docker

OpenMM Docker Build

Instructions on how to build a Docker Container with OpenMM.

Build System Requirements

• Git
• Docker

Inputs

Possible build-arg for the Docker build command

• IMAGE

  Default: rocm_gpu:5.7

  Note:
  This container needs to be build using Base ROCm GPU.

• OPENMM_BRANCH

  Default: 8.0.0
  Branch/Tag found: OpenMM repo

• OPENMMHIP_BRANCH

  Default: Master
  Branch/Tag found: OpenMM repo

Building OpenMM Container:

Download the Dockerfile

To run the default configuration:

docker build -t mycontainer/OpenMM -f /path/to/Dockerfile . 

Notes:

• mycontainer/OpenMM is an example container name.
• the . at the end of the build line is important! It tells Docker where your build context is located!
• -f /path/to/Dockerfile is only required if your docker file is in a different directory than your build context. If you are building in the same directory it is not required.

To run a custom configuration, include one or more customized build-arg
DISCLAIMER: This Docker build has only been validated using the default values. Using a different base image or branch may result in build failures or poor performance.

docker build \
    -t mycontainer/openmm \
    -f /path/to/Dockerfile \
    --build-arg OPENMM_BRANCH=main
    . 

Running OpenMM Container

This section describes how to launch the containers. It is assumed that up-to-versions of Docker and/or Singularity is installed on your system. If needed, please consult with your system administrator or view official documentation.

To run the OpenMM Benchmarks, just replace the <OpenMM Command> the examples in Running OpenMM Benchmarks section of the OpenMM readme. The commands can be run directly in an interactive session as well.

Docker

Docker Interactive

To run the container interactively, run the following command:

docker run --device=/dev/kfd \
           --device=/dev/dri \
           --security-opt seccomp=unconfined \
           -it  mycontainer/openmm  bash

Docker Single Command

To run the container as part of a batch script in a single command

docker run --device=/dev/kfd \
           --device=/dev/dri \
           --security-opt seccomp=unconfined \
           -it  mycontainer/openmm \
           <OpenMM Command>

Singularity

To build a singularity container from a docker container run the following command:

singularity build openmm.sif docker-daemon://mycontainer/openmm

Singularity Interactive

To launch a singularity container interactively run the following command:

singularity shell \
    --pwd /opt/openmm/examples/ \
    --no-home \
    --writable-tmpfs \
    openmm.sif

Singularity Single Command

Run the following command:

singularity run \
    --pwd /opt/openmm/examples/ \
    --no-home \
    --writable-tmpfs \
    openmm.sif \
    <OpenMM Command>

Custom Simulation

To run a custom simulation, included any scripts and data files in the container at build time adding Docker Copy commands in the provided Dockerfile or mounting the files into the container at runtime with Docker Volumes or Singularity Mount.