Bootstrapping Secure HPC Nodes with WireGuard and Cloud-Init

High-Performance Computing (HPC) clusters are the workhorses of scientific discovery, weather modeling, and countless other compute-intensive fields. Unlike typical server environments, where each machine might maintain its own persistent operating system and configuration, HPC clusters are built for speed, consistency, and efficiency.

In many HPC systems, nodes don’t have local disks for the operating system. Instead, they boot from a single, shared, read-only system image delivered across the network. This ensures uniformity and drastically reduces maintenance overhead—one image can be updated and deployed to thousands of nodes at once. However, it also introduces a unique challenge: personalization. Each node must configure itself on every boot to apply role-specific settings like network addresses, hostname, and specialized software.

This is where tools like cloud-init shine, handling the personalization process with ease. Coupled with WireGuard, a modern VPN protocol, we’ve built a workflow to securely and efficiently bootstrap these stateless nodes, ensuring they are fully configured and ready for their role in the cluster. Let’s explore how this system works and why it’s perfectly suited for HPC environments.

Bootstrapping HPC Nodes: The Workflow

When an HPC node boots, its first job is to contact the cluster’s central server. Without a persistent disk to store long-term configuration, the node starts fresh every time. To ensure secure communication, it generates a public-private key pair for WireGuard. This lightweight VPN protocol establishes a secure, encrypted tunnel between the node and the server.

The node sends its public key and metadata—information like its hostname or network address—to the server. If the server recognizes the node, it responds with its own WireGuard public key and configuration details. With this exchange complete, a secure tunnel is established, creating a private connection over which the node can safely receive its configuration data.

Next, the node downloads its cloud-init data through this tunnel. Cloud-init provides all the information the node needs to personalize itself: network settings, software packages, and sensitive data like SSH keys or workload manager keys. After cloud-init has completed its work, the node signals the server with a “phone-home” message to confirm that initialization is complete. Both the server and the node then remove all traces of the WireGuard tunnel, leaving no unnecessary connections behind.

Why Cloud-Init is Perfect for HPC

HPC clusters rely on consistency to achieve peak performance, and cloud-init is designed with this in mind. It provides a standardized way to personalize nodes, ensuring that every system is configured exactly as needed without manual intervention.

When the node boots, cloud-init kicks in early, well before the operating system is fully operational. It fetches configuration data from a designated source, which in our setup is a secure HTTP server accessed via WireGuard. This data contains everything from network configurations to user accounts and initialization scripts.

Once cloud-init retrieves the data, it processes it in several stages. First, it applies basic configurations like setting the hostname and network interfaces. Then, it moves on to more advanced tasks, such as creating users, injecting SSH keys, and installing software. If custom scripts are included, they run during the final stage, enabling precise, node-specific configuration.

Handling Secrets Securely

One of the standout features of cloud-init is its ability to handle secrets securely. For HPC clusters, this often includes delivering sensitive information like API keys, private keys, or tokens that enable the node to interact with external systems.

Cloud-init ensures secrets are stored only in memory or temporary filesystems (like /run/cloud-init) during the initialization process. By default, these files are cleared after use, ensuring that secrets don’t linger longer than necessary. If you need additional control, cloud-init allows you to explicitly purge data and logs, further reducing the risk of exposure.

Why WireGuard Complements Cloud-Init

While cloud-init handles the heavy lifting of node personalization, WireGuard ensures that this process remains secure. Its simplicity and performance make it ideal for HPC clusters, where hundreds or thousands of nodes may need to bootstrap simultaneously.

The WireGuard tunnel is ephemeral by design. Once the node retrieves its configuration data and cloud-init completes its tasks, the tunnel is torn down. This reduces the attack surface and ensures that no lingering connections exist to compromise the system.

Why This Workflow is Ideal for HPC

The workflow we’ve built leverages the strengths of both cloud-init and WireGuard to solve the unique challenges of HPC environments. With no persistent storage on the nodes, every reboot requires a fresh start. Cloud-init provides the automation needed to personalize each node efficiently, while WireGuard guarantees the secure delivery of configuration data.

By relying on a shared, read-only system image, we eliminate inconsistencies between nodes. Every system runs the exact same base environment, minimizing troubleshooting and maintenance. This uniformity also ensures that updates can be applied quickly across the entire cluster.

A Path Forward: Enhancing Security and Scalability

While this workflow is robust, there’s always room for improvement. One area we’re exploring is improving the node identity process. Today, we trust that if a request is coming in on the right network and from the right IP address, it is coming from a known HPC node. Relying on the network isn’t enough for us. We want cryptographic certainty which node is initiating the tunnel. Modern servers allow us to do this using special hardware called the Trusted Platform Module (TPM) which can generate keys and handle signatures without allowing the private key to be accessible to the Operating System. Using a TPM, nodes can prove their authenticity to the server before even initiating a WireGuard tunnel. This would further enhance trust and security across the cluster.

Final Thoughts

Bootstrapping HPC nodes is a unique challenge, but with the right tools and workflow, it becomes a seamless process. By combining the simplicity of WireGuard with the flexibility of cloud-init, we’ve built a system that is secure, efficient, and perfectly suited for the stateless nature of HPC clusters. As we look to the future, adding hardware-backed security and advanced secrets management will take this workflow to the next level.

If you’re managing an HPC cluster or exploring ways to simplify node provisioning, we’d love to hear how you’re tackling these challenges. Share your insights in the comments below, or reach out to join the conversation!