I'm not an expert, but I've never heard of a db getting slower after an
index rebuild. It's possible that's just a red herring.
You've been speaking generally about things being slower, I'd suggest you
get specific. Track down the queries are slow now, use EXPLAIN on them to
see what indexes that are using (or not). There a way to log slow queries
in MySQL, that might help.
Perhaps usage has just shifted and there are now a lot of writers and
readers to the same table - run "mysqladmin pr" and look to see if some
servers are waiting due to table locks. "mysqladmin -i3 pr" is good to do
continuous monitoring.
-bill
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