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.
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