Palmetto Apptainer Sandbox Builds

To use Apptainer on the Palmetto cluster, you must first request an interactive node.

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What is Apptainer?

Apptainer is an open-source container platform designed to be simple, fast, and secure. It provides portable and reproducible container environments, making it widely used in both industry and academia. Apptainer is not a veirtual machine (VM). Apptainer containers share the host OS kernel, making them faster and more lightweight than VMs. They isolate applications but don’t virtualize hardware.

Key distinctions: Performance: Containers like Apptainer have near-native performance since they bypass hardware virtualization . Overhead: VMs require more resources (e.g., full OS copies), while Apptainer containers only package applications and dependencies . Security: Apptainer uses the host’s kernel but enforces isolation via Linux namespaces and user permissions, unlike VMs which rely on hypervisor isolation .

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Tested Builds

MoDELib2 Apptainer

To build a sandbox on Palmetto, run:

sbatch buildSandbox.sh

freeFEM Apptainer

To build a sandbox on Palmetto, run:

sbatch buildSandbox.sh

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Interacting with Apptainer Directly

Start an interactive shell in a writable sandbox:

apptainer shell --writable --fakeroot ${SANDBOX_DIRECTORY_PATH}

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Managing Packages

Search for available packages in the Arch repository:

pacman -Ss ${PACKAGE_NAME}

Install a package:

pacman -S ${PACKAGE_NAME}

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Executing Programs Through Apptainer

Run commands inside the sandbox (e.g., cmake or Python scripts):

apptainer exec ${SANDBOX_DIRECTORY_PATH} cmake ..
apptainer exec ${SANDBOX_DIRECTORY_PATH} python mycode.py

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Need More Help?

Request an interactive session:

salloc

View the Apptainer manual:

man apptainer

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