b. Set up AWS ParallelCluster foundation

Typically, to configure AWS ParallelCluster, you use the interactive command pcluster configure to provide the information, such as the AWS Region, VPC, Subnet, and Amazon EC2 Instance Type. For this workshop, you will create a custom configuration file to include the HPC specific options for this lab.

In this section, you will set up the foundation (for example network, scheduler, …) required to build the ParallelCluster config file in the next section.

Don’t skip these steps, it is important to follow each step sequentially, copy paste and run these commands

Retrieve network information and set environment variables. In these steps you will also be writing these environment variables into a file in your working directory which can be sourced and set again in case you logout of the session.

  1. Set AWS Region
AWS_REGION=$(curl --silent
echo "export AWS_REGION=${AWS_REGION}" >> env_vars
  1. Set Amazon EC2 instance types that be will be used through this lab for head and compute nodes in the following sections (sections c)
  1. Retrieve network information

Your HPC cluster configuration will need network information such as VPC ID, Subnet ID and create a SSH Key. To ease the setup, you will use a script for settings of those parameters. If you have time and are curious, you can examine the different steps of the script.

Retrieve the script.

curl -O https://raw.githubusercontent.com/aws-samples/awsome-hpc/main/apps/wrf/scripts/setup/sc21_create_parallelcluster_config.sh

Execute the script to retrieve network information.

. ./sc21_create_parallelcluster_config.sh
  1. Store the SSH key in AWS Secrets Manager as a failsafe in the event that the private SSH key is lost
b64key=$(base64 ~/.ssh/${SSH_KEY_NAME})
aws secretsmanager create-secret --name ${SSH_KEY_NAME} \
    --description "Private key file" \
    --secret-string "$b64key" \
    --region ${AWS_REGION}

Next, you build a configuration to generate a cluster to run HPC applications.

Optional Step: Please run this command ONLY in the event that you lose your SSH private key and need to retrieve it from the secrets manager

aws secretsmanager get-secret-value --secret-id ${SSH_KEY_NAME} \
    --query 'SecretString' \
    --region ${AWS_REGION} \
    --output text | base64 --decode > ~/.ssh/${SSH_KEY_NAME}

chmod 400 ~/.ssh/${SSH_KEY_NAME}