Windows comes with a lot of extra baggage that is only useful sometimes on desktop machines (extra drivers, services, etc.) but are a total waste on supercomputers, where you usually strip down the OS to the bare minimum you need to run the specialized software required for the computations.
Among those baggages there’s graphics. Windows is *heavily* designed around graphical user interfaces, and even when building custom images using specialized tools, you can remove some of that graphics dependency from the OS, but a ton of code needs to stay because it’s part of the kernel (the core of the OS).
Another aspect that others have mentioned is the performance. On the same hardware, a fine tuned Linux doesn’t just kick ass to Windows, it’s simply on another level, like comparing fast cars with a supersonic plane, and I’m not exaggerating (too much, at least).
On Linux there are several dozens of options just for the file system, which can be picked and choosed to tailor them to the specific workload (e.g.: many small files vs fewer but very large ones, network distributed filesystems, etc.). On the other hand, the default Windows filesystem, NTFS, can be easily brought to its knees by a single user on a desktop, and on Linux tools to defrag the disk are considered in rare and esoteric cases.
Microsoft put some effort on allowing more optimization, but for the few supercomputers that run Widows, it took a dedicated team of Microsoft specialists to help them with the process, literally hacking the OS. The same could be done on Linux simply by an experienced sys admin. Also beyond a certain point, Windows simply doesn’t scale that well. Windows 11 Pro supports up to 4 CPUs with up to 256 cores in total. A minimally customized Linux can support up to 8192 cores.
This means that when using Windows you’re bound to be inefficient, and even if it’s less than 30% less efficient than it could be on Linux (very optimistic), who would take that cut?
Interestingly, Microsoft knows this very well since it runs almost exclusively Linux on Azure, their cloud computing (speaking about eating their own dog food).
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