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Molecular Simulation with OpenMM and Bacalhau

Introduction

In this tutorial example, we will showcase how to containerize an OpenMM workload so that it can be executed on the Bacalhau network and take advantage of the distributed storage & compute resources. OpenMM is a toolkit for molecular simulation. It is a physic-based library that is 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.

In this example tutorial, our focus will be on running OpenMM molecular simulation with Bacalhau.

Prerequisite

To get started, you need to install the Bacalhau client, see more information here

Running Locally

Downloading Datasets

We use a processed 2DRI dataset that represents the ribose binding protein in bacterial transport and chemotaxis. The source organism is the Escherichia coli bacteria.

Protein data can be stored in a .pdb file, this is a human-readable format. It provides for the description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. See more information about PDB format here. For the original, unprocessed 2DRI dataset, you can download it from the RCSB Protein Data Bank here.

The relevant code of the processed 2DRI dataset can be found here. Let's print the first 10 lines of the 2dri-processed.pdb file. The output contains a number of ATOM records. These describe the coordinates of the atoms that are part of the protein.

head ./dataset/2dri-processed.pdb

Expected Output
    REMARK   1 CREATED WITH OPENMM 7.6, 2022-07-12
    CRYST1   81.309   81.309   81.309  90.00  90.00  90.00 P 1           1 
    ATOM      1  N   LYS A   1      64.731   9.461  59.430  1.00  0.00           N  
    ATOM      2  CA  LYS A   1      63.588  10.286  58.927  1.00  0.00           C  
    ATOM      3  HA  LYS A   1      62.707   9.486  59.038  1.00  0.00           H  
    ATOM      4  C   LYS A   1      63.790  10.671  57.468  1.00  0.00           C  
    ATOM      5  O   LYS A   1      64.887  11.089  57.078  1.00  0.00           O  
    ATOM      6  CB  LYS A   1      63.458  11.567  59.749  1.00  0.00           C  
    ATOM      7  HB2 LYS A   1      63.333  12.366  58.879  1.00  0.00           H  
    ATOM      8  HB3 LYS A   1      64.435  11.867  60.372  1.00  0.00           H

Writing the Script

To run the script above all we need is a Python environment with the OpenMM library installed.

# run_openmm_simulation.py
import os
from openmm import *
from openmm.app import *
from openmm.unit import *

# Input Files
input_path = '/inputs/2dri-processed.pdb'
os.path.exists(input_path) # check if input file exists
pdb = PDBFile(input_path)
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')

# Output
output_path = '/outputs/final_state.pdbx'
if not os.path.exists(os.path.dirname(output_path)): # check if output dir exists
    os.makedirs(os.path.dirname(output_path))

# System Configuration

nonbondedMethod = PME
nonbondedCutoff = 1.0*nanometers
ewaldErrorTolerance = 0.0005
constraints = HBonds
rigidWater = True
constraintTolerance = 0.000001
hydrogenMass = 1.5*amu

# Integration Options

dt = 0.002*picoseconds
temperature = 310*kelvin
friction = 1.0/picosecond
pressure = 1.0*atmospheres
barostatInterval = 25

# Simulation Options

steps = 10
equilibrationSteps = 0
#platform = Platform.getPlatformByName('CUDA')
platform = Platform.getPlatformByName('CPU')
#platformProperties = {'Precision': 'single'}
platformProperties = {}
dcdReporter = DCDReporter('trajectory.dcd', 1000)
dataReporter = StateDataReporter('log.txt', 1000, totalSteps=steps,
    step=True, time=True, speed=True, progress=True, elapsedTime=True, remainingTime=True, potentialEnergy=True, kineticEnergy=True, totalEnergy=True, temperature=True, volume=True, density=True, separator='\t')
checkpointReporter = CheckpointReporter('checkpoint.chk', 1000)

# Prepare the Simulation

print('Building system...')
topology = pdb.topology
positions = pdb.positions
system = forcefield.createSystem(topology, nonbondedMethod=nonbondedMethod, nonbondedCutoff=nonbondedCutoff,
    constraints=constraints, rigidWater=rigidWater, ewaldErrorTolerance=ewaldErrorTolerance, hydrogenMass=hydrogenMass)
system.addForce(MonteCarloBarostat(pressure, temperature, barostatInterval))
integrator = LangevinMiddleIntegrator(temperature, friction, dt)
integrator.setConstraintTolerance(constraintTolerance)
simulation = Simulation(topology, system, integrator, platform, platformProperties)
simulation.context.setPositions(positions)

