HPC on Kubernetes

This lab requires an AWS Cloud9 IDE. If you do not have an AWS Cloud9 IDE set up, complete all of the steps in the Preparation section of the workshop.

In this lab, you depoy and use a container orchestrator such as Kubernetes for running HPC applications. You will run a high-performance application for molecular dynamics, GROMACS, that reads and writes data from/to a managed Lustre parallel file system, Amazon FSx for Lustre.

The deployment of Kubernetes is a challenging endeavour when done on your own. In the cloud, managed services simplify the installation, operation, and maintenance of Kubernetes. Amazon Elastic Kubernetes Service (Amazon EKS) is a managed Kubernetes service on AWS.

About Amazon EKS

Amazon EKS is is a managed service that you can use to run Kubernetes on AWS without needing to install, operate, and maintain your own Kubernetes control plane or nodes. In the cloud, Amazon EKS automatically manages the availability and scalability of the Kubernetes control plane nodes responsible for scheduling containers, managing application availability, storing cluster data, and other key tasks. With Amazon EKS, you can take advantage of all the performance, scale, reliability, and availability of AWS infrastructure, as well as integrations with AWS networking and security services. On-premises, EKS Anywhere provides a consistent, fully-supported Kubernetes solution with integrated tooling and simple deployment to AWS Outposts, virtual machines, or bare metal servers.

As part of this lab, you will deploy the below architecture to run GROMACS: Architecture

Lab workflow: