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Perl - MySQL/MariaDB - slow with no identifiable bottleneck

I am running a Perl script (using DBI) which reads from raw files from a hard disk, and updates MySQL database (which is on a separate SSD). My performance is rather slow (1000 files processed in ...
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DBD::mysql complains “Character set 'latin1' is not a compiled character set”

I think this boils down to "Am I doomed to upgrading mysql hoping the problem goes away?". I've seen a few of the same issues around the internet but with no guidance on a fix other than "Did you turn ...