If the tables really are InnoDB that's a problem. Winston doesn't
perform well with engines other than MyISAM.
Back up your database before you try this, but maybe this will help your
performance:
select concat('alter table ',table_schema,'.',table_name,'
engine=MyISAM;')
from information_schema.tables
where engine = 'InnoDB';
should get you a list of commands you can run to convert Winston to
MyISAM. (Obviously only run this on the Winston tables, this query will
show all tables that are InnoDB.)
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