layer: sha256:2408cc74d12b6cd092bb8b516ba7d5e290f485d3eb9672efc00f0583730179e8
INFO:    Creating SIF file...

A file called alpine_latest.sif should now be in your current directory.

How do I open a shell in an Apptainer container?​

If you have a .sif file in your current directory, you can open a shell in the container using apptainer shell.

For example, if you have a alpine_latest.sif file in your current directory, you can open a shell in the container using:

$ apptainer shell alpine_latest.sif

How can I run apptainer in my SLURM job script?​

Please find a sample SLURM job script running a container called gromacs_latest.sif.

#!/bin/bash
#SBATCH -p compute
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --mem 512M
#SBATCH -t 4-2:23 # time (D-HH:MM)
#SBATCH --job-name="hello_test"
#SBATCH -o slurm.%j.out
#SBATCH -e slurm.%j.err
#SBATCH --mail-user=<username>@hyderabad.bits-pilani.ac.in
#SBATCH --mail-type=ALL
srun apptainer exec gromacs_latest.sif sample.sh

How can I use a GPU in an Apptainer container?​

If you want to use a GPU in an Apptainer container, pass the --nv flag to your apptainer command.

For example, a typical exec command on a GPU container would be something like:

$ apptainer exec --nv cuda_latest.sif my_scipt.py
info

The --nv flag can be passed to exec, run, and shell.

We recommend the following registry websites: