Apptainer usage

Owned by Alan Chapman, created
Last updated: May 15, 2024 by rahull1
3 min read

 

Overview

Apptainer and Singularity refer to the same container technology, with Apptainer being the current branding. Apptainer binaries are available on all compute nodes. You can use a login node to execute the following instructions, which will start the container on a compute node.

Steps

Step 1: Identify the Apptainer Image for Use

To display all available images, you can use the following command from any Sol node:

$ showsimg Available Images: afni-22.2.12.sif megahit-1.2.9.sif alphafold.sif metaphage.sif aspect.sif metaphage-v2.sif aspect-tester.sif neo4j_4.4.27-community.sif beast-1.10.4.sif nfcore-eager-2.4.7.sif carla-0.9.15.sif nfcore-eager-2.5.0.sif carla_latest.sif nvhpl.sif centos-6.sif parabricks-4.0.sif centos-7.9.sif pecube-d.sif centos-8.sif persvade_v1.02.6.sif clara-parabricks_4.1.0-1.sif polysolver.sif debian-11.3.sif polysolver-singularity_v4.sif deepvariant_1.5.0-gpu.sif python deepvariant_1.5.0.sif qe-7.1.sif ensembl-vep-108.2.sif qsiprep.sif ensembl-vep.sif rhel-8.sif flexbar-3.5.0.sif rhel-9.sif fmriprep.sif spy gamess_17.09.sif spython.sif gemBS stablediffusion_automatic1111.sif gemBS.sif tensorflow_latest-gpu.sif google_colab.sif ubuntu-22.04.sif gromacs_2022.3.sif vep.sif irods-icommands.sif yade-2023.02a.sif llm.sif Syntax: $ SIMG=ubuntu-22.04 interactive $

Step 2: Launch the Apptainer Container and Enter a Terminal Prompt

To launch one of the images onto a compute node for interactive work you can do the following, as described at the bottom of the previous output:

SIMG=ubuntu-22.04 interactive

Of course, depending on the application you are interested in, you will want to change the image and interactive parameters to suit your workflow, for example:

$ SIMG=fmriprep.sif interactive -c 4 $ SIMG=tensorflow_latest-gpu.sif interactive --gres=gpu:a100:4

Step 3: Using the Container Image

Once your job has been allocated resources, you will be presented with a new prompt, indicating you are inside the container:

As the above output shows, though your terminal prompt is different, your user remains the same as your logged-in ASURITE. This means the applications (which are still inside the container) can read, write, and modify files within your Sol $HOME and scratch directories. Only files saved to these locations will be kept when you leave the container.

For additional examples of using Apptainer containers:

Parabricks

Gromacs

GAMESS 17

Additional Help

 

Arizona State University