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Let's see the slowest query in the system. Quite likely, fixing it (adding an index, reformulating the SELECT, etc) is the best solution. You mentioned SHOW FULL PROCESSLIST -- That is likely to show the naughty queries; let's see them, plus the associated SHOW CREATE TABLEs. query_cache_size = 128M -- too big; no more than 50M. A big value slows ...


The problem was caused by an inactive legacy website hosted on this server. It was a target of heavy spamming. I solved this issue by putting some tables in read-only mode.

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