5.5 running tiny queries much slower than 5.0

[Andrew Leonard]

I'm really confused. We have a process - admittedly inefficient, and I'm fixing it - that runs about a quarter million tiny update queries. These finished on our MySQL 5.0 master in half an hour; the newly-upgraded 5.5 slave has been working on them for six hours. The key seems to be "query end" - each one spends over a tenth of a second in this state on the slave, which is really dragging things down as 10 queries a second means, well... six hours. The master spends less well under a tenth of a second in the entire query, and this one is spending .13 seconds (89% of the query) in "query end". Sometimes it's as high as half a second.

Did 5.5 change something that my 5.0 configuration is interfering with? I haven't optimized it for 5.5 yet, just using MyISAM for now until we get everything set up so it's not an InnoDB problem. Is there some 5.0 setting that could be causing this, or a new 5.5 setting I'm missing? I'm at my wits end, as this is really starting to slow down some reports we have that are inefficient like this. I will change the reports, but I also want to find out what went wrong.