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    <p>I have noticed the same phenomenon on my systems. Queries which normally take a millisecond will suddenly take 1-2 seconds. All of my cases are simple, single table INSERT/UPDATE/REPLACE statements --- not on any SELECTs. No load, locking, or thread build up is evident. </p> <p>I had suspected that it's due to clearing out dirty pages, flushing changes to disk, or some hidden mutex, but I have yet to narrow it down.</p> <p><strong>Also Ruled Out</strong></p> <ul> <li>Server load -- no correlation with high load</li> <li>Engine -- happens with InnoDB/MyISAM/Memory</li> <li>MySQL Query Cache -- happens whether it's on or off</li> <li>Log rotations -- no correlation in events</li> </ul> <p>The only other observation I have at this point is derived from the fact I'm running the same db on multiple machines. I have a heavy read application so I'm using an environment with replication -- most of the load is on the slaves. I've noticed that even though there is minimal load on the master, the phenomenon occurs more there. Even though I see no locking issues, maybe it's Innodb/Mysql having trouble with (thread) concurrency? Recall that the updates on the slave will be single threaded.</p> <p>MySQL Verion 5.1.48</p> <p><strong>Update</strong></p> <p>I think I have a lead for the problem on my case. On some of my servers, I noticed this phenomenon on more than the others. Seeing what was different between the different servers, and tweaking things around, I was lead to the <a href="http://dev.mysql.com/doc/refman/5.1/en/innodb-parameters.html#sysvar_innodb_flush_log_at_trx_commit" rel="noreferrer">MySQL innodb system variable</a> <code>innodb_flush_log_at_trx_commit</code>.</p> <p>I found the doc a bit awkward to read, but <code>innodb_flush_log_at_trx_commit</code> can take the values of 1,2,0:</p> <ul> <li>For 1, the log buffer is flushed to the log file for every commit, and the log file is flushed to disk for every commit.</li> <li>For 2, the log buffer is flushed to the log file for every commit, and the log file is flushed to disk approximately every 1-2 seconds.</li> <li>For 0, the log buffer is flushed to the log file every second, and the log file is flushed to disk every second.</li> </ul> <p>Effectively, in the order (1,2,0), as reported and documented, you're supposed to get with increasing performance in trade for increased risk.</p> <p>Having said that, I found that the servers with <code>innodb_flush_log_at_trx_commit=0</code> were performing worse (i.e. having 10-100 times more "long updates") than the servers with <code>innodb_flush_log_at_trx_commit=2</code>. Moreover, things immediately improved on the bad instances when I switched it to 2 (note you can change it on the fly).</p> <p>So, my question is, what is yours set to? Note that I'm not blaming this parameter, but rather highlighting that it's context is related to this issue.</p>
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    1. POWhy does an insert query occasionally take so long to complete?
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    1. COI recently upgraded to 5.1.48. I think it was the query cache. I turned it off and things started performming much better.
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      1. USDaniel
    2. COI did have a similar problem about a year ago when my query_cache was too large, so when a big chunk of data was invalidated, the whole server would lock up for up to 30 seconds. On that note, see: http://dom.as/2009/07/08/query-cache-tuning/
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    3. COinnodb_flush_log_at_trx_commit=2 is also worked for me.
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