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OpenFOAM on AWS ParallelCluster

OpenFOAM on AWS ParallelCluster provides steps and code samples to build and run OpenFOAM on AWS using AWS ParallelCluster. It is targeted for Intel and AMD CPU Platform from Haswell and onward.

OpenFOAM On AWS

Architecture

OpenFOAM ParallelCluster Architecture

Deploying OpenFOAM on AWS

AWS Cloud9 Environment

AWS Cloud9 is a cloud-based integrated development environment (IDE) that lets you write, run, and debug your code with just a browser.

AWS Cloud9 contains a collection of tools that let you code, build, run, test, debug, and release software in the cloud using your internet browser. The IDE offers support for python, pip, AWS CLI, and provides easy access to AWS resources through Identity and Access Management (IAM) user credentials. The IDE includes a terminal with sudo privileges to the managed instance that is hosting your development environment. This makes it easy for you to quickly run commands and directly access AWS services.

Create an AWS Cloud9 environment:

The link below will create an AWS Cloud9 environment from which you will be able to create your cluster.

Launch Stack

  1. Open the AWS Cloud9 console.
  2. Select MyCloud9Env.
  3. Choose Open IDE.

Disable AWS managed temporary credentials:

  1. Once the Cloud9 environment is created.
  2. Choose the gear icon in the top right to open the Prefences tab.
  3. In the Preferences tab, choose AWS SETTINGS.
  4. Turn off the AWS managed temporary credentials.
  5. Close the Preferences tab.

Prerequisites

Let start by downloading the OpenFOAM repository containing the Infrastructure as Code on your Cloud9 instance.

On the Cloud9 instance terminal, run the script below to install the prerequisited software:

wget https://github.com/aws-samples/awsome-hpc/archive/refs/heads/main.tar.gz
mkdir -p AWSome-hpc
tar -xvzf main.tar.gz -C AWSome-hpc --strip-components 1
cd AWSome-hpc/apps/openfoam
bash ./scripts/setup/install_prerequisites.sh

The script will install the following on the Cloud9 instance:

Install AWS ParallelCluster

Create your Python3 virtual environment

python3 -m venv .env
source .env/bin/activate

Install AWS ParallelCluster

pip3 install aws-parallelcluster==3.4.1

Set AWS Region The command below will query the metadata of the AWS Cloud9 instance to determine in which region it has been created.

export AWS_REGION=`curl --silent http://169.254.169.254/latest/meta-data/placement/region`

Building OpenFOAM Image using Packer on AWS

The sample relies on packer to build an AWS Machine Image (AMI) containing an installation of OpenFOAM. It is compiled and optimized for Intel Xeon Scalable Processor using the following compiler and MPI combination:

  • Intel oneAPI compiler and Intel oneAPI MPI 2022.2.0

The packer scripts are located in the amis folder and are organized by Operating System (OS) such as \[OS\]-pc-openfoam. The available OS for this solution are:

  • Amazon Linux 2

The AMI name is generated as [company_name]-[OS]-parallelcluster-[parallel_cluster_version]-[application_name]-[application_version]-[isotime YYYMMDDHHmmss].

Different variables are passed to packer to build the OpenFOAM AMI. For simplicity, they have preset values and you can find the list and description of the variables in this document.

Build an AMI

Navigate to the amis folder, choose the desired OS, build the AMI using packer. You can accomplish this by typing:

# Set OS for OpenFOAM to be amzn2 or CentOS 7
COMPANY_NAME=AnyCompany
OS_TYPE=amzn2

# Go to the corresponding folder
cd amis/${OS_TYPE}-pc-openfoam

# Build the ami using packer
packer build \
    -var-file variables.json \
    -var aws_region=${AWS_REGION} \
    -var parallel_cluster_version=`pcluster version | jq -r '.version'` \
    -var company_name=${COMPANY_NAME} \
    ${OS_TYPE}-pc-openfoam.json

Deploy AWS ParallelCluster with OpenFOAM

Create the AWS ParallelCluster Configuration file. Instances that will be used are c5n.18xlarge

# Going back from where you started
cd ../../

. ./scripts/setup/create_parallelcluster_config.sh

Create the OpenFOAM Cluster

CLUSTER_NAME="openfoam-cluster"
pcluster create-cluster -n ${CLUSTER_NAME} -c config/openfoam-x86-64.yaml --region ${AWS_REGION}

Connect to the cluster

pcluster ssh -n ${CLUSTER_NAME} -i ~/.ssh/${SSH_KEY_NAME} --region ${AWS_REGION}

Run OpenFOAM

In this section, you will go through the steps to run test case(s) provided by OpenFOAM on AWS ParallelCluster.

Once you are connected to the OpenFOAM cluster, you should navigate to the /fsx directory. Here are the steps:

MotorBike 4 Million Cells

In this section, you will learn how to run simpleFoam from OpenFoam on a Motorobike test case.

Run simpleFoam

Create a work directory on FSx for Lustre, /fsx

export MOTORBIKE_DIR="/fsx/motorBikeDemo"
mkdir -p ${MOTORBIKE_DIR}

Load OpenFoam environment for Intel oneAPI compiler.

module load openfoam/2012-intel-2022.2.0

Copy MotorBike tutorial case to FSx for Lustre

cp -r $FOAM_TUTORIALS/incompressible/simpleFoam/motorBike/* ${MOTORBIKE_DIR}/

Create a script to change the default tutorial Motorbike case to 4 Million cells.

cat > ~/change_motorbike.sh << EOF
#Change the number of subdomains to 192 to run on 192 cores.

sed  's%numberOfSubdomains.*$%numberOfSubdomains 192;%g;s%(.*$%(8 6 4);%g' \${MOTORBIKE_DIR}/system/decomposeParDict.6 > \${MOTORBIKE_DIR}/system/decomposeParDict.hierarchical

cat > \${MOTORBIKE_DIR}/system/decomposeParDict.ptscotch  << EOF2
FoamFile
{
    version     2.0;
    format      ascii;
    class       dictionary;
    object      decomposeParDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

numberOfSubdomains 192;

method          ptscotch;
EOF2


#Change the maximum number of cells per core and total for the domain to obtain a 4 million cells domain.
sed  -i -e 's%maxLocalCells.*$%maxLocalCells 10000000;%g'\
    -e 's%maxGlobalCells.*$%maxGlobalCells 200000000;%g' \
    -e 's%finalLayerThickness.*%finalLayerThickness 0.5;%g' \
    -e 's% minThickness.*% minThickness 0.2;%g' \
    -e 's%levels.*%levels ((1E15 5));%g' \${MOTORBIKE_DIR}/system/snappyHexMeshDict


#Change the simulaion time and the interval to save results.
sed  -i 's%writeInterval.*$%writeInterval 50;%g;s%endTime .*$%endTime 50;%g' \${MOTORBIKE_DIR}/system/controlDict

#Change the number of cells per axis.
sed  -i 's%hex (.*$%hex (0 1 2 3 4 5 6 7) (30 12 12) simpleGrading (1 1 1)%g' \${MOTORBIKE_DIR}/system/blockMeshDict
EOF

Execute the script to create a 4 Million cells motorbike case.

bash ~/change_motorbike.sh

Create a slurm submission script

cat > slurm-hpc6a-openfoam-motorbike.sh << EOF
#!/bin/bash
#SBATCH --job-name=foam-192
#SBATCH --ntasks=192
#SBATCH --output=%x_%j.out
#SBATCH --error=%x_%j.err
#SBATCH --partition=queue0
#SBATCH --constraint=hpc6a.48xlarge

export I_MPI_OFI_LIBRARY_INTERNAL=0

module load libfabric-aws
module load openfoam/2012-intel-2022.2.0

export FI_EFA_FORK_SAFE=1
export I_MPI_OFI_PROVIDER=efa
export I_MPI_FABRICS=shm:ofi


cd ${MOTORBIKE_DIR}
mkdir -p log
cp \$FOAM_TUTORIALS/resources/geometry/motorBike.obj.gz constant/triSurface/

surfaceFeatureExtract  > ./log/surfaceFeatureExtract.log 2>&1
blockMesh  > ./log/blockMesh.log 2>&1
decomposePar -decomposeParDict system/decomposeParDict.hierarchical  > ./log/decomposePar.log 2>&1
mpirun snappyHexMesh -parallel -overwrite -decomposeParDict system/decomposeParDict.hierarchical   > ./log/snappyHexMesh.log 2>&1
mpirun checkMesh -parallel -allGeometry -constant -allTopology -decomposeParDict system/decomposeParDict.hierarchical > ./log/checkMesh.log 2>&1
mpirun redistributePar -parallel -overwrite -decomposeParDict system/decomposeParDict.ptscotch > ./log/decomposePar2.log 2>&1
mpirun renumberMesh -parallel -overwrite -constant -decomposeParDict system/decomposeParDict.ptscotch > ./log/renumberMesh.log 2>&1
mpirun patchSummary -parallel -decomposeParDict system/decomposeParDict.ptscotch > ./log/patchSummary.log 2>&1
ls -d processor* | xargs -i rm -rf ./{}/0
ls -d processor* | xargs -i cp -r 0.orig ./{}/0
mpirun potentialFoam -parallel -noFunctionObjects -initialiseUBCs -decomposeParDict system/decomposeParDict.ptscotch > ./log/potentialFoam.log 2>&1
mpirun simpleFoam -parallel  -decomposeParDict system/decomposeParDict.ptscotch > ./log/simpleFoam.log 2>&1
EOF

Run the MotorBike test case on 2 x hpc6a.48xlarge instances

sbatch slurm-hpc6a-openfoam-motorbike.sh

The job should complete in a couple of minutes with the output and log files located in the /fsx directory.

Visualize Motorbike Results

Once the simulation is completed, you can visualize the results using Paraview

Download and extract Paraview archive

curl -o ~/ParaView-5.10.1-MPI-Linux-Python3.9-x86_64.tar.gz "https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.10&type=binary&os=Linux&downloadFile=ParaView-5.10.1-MPI-Linux-Python3.9-x86_64.tar.gz" && \
tar -xvzf ~/ParaView-5.10.1-MPI-Linux-Python3.9-x86_64.tar.gz

Let's exit the head node of AWS ParallelCluster to return to AWS Cloud9 environment.

exit

To visualize the results of the motorbike test case, you will create remote visualization session using DCV

pcluster dcv-connect -n ${CLUSTER_NAME} --key-path ~/.ssh/${SSH_KEY_NAME} --region ${AWS_REGION}

You should obtain a reponse like this. DCV link

Copy and Paste the https link to a new tab of your web brower. It will create a remote visualization session. Launch Paraview by navigating to ~/ParaView-5.10.1-MPI-Linux-Python3.9-x86_64/bin/paraview

Through Paraview, open the file at /fsx/motorBikeDemo/postProcessing/cuttingPlane/50/yNormal.vtp. Select the '+Y' option. Paraview

You'll get the view of the fluid flow on the motorbike. Paraview

Cleanup your cluster

To avoid unexpected charges to your account relative to the OpenFOAM cluster, make sure you delete the cluster and associated resources.

Delete the cluster.

pcluster delete-cluster -n ${CLUSTER_NAME} --region ${AWS_REGION}

The steps below are optional if you plan to deploy a cluster with OpenFOAM in the future.

Delete remaining components of the OpenFOAM solution

. ./scripts/cleanup/cleanup_solution_components.sh

Delete the AWS Cloud9 environment:

  1. Open the AWS CloudFormation.
  2. Select hpcsolutions-cloud9.
  3. Choose Delete.
  4. Choose Delete to confirm deletion.