I recently did some performance testing with a few big tables on mysql/5.0.45 under CentOS and noticed a sharp drop in query speed a few minutes after restarting mysql. More tests showed mysql/5.0.51a or newer don’t have this problem. OK, I guess a picture is worth a thousand words… (SELECT queries only, and also mysql buffer size is huge, so disk I/O is minimal during test.)
It’s most likely due to mysql bug 21074 (fixed in mysql/5.0.50). Unfortunately mysql/5.0.45 is the version that ships with CentOS 5.3 and some other Redhat-derived Linux distro. Consider upgrading if you are using mysql/5.0.45 and your mysql server appears to be heavily CPU-bound.