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Format a 512e drive to 4096 on Linux
(piefed.blahaj.zone)
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I'm pretty sure OP is confused themselves, but I read this as referring to the physical sector size.
Fair enough, I probably explained it poorly. The problem is that pages don't mean anything to the filesystem, but the way the filesystem is layed out means a lot to the pages. With 512e, the SSD has to buffer each write until it can make up the whole 4K page. It'll also buffer a read until the whole 4K page is read. So if those buffers never become full/read, such as when the filesystem isn't aligned to it's pages, or the read/writes aren't in the right sequence, then it destroys your performance.
This also happens with HDDs, but they're slow enough to be able to rearrange operations, though an unaligned filesystem will still cause unnecessary reads before writes.