[Bioperl-l] Memory leak in Bio::Root::Root?
Mike Muratet
muratem at eng.uah.edu
Thu Dec 15 14:47:54 EST 2005
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"
>
>
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