There is a really nice article by Pep Pla, over at the Percona blog
about fragmentation in MySQL InnoDB tablespaces, which you should read.
The article discusses “fragmentation” of data in tables, which happens in a way similar to how it happens in filesystems.
InnoDB stores data by default in tablespaces, which by default are a file per table. These files are subject to the fragmentation and growth rules of your filesystem, but if you are smart, you are running MySQL on Linux on the XFS. In that case, filesystem fragmentation (and unexplained commit latency variance) are not an issue, because XFS takes care of handling this properly, and only database-internal fragmentation remains.
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