# Minimize and Equilibrate

print('Performing energy minimization...')
simulation.minimizeEnergy()
print('Equilibrating...')
simulation.context.setVelocitiesToTemperature(temperature)
simulation.step(equilibrationSteps)

# Simulate

print('Simulating...')
simulation.reporters.append(dcdReporter)
simulation.reporters.append(dataReporter)
simulation.reporters.append(checkpointReporter)
simulation.currentStep = 0
simulation.step(steps)

# Write a file with the final simulation state

state = simulation.context.getState(getPositions=True, enforcePeriodicBox=system.usesPeriodicBoundaryConditions())
with open(output_path, mode="w+") as file:
    PDBxFile.writeFile(simulation.topology, state.getPositions(), file)
print('Simulation complete, file written to disk at: {}'.format(output_path))

Running the Script

python run_openmm_simulation.py

Uploading the Data to IPFS

The simplest way to upload the data to IPFS is to use a third-party service to "pin" data to the IPFS network, to ensure that the data exists and is available. To do this, you need an account with a pinning service like Pinata or nft.storage. Once registered, you can use their UI or API or SDKs to upload files.

When you pin your data, you'll get a CID. Copy the CID as it will be used to access your data

Containerize Script using Docker

To build your own docker container, create a Dockerfile, which contains instructions to build your image.

See more information on how to containerize your script/app here

FROM conda/miniconda3

RUN conda install -y -c conda-forge openmm

WORKDIR /project

COPY ./run_openmm_simulation.py /project

LABEL org.opencontainers.image.source https://github.com/bacalhau-project/examples

CMD ["python","run_openmm_simulation.py"]

Build the container

We will run docker build command to build the container:

docker build -t <hub-user>/<repo-name>:<tag> .

Before running the command, replace:

hub-user with your docker hub username, If you don’t have a docker hub account follow these instructions to create docker account, and use the username of the account you created

repo-name with the name of the container, you can name it anything you want

tag this is not required but you can use the latest tag

In our case, this will be:

docker buildx build --platform linux/amd64 --push -t ghcr.io/bacalhau-project/examples/openmm:0.3 .

Push the container

Next, upload the image to the registry. This can be done by using the Docker hub username, repo name, or tag.

docker push <hub-user>/<repo-name>:<tag>

Run a Bacalhau Job

Now that we have the data in IPFS and the docker image pushed, we can run a job on the Bacalhau network.

export JOB_ID=$(bacalhau docker run \
    --input ipfs://bafybeig63whfqyuvwqqrp5456fl4anceju24ttyycexef3k5eurg5uvrq4 \
    --wait \
    --id-only \
    ghcr.io/bacalhau-project/examples/openmm:0.3 \
    -- python run_openmm_simulation.py)

Structure of the command

Lets look closely at the command above:

bacalhau docker run: call to Bacalhau
bafybeig63whfqyuvwqqrp5456fl4anceju24ttyycexef3k5eurg5uvrq4: here we mount the CID of the dataset we uploaded to IPFS to use on the job
ghcr.io/bacalhau-project/examples/openmm:0.3: the name and the tag of the image we are using
python run_openmm_simulation.py: the script that will be executed inside the container

When a job is submitted, Bacalhau prints out the related job_id. We store that in an environment variable so that we can reuse it later on.

Checking the State of your Jobs

Job status: You can check the status of the job using bacalhau list.

bacalhau list --id-filter=${JOB_ID} --no-style

When it says Published or Completed, that means the job is done, and we can get the results.

Job information: You can find out more information about your job by using bacalhau describe.

bacalhau describe ${JOB_ID}

Job download: You can download your job results directly by using bacalhau get. Alternatively, you can choose to create a directory to store your results. In the command below, we created a directory (results) and downloaded our job output to be stored in that directory.

rm -rf results && mkdir -p results
bacalhau get ${JOB_ID} --output-dir results # Download the results

Viewing your Job Output

To view the file, run the following command:

cat results/outputs/final_state.pdbx

Support

If you have questions or need support or guidance, please reach out to the Bacalhau team via Slack (#general channel).

Molecular Simulation with OpenMM and Bacalhau

Introduction

In this example tutorial, our focus will be on running OpenMM molecular simulation with Bacalhau.

