Unexplained "out of memory"

Dear list,

I am using DBD::Mysql to insert data into a InnoDB database, and I
stumbled on a problem recently.
My script is launching a high number of update queries on a huge table
(~ 110 Million lines). The queries are simple, for example :

$upd=$dbh->prepare("UPDATE affymetrixProbeset SET expressionId=? WHERE
geneId=? and affymetrixChipId=?;");
$upd->execute(..., ..., ...);
$upd->finish;

At one point of the script the following error occurs :

DBD::mysql::st execute failed: Out of memory (Needed 1106080 bytes) at
my_script.pl line 152.

It really seems to be due to the accumulation of queries, because the
beginning of the script works fine, and there is no problem when
restarting the script where it stopped.
Is it due to some buffer size or something?
I am not using a transaction to do the modifications since I didn't set
autocommit=0.

Any idea that could help?
Thanks a lot in advance
Julien

--
Julien Roux, PhD student
http://bioinfo.unil.ch/
Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4221 fax: +41 21 692 4165



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