Openmm Test

Background

OpenMM is a toolkit for molecular simulation. Physic based libraries like OpenMM are then useful for refining the structure and exploring functional interactions with other molecules. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.

Running the Demo

Example workload to validate OpenMM on Bacalhau via workload onboarding

To run on Bacalhau:

bacalhau docker run \
	-o output:/project/output \
	wesfloyd/bacalwow-openmm

bacalhau list

bacalhau describe [JOB_ID]

bacalhau get [JOB_ID]

To Build and test the docker image locally

git clone https://github.com/wesfloyd/openmm-test.git

docker build -t wesfloyd/bacalwow-openmm .

mkdir output

docker run \
	-v output:/project/output \
	wesfloyd/bacalwow-openmm

docker push wesfloyd/bacalwow-openmm

To create the Docker Image from scratch

docker run --name bacalwow-openmm -it conda/miniconda3

conda install -y -c conda-forge openmm
#python -m openmm.testInstallation


#this section will be omitted from Dockerfile
mkdir /project /project/output/ /project/input
cd /project
apt-get update && apt-get -y upgrade &&\
apt-get install -y wget sudo vim git
git clone https://github.com/wesfloyd/openmm-test.git
cp openmm-test/run_openmm_simulation.py  .
cp openmm-test/input/2dri-processed.pdb ./input
python run_openmm_simulation.py

#exit
#docker commit <CONTAINER_ID> wesfloyd/bacalwow-openmm
#docker push wesfloyd/bacalwow-openmm