Comments - Cluster node sizes are different
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Could you describe how are you measuring the content size? What is the storage engine for the tables?
I use innodb engine for tables, and using (du -sm *) in /var/lib/mysql to get all database sizes.
Can you provide the ls -lsR --block-size=1 /var/lib/mysql/* output from all 3 nodes, it is interesting where the difference is, there can be difference e.g. in error log size.