[Bioperl-l] Memory leak in Bio::Root::Root?
Stefan Kirov
skirov at utk.edu
Thu Dec 15 15:46:49 EST 2005
You should check find_cycle($self) and the same for seqobj. Also
shouldn't it be
my $tempseq = $seqobj->seq();
as opposed to
$tempseq = $seqobj->seq();
I don't see anything wrong with the regexp (your next post).
Stefan
Mike Muratet wrote:
>
>
> On Wed, 14 Dec 2005, Stefan Kirov wrote:
>
>> My two cents: have you looked for cyclic referencing. Then your
>> objects will not get destroyed properly. You can try Devel::Cycle to
>> track those. If you post some more code we may have better idea what
>> is going on.
>> Stefan
>>
>
> I included Devel::Cycle and tried find_cycle($polyn) and
> find_cycle($nmer_statistics) but got no output. Can I assume that no
> references were found?
>
> Here is the code for the max_polyn method:
>
> sub max_polyn {
>
> my $seqobj;
> my $_is_strict;
> my $_is_instance = 1 ;
> my $self = shift @_;
> my $object_argument = shift @_;
> my ($maxpolyn, $tempmaxpolyn, $polya,$polyc,$polyg,$polyt,
> $tempseq , $lpolya, $lpolyc, $lpolyg, $lpolyt);
>
>
> if (defined $object_argument) {
> $_is_instance = 0;
> }
>
> # If we are using an instance object...
> if ($_is_instance) {
> if ($maxpolyn = $self->{'_max_polyn'}) {
> return $maxpolyn; # return count if previously
> calculated
> }
> $_is_strict = $self->{'_is_strict'}; # retrieve "strictness"
> $seqobj = $self->{'_seqref'};
> } else {
> # otherwise...
> $seqobj = $object_argument;
>
> # Following two lines lead to error in "throw" routine
> $seqobj->isa("Bio::PrimarySeqI") ||
> $self->throw(" SeqStats works only on PrimarySeqI objects
> \n");
> # is alphabet OK? Is it strict?
> #$_is_strict = _is_alphabet_strict($seqobj);
> }
>
> $tempseq = $seqobj->seq();
> #$gccontent = 100 * ($gc_cnt =~
> tr/gcGC/gcGC/)/length($seqobj->seq());
>
> $maxpolyn = 0;
> my $lcount = 0;
> my $polyn;
> while ($lcount < length($seqobj->seq())) {
>
> ($polyn = $tempseq) =~ s/^\w{$lcount}(\w)\w*$/$1/;
>
> if ($polyn=~/a/i) {
> $lpolya++;
> $lpolyc = $lpolyg = $lpolyt = 0
> }elsif ($polyn =~/c/i) {
> $lpolyc++;
> $lpolya = $lpolyg = $lpolyt = 0;
> }elsif ($polyn =~/g/i) {
> $lpolyg++;
> $lpolya = $lpolyc = $lpolyt = 0;
> }elsif ($polyn =~/t/i) {
> $lpolyt++;;
> $lpolya = $lpolyc = $lpolyg = 0;
> }
> ($tempmaxpolyn ) = sort {$b <=> $a} $lpolya, $lpolyc, $lpolyg,
> $lpolyt;
> $maxpolyn = $tempmaxpolyn if ($tempmaxpolyn > $maxpolyn);
> $lcount++;
> }
>
> my ($rmaxpolyn) = \$maxpolyn;
> if ($_is_instance) {
> $self->{'_max_polyn'} = $rmaxpolyn; # Save in case called
> again later
> }
>
> return $rmaxpolyn;
> }
>
> Do you see anything that would create a memory leak?
>
> Thanks for the help
>
> Mike
>
>> 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
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> -- Stefan Kirov, Ph.D.
>> University of Tennessee/Oak Ridge National Laboratory
>> 5700 bldg, PO BOX 2008 MS6164
>> Oak Ridge TN 37831-6164
>> USA
>> tel +865 576 5120
>> fax +865-576-5332
>> e-mail: skirov at utk.edu
>> sao at ornl.gov
>>
>> "And the wars go on with brainwashed pride
>> For the love of God and our human rights
>> And all these things are swept aside"
>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
--
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov
"And the wars go on with brainwashed pride
For the love of God and our human rights
And all these things are swept aside"
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