[InterMine Dev] SNP script - timing out

Vallejos, Andrew avallejos at mcw.edu
Fri Aug 28 18:26:15 BST 2009


I commented out that line, no change.

I commented out the line I added:
location_item->set('subject', $snp_item);

After that the Perl script holds at ~293MB of RAM.

-----Original Message-----
From: dev-bounces at mail.intermine.org
[mailto:dev-bounces at mail.intermine.org] On Behalf Of Julie Sullivan
Sent: Friday, August 28, 2009 11:01 AM
To: dev at intermine.org
Subject: [InterMine Dev] SNP script - timing out

Andrew,

Can you test something for me?

In intermine/perl/lib/InterMine/Item.pm, comment out line 196:

	$other_item->set($field->reverse_reference_name(), $self);

This is the line setting the reverse reference for the item we're
saving.  We 
don't need it as we have the original reference, we were keeping it to
make the 
XML more human readable, I think.  The converter discards this reference
anyway.

The idea is that the objects are being kept in memory (even though they
are out 
of scope) because an object you do have in scope has references to these

objects.  So Perl never lets them go.  Removing this reference hopefully
will 
prevent that.

That's the idea anyway.

Let me know how that works out.

Cheers,
Julie

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