[Bioperl-l] Memory leak in Bio::Root::Root?

Stefan Kirov skirov at utk.edu
Wed Dec 14 12:37:42 EST 2005

My two cents: have you looked for cyclic referencing. Then your objects 
will not get destroyed properly. You can try Devel::Cycle to track 
those. If you post some more code we may have better idea what is going on.

Mike Muratet wrote:

> Jason
>> polyn returns a scalar object (blessed) or just some scalar data?
>> If you are really calling QStat->polyn( $obj) then 'new' is never 
>> called in the first place for the Qstat package.
> polyn returns a reference to some scalar data. My understanding is 
> that 'new' would not be called, but then I'm at a loss to explain 
> where all the extra memory goes.
>> Destructors are automatic, but you can create your own to see when/if 
>> the destructor is called.
>> sub DESTROY {
>> my $self =shift;
>> warn("I am calling destroy in the Qstat object\n");
>> $self->SUPER::DESTROY;
>> }
> I will try this.
>> You can also inherit from Bio::Root::RootI and call bless on your own 
>> if you want to play with whether this is Bio::Root::Root induced 
>> behavior.  I'm not sure I understand enough of how it works to tell 
>> you where else to look.
> I will try this, too.
>> Is a new $seq_obj getting created every iteration of the loop?  Are 
>> these getting cleaned up or is Qstat keeping references  to them, and 
>> they are sticking around?  Devel::Cycle doesn't show any memory cycles?
> A new $seq_obj gets created in every loop of the method that calls 
> QStats with the $seq_obj as an argument, but I undef it at the bottom 
> of the loop. Should this not be enough to get perl to recycle the 
> memory? I haven't tried Devel::Cycle but I will include it to see what 
> it says.
> I saw on some of the perl lists a reference to a memory leak in perl 
> 5.8 with the s/// operator. Have you heard about such a problem?
> Thanks for the help
> Mike
>> On Dec 13, 2005, at 11:32 AM, Mike Muratet wrote:
>>> Greetings all
>>> I have a problem that surpasses what I know and what I've been able 
>>> to glean from perltoot,perboot,etc. Maybe it's a question for a perl 
>>> list, but here goes...
>>> I was given a package that calculates some statistics regarding base 
>>> repeats in a sequence. It inherits from Bio::Root::Root presumbably 
>>> to obtain the exception behavior bestowed by the class judging from 
>>> the perldocs and to enforce that the argument is a PrimarySeq 
>>> object. It has
>>> two methods which get called thus:
>>> my $polyn = QStat->polyn($seq_obj);
>>> my $nstat = QStat->nmer_stat($seq_obj);
>>> where the returned values are scalar references. The problem is that 
>>> script quickly uses up all of the 4GB address space (processing lots 
>>> of oligos) and crashes.
>>> I have used Devel::Size to determine the size of these variables and 
>>> get 3.8K and 7K. I have tried to undef them at the end of the loop 
>>> but it has no effect. I commented out the calls and the problem goes 
>>> away so the problem is associated with the QStat object.
>>> The QStat class has a constructor that calls the base constructor:
>>>     my $self = $class->SUPER::new(@args);
>>> would this demand a destructor somewhere?
>>> Does calling a method out of a class like this invoke all the class 
>>> machinery without creating the object with new?
>>> Can someone with experience deriving from Bio::Root::Root offer some 
>>> suggestions on how to get the memory back?
>>> Thanks
>>> Mike
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> -- 
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
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Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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