Containers

Overview

Apptainer is an HPC-focused container platform that runs containers as the calling user (no root required). It seamlessly converts and runs images from DockerHub and Sylabs Cloud.

Why use containers on HPC?

Reproducible environments across different systems
Pre-packaged software without complex installations
Data access through bind mounting

Apptainer is pre-installed on Camber. Check version:

apptainer --version

Pulling Images

Download container images from DockerHub or Sylabs Cloud:

# From DockerHub (most common)
apptainer pull docker://python:3.11
apptainer pull docker://ubuntu:22.04

# From Sylabs Cloud
apptainer pull library://lolcow:latest

Example output:

[user@login ~]$ apptainer pull docker://alpine:latest
INFO:    Converting OCI blobs to SIF format
WARNING: 'nodev' mount option set on /tmp, it could be a source of failure during build process
INFO:    Starting build...
INFO:    Fetching OCI image...
3.6MiB / 3.6MiB [=======================================] 100% 0s
INFO:    Extracting OCI image...
INFO:    Creating SIF file...
[=======================================] 100% 0s

Images are converted to SIF (Singularity Image Format) files locally.

Running Containers

Execute specific commands:

apptainer exec python_3.11.sif python --version
apptainer exec ubuntu_22.04.sif apt list --installed

Interactive shell:

apptainer shell python_3.11.sif  # Enter container interactively

Run default command:

apptainer run python_3.11.sif    # Runs container's default command
./lolcow_latest.sif               # Direct execution (some containers)

Example output from direct execution:

 ______________________________
< Tue Aug 12 03:45:38 UTC 2025 >
 ------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Data Access

Default access: Your $HOME directory is automatically available inside containers:

apptainer exec alpine_latest.sif ls -ld $HOME
# Output: drwx------ 6 username username 6144 Aug 12 03:45 /camber/home/username

Mount additional directories:

# Mount host directory inside container
apptainer exec -B $HOME/data:/data python_3.11.sif python /data/script.py

# Mount multiple directories
apptainer exec -B $HOME/data:/data,$HOME/results:/results python_3.11.sif python /data/analysis.py

Example with outputs directory:

# First, check the host directory contents
ls -l $HOME/outputs/
# Output: -rw-r--r-- 1 username username 0 Aug 12 03:54 test.txt

# Bind mount it to /lustre inside the container
apptainer exec -B $HOME/outputs:/lustre alpine_latest.sif ls -l /lustre
# Output: -rw-r--r-- 1 username username 0 Aug 12 03:54 test.txt

Syntax:

apptainer exec -B /host/path:/container/path image.sif command

Container Information

Inspect container metadata, labels, environment variables, and other properties:

# Basic metadata
apptainer inspect python_latest.sif

Example output:

org.label-schema.build-arch: amd64
org.label-schema.build-date: Tuesday_12_August_2025_3:58:51_UTC
org.label-schema.schema-version: 1.0
org.label-schema.usage.apptainer.version: 1.4.2-1
org.label-schema.usage.singularity.deffile.bootstrap: docker
org.label-schema.usage.singularity.deffile.from: python:latest

Environment variables: View environment variables defined in the container:

apptainer inspect -e python_latest.sif

Example output:

# === /.singularity.d/env/10-docker2singularity.sh ===
#!/bin/sh
export PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
export GPG_KEY="${GPG_KEY:-7169605F62C751356D054A26A821E680E5FA6305}"
export PYTHON_VERSION="${PYTHON_VERSION:-3.13.6}"
export PYTHON_SHA256="${PYTHON_SHA256:-17ba5508819d8736a14fbfc47d36e184946a877851b2e9c4b6c43acb44a3b104}"

# === /.singularity.d/env/90-environment.sh ===
#!/bin/sh
# Copyright notices and custom environment code follow...

Quick Reference

# Pull from DockerHub
apptainer pull docker://ubuntu:22.04

# Run with data access
apptainer exec -B $HOME/data:/data ubuntu_22.04.sif python3 /data/script.py

# Interactive session
apptainer shell ubuntu_22.04.sif

# Check container info
apptainer inspect ubuntu_22.04.sif

Software Support