Apptainer usage
- Alan Chapman
- Josh Burks
- achiquet
- rahull1
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 classic-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 classic-interactiveOf 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 classic-interactive -c 4
$ SIMG=tensorflow_latest-gpu.sif classic-interactive --gres=gpu:a100:4Step 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:
Additional Help