I have a hefty db server with lots of very similar InnoDB databases. A query that I run often simply updates a timestamp on one row in a small table. This takes like 1-2 ms most of the time. Occasionally, at night, probably while backups and maatkit replication tools are running, one or more of these queries may show “Updating” for several minutes. During this time, other queries, including maatkit queries, seem to be proceeding normally, and no other queries seem to be executing. I have been unable to explain or fix this.
We are using mysql 4.1.22 and gentoo 2.6.21 on a pair of 4-way Xeon with 16gig of RAM and RAIDed drives for storage. Replication is in place and operating well with maatkit confirming replication nightly. InnoDB is using most of the RAM and the cpu’s are typically 70-80% idle. The table in question has about 100 rows of about 200 bytes each. I’ve tried with and without an index on the WHERE clause with no discernible change. No unusual log messages have been found (checked system messages and mysql errors).
Has anybody else heard of this? Solved something like this? Any ideas of how to investigate?
Using some of the information offered in the responses, we continued investigating and found some disturbing behavior on our server. A simple “check table” on any table in any database caused simple update queries to lock in other databases and other tables. I don’t have any idea why this would happen, though we could not reproduce it on MySQL v5.1, so we intend to upgrade our database server.
I don’t think maatkit’s mk-table-checksum does a “check table” but it is having a similar effect. Turning off this script reduced the problems significantly, but we believe that we cannot live without this script.
I’m going to mark this as the answer to my question. Thanks for the help.