10APR2021

THE FUNDAMENTALS OF BUILDING AN HPC CLUSTER

Jeff Layton

The King in Alice in Wonderland said it best, “Begin at the beginning ….” The general goal of HPC is either to run applications faster or to run problems that can’t or won’t run on a single server. To do this, you need to run parallel applications across separate nodes. Although you could use a single node and then create two VMs, it’s important to understand how applications run across physically different servers and how you administer a system of disparate physical hardware.

https://sites.google.com/view/how-to-build-a-pc-now

https://sites.google.com/view/how-to-build-a-pc-now

With this goal in mind, you can make some reasonable assumptions about the HPC system. If you are interested in parallel computing using multiple nodes, you need at least two separate systems (nodes), each with its own operating system (OS). To keep things running smoothly, the OS on both nodes should be identical. (Strictly speaking, it doesn’t have to be this way, but otherwise, it is very difficult to run and maintain.) If you install a package on node 1, then it needs to be installed on node 2 as well. This lessens a source of possible problems when you have to debug the system.

The second thing your cluster needs is a network to connect the nodes so they can communicate to share data, the state of the solution to the problem, and possibly even the instructions that need to be executed. The network can theoretically be anything that allows communication between nodes, but the easiest solution is Ethernet. In this article, I am initially going to consider a single network, but later I will consider more than one.

Storage in each node can be as simple as an SD card to hold the OS, the applications, and the data. In addition to some basic storage, and to make things a bit easier, I’ll create a shared filesystem from the master node to the other nodes in the cluster.

The most fundamental HPC architecture and software is pretty unassuming. Most distributions have the basic tools for making a cluster work and for administering the tools; however, you will most likely have to add the tools and libraries for the parallel applications (e.g., a message-passing interface [MPI] library or libraries, compilers, and any additional libraries needed by the application). Perhaps surprisingly, the other basic tools are almost always installed by default on an OS; however, before discussing the software, you need to understand the architecture of a cluster.

Architecture

The architecture of a cluster is pretty straightforward. You have some servers (nodes) that serve various roles in a cluster and that are connected by some sort of network. That’s all. It’s that simple. Typically the nodes are as similar as possible, but they don’t have to be; however, I highly recommend that they be as similar as possible because it will make your life much easier. Figure 1 is a simple illustration of the basic architecture.