Prerequisite

To get started, you need to install the Bacalhau client, see more information here

Running Locally

Downloading Datasets

We use a processed 2DRI dataset that represents the ribose binding protein in bacterial transport and chemotaxis. The source organism is the Escherichia coli bacteria.

head ./dataset/2dri-processed.pdb

Expected Output
    REMARK   1 CREATED WITH OPENMM 7.6, 2022-07-12
    CRYST1   81.309   81.309   81.309  90.00  90.00  90.00 P 1           1 
    ATOM      1  N   LYS A   1      64.731   9.461  59.430  1.00  0.00           N  
    ATOM      2  CA  LYS A   1      63.588  10.286  58.927  1.00  0.00           C  
    ATOM      3  HA  LYS A   1      62.707   9.486  59.038  1.00  0.00           H  
    ATOM      4  C   LYS A   1      63.790  10.671  57.468  1.00  0.00           C  
    ATOM      5  O   LYS A   1      64.887  11.089  57.078  1.00  0.00           O  
    ATOM      6  CB  LYS A   1      63.458  11.567  59.749  1.00  0.00           C  
    ATOM      7  HB2 LYS A   1      63.333  12.366  58.879  1.00  0.00           H  
    ATOM      8  HB3 LYS A   1      64.435  11.867  60.372  1.00  0.00           H

Writing the Script

To run the script above all we need is a Python environment with the OpenMM library installed.

# run_openmm_simulation.py
import os
from openmm import *
from openmm.app import *
from openmm.unit import *

# Input Files
input_path = '/inputs/2dri-processed.pdb'
os.path.exists(input_path) # check if input file exists
pdb = PDBFile(input_path)
forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')

# Output
output_path = '/outputs/final_state.pdbx'
if not os.path.exists(os.path.dirname(output_path)): # check if output dir exists
    os.makedirs(os.path.dirname(output_path))

# System Configuration

nonbondedMethod = PME
nonbondedCutoff = 1.0*nanometers
ewaldErrorTolerance = 0.0005
constraints = HBonds
rigidWater = True
constraintTolerance = 0.000001
hydrogenMass = 1.5*amu

# Integration Options

dt = 0.002*picoseconds
temperature = 310*kelvin
friction = 1.0/picosecond
pressure = 1.0*atmospheres
barostatInterval = 25

# Simulation Options

steps = 10
equilibrationSteps = 0
#platform = Platform.getPlatformByName('CUDA')
platform = Platform.getPlatformByName('CPU')
#platformProperties = {'Precision': 'single'}
platformProperties = {}
dcdReporter = DCDReporter('trajectory.dcd', 1000)
dataReporter = StateDataReporter('log.txt', 1000, totalSteps=steps,
    step=True, time=True, speed=True, progress=True, elapsedTime=True, remainingTime=True, potentialEnergy=True, kineticEnergy=True, totalEnergy=True, temperature=True, volume=True, density=True, separator='\t')
checkpointReporter = CheckpointReporter('checkpoint.chk', 1000)

# Prepare the Simulation

print('Building system...')
topology = pdb.topology
positions = pdb.positions
system = forcefield.createSystem(topology, nonbondedMethod=nonbondedMethod, nonbondedCutoff=nonbondedCutoff,
    constraints=constraints, rigidWater=rigidWater, ewaldErrorTolerance=ewaldErrorTolerance, hydrogenMass=hydrogenMass)
system.addForce(MonteCarloBarostat(pressure, temperature, barostatInterval))
integrator = LangevinMiddleIntegrator(temperature, friction, dt)
integrator.setConstraintTolerance(constraintTolerance)
simulation = Simulation(topology, system, integrator, platform, platformProperties)
simulation.context.setPositions(positions)

# Minimize and Equilibrate

print('Performing energy minimization...')
simulation.minimizeEnergy()
print('Equilibrating...')
simulation.context.setVelocitiesToTemperature(temperature)
simulation.step(equilibrationSteps)

# Simulate

print('Simulating...')
simulation.reporters.append(dcdReporter)
simulation.reporters.append(dataReporter)
simulation.reporters.append(checkpointReporter)
simulation.currentStep = 0
simulation.step(steps)

# Write a file with the final simulation state

state = simulation.context.getState(getPositions=True, enforcePeriodicBox=system.usesPeriodicBoundaryConditions())
with open(output_path, mode="w+") as file:
    PDBxFile.writeFile(simulation.topology, state.getPositions(), file)
print('Simulation complete, file written to disk at: {}'.format(output_path))

Running the Script

python run_openmm_simulation.py

Uploading the Data to IPFS

When you pin your data, you'll get a CID. Copy the CID as it will be used to access your data

Containerize Script using Docker

To build your own docker container, create a Dockerfile, which contains instructions to build your image.

See more information on how to containerize your script/app here

FROM conda/miniconda3

RUN conda install -y -c conda-forge openmm

WORKDIR /project

COPY ./run_openmm_simulation.py /project

LABEL org.opencontainers.image.source https://github.com/bacalhau-project/examples

CMD ["python","run_openmm_simulation.py"]

Build the container

We will run docker build command to build the container:

docker build -t <hub-user>/<repo-name>:<tag> .

Before running the command, replace:

hub-user with your docker hub username, If you don’t have a docker hub account follow these instructions to create docker account, and use the username of the account you created

repo-name with the name of the container, you can name it anything you want

tag this is not required but you can use the latest tag

In our case, this will be:

docker buildx build --platform linux/amd64 --push -t ghcr.io/bacalhau-project/examples/openmm:0.3 .

Push the container

Next, upload the image to the registry. This can be done by using the Docker hub username, repo name, or tag.

docker push <hub-user>/<repo-name>:<tag>

Run a Bacalhau Job

Now that we have the data in IPFS and the docker image pushed, we can run a job on the Bacalhau network.

export JOB_ID=$(bacalhau docker run \
    --input ipfs://bafybeig63whfqyuvwqqrp5456fl4anceju24ttyycexef3k5eurg5uvrq4 \
    --wait \
    --id-only \
    ghcr.io/bacalhau-project/examples/openmm:0.3 \
    -- python run_openmm_simulation.py)

Structure of the command

Lets look closely at the command above:

bacalhau docker run: call to Bacalhau
bafybeig63whfqyuvwqqrp5456fl4anceju24ttyycexef3k5eurg5uvrq4: here we mount the CID of the dataset we uploaded to IPFS to use on the job
ghcr.io/bacalhau-project/examples/openmm:0.3: the name and the tag of the image we are using
python run_openmm_simulation.py: the script that will be executed inside the container

When a job is submitted, Bacalhau prints out the related job_id. We store that in an environment variable so that we can reuse it later on.

Checking the State of your Jobs

Job status: You can check the status of the job using bacalhau list.

bacalhau list --id-filter=${JOB_ID} --no-style

When it says Published or Completed, that means the job is done, and we can get the results.

Job information: You can find out more information about your job by using bacalhau describe.

bacalhau describe ${JOB_ID}

rm -rf results && mkdir -p results
bacalhau get ${JOB_ID} --output-dir results # Download the results

Viewing your Job Output

To view the file, run the following command:

cat results/outputs/final_state.pdbx

Support

If you have questions or need support or guidance, please reach out to the Bacalhau team via Slack (#general channel).

Molecular Simulation with OpenMM and Bacalhau

Introduction

Prerequisite​

Running Locally​

Downloading Datasets​

Writing the Script​

Running the Script​

Uploading the Data to IPFS​

Containerize Script using Docker​

Build the container​

Push the container​

Run a Bacalhau Job​

Structure of the command​

Checking the State of your Jobs​

Viewing your Job Output​

Support​

Molecular Simulation with OpenMM and Bacalhau

Introduction

Prerequisite​

Running Locally​

Downloading Datasets​

Writing the Script​

Running the Script​

Uploading the Data to IPFS​

Containerize Script using Docker​

Build the container​

Push the container​

Run a Bacalhau Job​

Structure of the command​

Checking the State of your Jobs​

Viewing your Job Output​

Support​

Prerequisite

Running Locally

Downloading Datasets

Writing the Script

Running the Script

Uploading the Data to IPFS

Containerize Script using Docker

Build the container

Push the container

Run a Bacalhau Job

Structure of the command

Checking the State of your Jobs

Viewing your Job Output

Support

Prerequisite

Running Locally

Downloading Datasets

Writing the Script

Running the Script

Uploading the Data to IPFS

Containerize Script using Docker

Build the container

Push the container

Run a Bacalhau Job

Structure of the command

Checking the State of your Jobs

Viewing your Job Output

Support