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:
$ SIMG=fmriprep.sif interactive Waiting for JOBID 9899771 to start Apptainer> ls .bashrc .bash_profile .bash_history myscript.sh Apptainer> fmriprep --help ... omitted extra lines ... fMRIPrep: fMRI PREProcessing workflows v21.0.3 Apptainer> whoami wdizon Apptainer> ls /scratch/wdizon/ letsbuildwrf/ wrf_compiles/
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
If you require further assistance on this topic, please don't hesitate to contact the Research Computing Team. To create a support ticket, kindly send an email to rtshelp@asu.edu. For quick inquiries, you're welcome to reach out via our #rc-support Slack Channel or attend our office hours for live assistance