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Oh my god, the DBMS uses a lot of memory while running!
Show the settings, most likely this is completely normal behavior.
well, there is a lot of data in the database and you work with it very well, this is normal
Install mysqltuner and see its output. And yes, if there is a lot of data and little RAM, you can only make things worse.
Enable slowlog, analyze it with percona tools, you may need to add a couple of other indexes. Lots of options.
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