You would include a slow query , for example. add this to your my.cnf in the [mysqld] section
set-variable=slow_query_log=on set-variable=long_query_time=20
This will log all requests taking 20 seconds or more, with the name "hostname" -slow.log, for example. / var / lib / mysql / localhost -slow.log
Then you check these queries and at least run EXPLAIN and find out what slows down, for example. add indexes, rewrite SQL, etc., although optimizing queries are a whole different book.
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