simpson-docker

Dockerfile for the Simpson code. This image will be pushed to Docker Hub as jkshenton/simpson:

Overview

This project provides a Docker/Podman container for running the SIMPSON (SIMulation Package for SOlid-state NMR) application without installing it directly on your system.

Running the Container

To run the container directly from Docker Hub:

```bash

Pull the image from Docker Hub

docker pull jkshenton/simpson

Using Docker: Run the image directly

docker run -v $(pwd):/workspace jkshenton/simpson simpson test.in

Using Podman

podman run -v $(pwd):/workspace jkshenton/simpson simpson test.in ```

Instructions for Windows Users

When using PowerShell, replace $(pwd) with ${PWD} or use an absolute path.

```powershell

Pull the image from Docker Hub

docker pull jkshenton/simpson

Run using Docker in PowerShell

docker run -v ${PWD}:/workspace jkshenton/simpson simpson test.in ```

Using with Singularity/Apptainer

On HPC systems where Singularity/Apptainer is available, you can use this container in several ways:

Pull directly from Docker Hub

```bash

Convert Docker image to Singularity image

singularity pull simpson.sif docker://jkshenton/simpson

Or with newer Apptainer syntax

apptainer pull simpson.sif docker://jkshenton/simpson ```

Running with Singularity/Apptainer

```bash

The current directory is automatically mounted

singularity run simpson.sif simpson test.in

Or with newer Apptainer syntax

apptainer run simpson.sif simpson test.in ```

Note: Unlike Docker/Podman, Singularity/Apptainer automatically mounts the current directory, so you don't need to specify the -v flag.

Building and running the container locally

```bash

Using Docker

docker build -t simpson .

Using Podman

podman build -t simpson . ```

Running the Container

```bash

Using Docker

docker run -v $(pwd):/workspace simpson simpson test.in

Using Podman

podman run -v $(pwd):/workspace simpson simpson test.in

```

Using the wrapper script

1. Make the script executable bash chmod +x simpson.sh

2. Run the script bash ./simpson.sh test.in

The script will automatically mount the current directory to the /workspace directory in the container and run the simpson command with the provided input file.

You can add the script to your PATH to run it from anywhere. For example, you can copy the script to /usr/local/bin and rename it to simpson: bash sudo cp simpson.sh /usr/local/bin/simpson

Controlling CPU Cores

To limit the number of CPU cores SIMPSON uses, set the SIMPSON_NUM_CORES environment variable:

```bash

Using Docker

docker run -e SIMPSONNUMCORES=4 -v $(pwd):/workspace jkshenton/simpson simpson test.in

Using Podman

podman run -e SIMPSONNUMCORES=4 -v $(pwd):/workspace jkshenton/simpson simpson test.in

Using Singularity/Apptainer

apptainer run --env SIMPSONNUMCORES=4 simpson.sif simpson test.in ```

Note: This container uses the fork-based parallelization method which works on Linux and macOS systems. MPI-based parallelization is not (yet) included in this container build.

Disclaimer

This repository is not affiliated with the SIMPSON development team. This Docker container is an independent project created to simplify the installation and usage of SIMPSON.

The SIMPSON software is developed and maintained by the NMR group at Aarhus University. For the official SIMPSON software, support, and documentation, please visit https://inano.au.dk/about/research-centers-and-projects/nmr/software/simpson.

This Docker container is provided "as is", without warranty of any kind. While efforts have been made to ensure compatibility, I am not responsible for any issues that may arise from using this container in your research or production environment. Use at your own risk.