OpenMM

OpenMM is a high performance toolkit for molecular simulation and can be used as a library or as an application. OpenMM is built upon two levels, a low level computational library (C++) and a high level application layer (Python). The goal in this is to address several distinct types of users: biologists and chemists who use the OpenMM application to study biological or chemical simulations, application developers who use the OpenMM library to create molecular simulation applications, and lastly, algorithm developers who use the application, library, and OpenMM's other unique featues like custom forces and custom integrators to develop new methodologies and molecular simulation algorithms.

System requirements

Before running the NGC OpenMM container please ensure your system meets the following requirements.

• One of the following container runtimes
  • nvidia-docker
  • Singularity >= 3.1
• One of the following NVIDIA GPU(s)
  • Pascal(sm60)
  • Volta (sm70)
  • Ampere (sm80)
  • Hopper (sm90)

x86_64

• One of the following CUDA driver versions
  • >= r525.60.13
  • > r470 (>=.57.02)

arm64

• Neoverse-n1 CPU
• CUDA driver version >= r525.60.13

Examples

The following examples will use the OpenMM NGC container to test both the application and computational layer. Ensure you're running the correct container version by replacing x.y.z with the appropriate container tag.

Running with nvidia-docker

export TEST_TYPE=gbsa|apoa1rf|pme|amoebapme|apoa1pme # Select a single test from this list you'd like to run
docker run --rm --gpus all -v $PWD:/host_pwd -w /usr/local/openmm/examples/ nvcr.io/hpc/openmm:x.y.z python benchmark.py --platform=CUDA --test=$TEST_TYPE --seconds=60

Running with Singularity

export TEST_TYPE=gbsa|apoa1rf|pme|amoebapme|apoa1pme # Select a single test from this list you'd like to run
singularity exec --nv -B $PWD:/host_pwd --pwd /usr/local/openmm/examples/ docker://nvcr.io/hpc/openmm:x.y.z python benchmark.py --platform=CUDA --test=$TEST_TYPE --seconds=60

Suggested Reading

OpenMM website

OpenMM Users Guide

OpenMM Advanced Simulations Examples

OpenMM Github.