Johan, I think you are right about this. The problem does not appear to be with the database at all, but with the undo log. Thanks for pointing me in the right direction.
From: Johan De Meersman [mailto:vegivamp@stripped]
Sent: Tuesday, November 01, 2011 10:01 AM
To: Rozeboom, Kay [DAS]
Subject: Re: Reusing "ibdata1" space
----- Original Message -----
> From: "Kay Rozeboom [DAS]" <KAY.ROZEBOOM@stripped>
> I realize that this would not return the unused space to the operating
> system. But would it return it to MySQL so that it could be re-used
> for subsequent inserts, instead of extending "ibdata1"
That should normally already happen. An occasional optimize table might help defragment the tablespace, but space from properly deleted records should be reused anyway (save for really small fragments).
I recommend you keep track of the innodb free tablespace for a while, and see how that evolves - it should go relatively low before the tablespace expands on disk.
Bier met grenadyn
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Hy die't drinkt, is ras een ezel