Re: memory leak in Bio::Species

Looks like a 'self-as-descendant' idea in the data structure. If the algorithms depend on that, I'm sure the right person could add a strategic weaken.

On Fri, Sep 12, 2014 at 2:22 PM, Dmitry Karasik <[email protected] > wrote:

Dear all,

I've hit a memory leak issue that OOMs our daemons once in a while, and what is

worse, I don't have the BioPerl expertise to fix it (I would send a patch

otherwise ). The problem is that Bio::Species and/or the modules it uses forms

cyclic references, which are never killed by perl automatically. I guess

either some internal data structure has to be reworked, or there should be some

strategic placing of Scalar::Util::weaken, but I have no idea where (or rather,

I could devise a hack that hammers weaken() instantly, but I don't think

this is the right approach).

It's very simple to reproduce, f.ex. by this:

use Devel::Cycle;

use Bio::Species;

find_cycle(Bio::Species->new(-classification => ['A']));

which outputs

Cycle (1):

$Bio::Species::A->{'taxon'} => \%Bio::Taxon::B

$Bio::Taxon::B->{'_ancestor'} => \%Bio::Taxon::C

$Bio::Taxon::C->{'_desc'} => \%D

$D->{'1'} => \%Bio::Taxon::B

Cycle (2):

$Bio::Species::A->{'tree'} => \%Bio::Tree::Tree::E

$Bio::Tree::Tree::E->{'_rootnode'} => \%Bio::Taxon::C

$Bio::Taxon::C->{'_desc'} => \%D

$D->{'1'} => \%Bio::Taxon::B

$Bio::Taxon::B->{'_ancestor'} => \%Bio::Taxon::C

whereas I would expect it would print nothing.

I should really much like to ask the devs for a closer look. It's here on

github: https://github.com/bioperl/bioperl-live/issues/81

Thank you in advance!

--

Sincerely,

Dmitry Karasik

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