foam-extend-4.1: Docker & Apptainer Containerization for HPC

This repository provides everything needed to build and run a containerized version of foam-extend-4.1 for both Docker and Apptainer (Singularity) environments, suitable for HPC clusters.

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Recent Changes

• Dockerfiles now use Ubuntu 16.04 and GCC 4.9 (per official release notes).
• Build scripts (build-foamextended.sh, build-foamextended-optimized.sh) now load images locally by default (--load), with a --no-load option to disable this.
• Apptainer support: Added Singularity.def, build-foam-extend-apptainer.sh, and run-foam-extend-apptainer.sh for easy container creation and execution on HPC systems.

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Docker Workflow

Dockerfile

• Base image: ubuntu:16.04
• Compiler: gcc-4.9 and g++-4.9
• Builds: foam-extend-4.1 from source, applies all required patches and environment setup.
• Entrypoint: Automatically configures the shell for foam-extend.

Build Scripts

build-foamextended.sh

Automates building the Docker image.
Now loads the image locally by default (--load).
Add --no-load to skip loading.

Usage:

./build-foamextended.sh [options]

Options:

• -u, --username Docker Hub username (default: acchapm1)
• -i, --image-name Image name (default: foam-extend)
• -v, --version Image version tag (default: 4.1)
• -p, --platform Target architecture (default: linux/amd64)
• --no-load Do not load the image locally after build
• -h, --help Show help

build-foamextended-optimized.sh

Supports multiple optimization levels and flattening.
Loads image locally by default unless --no-load is specified.
Use --push to push to Docker Hub.

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Apptainer (Singularity) Workflow

Singularity Definition File

• File: Singularity.def
• Base: Ubuntu 16.04, GCC 4.9, all dependencies, builds foam-extend-4.1
• Environment: Sets up all necessary variables for foam-extend

Build the Apptainer Image

Use the provided script:

./build-foam-extend-apptainer.sh [output_image.sif]

(Default output: foam-extend-4.1.sif)

Or manually:

apptainer build foam-extend-4.1.sif Singularity.def

Run the Apptainer Container

Use the provided script:

./run-foam-extend-apptainer.sh [image.sif] [host_workdir] [extra_args...]

• image.sif (optional): Apptainer image (default: foam-extend-4.1.sif)
• host_workdir (optional): Host directory to mount as /work (default: current directory)
• extra_args...: Any extra arguments to pass to the container

Example:

./run-foam-extend-apptainer.sh foam-extend-4.1.sif $PWD icoFoam -help

Or run interactively:

apptainer shell foam-extend-4.1.sif

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Example: Running on HPC with Apptainer

#!/bin/bash
#SBATCH --job-name=foam_test
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem=4G
#SBATCH --time=01:00:00

CASE_DIR="/path/to/your/case"
SIF_FILE="/path/to/foam-extend-4.1.sif"

apptainer exec --bind "${CASE_DIR}:/work" "${SIF_FILE}" icoFoam

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Summary

• Docker: Build and run locally or on any Docker-enabled system.
• Apptainer: Build and run on any HPC system with Apptainer/Singularity.
• Scripts: Provided for both build and run workflows, with flexible options.

See individual script comments and the Singularity.def for further details.