Acquire and deploy hardware

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Here is our recommendation of how to build a computer cluster that will work well for molecular docking and cheminformatics. This document can be used whether you already own hardware, or whether you are planning to buy new. This is part of a series of articles called So you want to set up a lab.

Buying CPU and disk

We describe several sizes of cluster in Cluster Theory.

Setting up a network

Managed 24 port GigE switch with VPN support. About $250. This is not a full layer 3 switch, but it should do for most circumstances. Allows you to run both private and public networks. We do know why people spend $2500 for a full layer 3 switch (compatibility with and isolation from a complex networking environment). You should not have to buy the fancy $2500 switch. Suggest starting with the $250 switch, and then upgrade if you must (and now you've got a backup switch!)

Network topology will depend on your circumstances. We recommend running a private network, and keeping any machines that don't have to be on the public network off it for security. We recommend using a portal computer and ssh keys for remote access.

Minimum requirements for legacy equipment

At the very least, you really need 24 cores at 1GB/core and 10TB of RAID10 formatted disk space to get started. There have been substantial improvements in disk price/performance and CPU-core/dollar performance in the past 24 months that we really recommend getting new equipment if you can. If you do not have a 24 core / 48 GB / 4 TB disk system to run the hypervisor and core services, then you will need to reserve 3 older 2, 4 or 8 core machines to run central services. You can use two cheap switches to run private and public networks separately.

If you have more money

Our recommended CPU machine costs $20K (128 cores). Our recommended disk machine costs $20K (96 TB raw). We recommend just buying these two machines in a proportion that makes sense for your research. A single switch will handle an entire rack. If you have a lot more money, ask us. Don't forget about cooling, UPS and power.

Physical setup

You can fit everything described here in one rack. You only need a rack when you buy the third computer. Put the switch in the middle for neater cabling.


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