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#9 Memory leak when creating Chemistry::MacroMol files

open
nobody
None
5
2008-12-23
2008-12-23
Anonymous
No

Looping through every pdb file in a directory and reading
them into the same Chemistry::MacroMol variable caused a
linear increase in RAM usage, which shouldn't happen since I
was reusing the variable.

The following snippet should reproduce this behaviour, given
that the working directory has several pdb files:

use Chemistry::File::PDB;
use Chemistry::MacroMol;

# The directory should have several pdb files
my @files = <*.pdb>;

for my $file (@files) {
my $structure = Chemistry::MacroMol->read( $files[0] );
}

This also happens if one tries to undef $structure
explicitly. To confirm the leak and have more information on
the actual modules causing it, I used Devel::Leak::Object
with a one atom pdb file:

This is the content of the file 'atom.pdb'
ATOM 1 N VAL L 1 9.069 116.493 216.070 12 1 1.63 -0.15

This is the code to detect the circular references:

use Devel::Leak::Object qw( GLOBAL_bless );
use Chemistry::File::PDB;
use Chemistry::MacroMol;

my $structure = Chemistry::MacroMol->read( 'atom.pdb' );

And this is are the detected objects that were not
garbage-collected:

Chemistry::Atom 1
Chemistry::Domain 1
Config 1
FileHandle 3
Math::VectorReal 1

Even more information comes from applying diagnostics with
the module Devel::Cycle, which shows explicitely what the
circular references are. I applied the following code:

use Devel::Cycle;
use Chemistry::File::PDB;
use Chemistry::MacroMol;

my $structure = Chemistry::MacroMol->read( 'atom.pdb' );
find_cycle($structure);

which produced a 63-line output with 8 cycles (attached).
Repeating the analysis replacing 'find_cycle' with
'find_weakened_cycle' produced a 127-line output with 18
cycles (attached). I am aware that this weakened cycles are
not unintentional, and are not producing the leakage, but
the first ones might be the cause of the observed memory
increase.

Discussion

  • Circular references detected by Devel::Cycle when parsing the file atom.pdb

     
    Attachments
  • Sorry, the 7th. line of first code snippet should be:

    my $structure = Chemistry::MacroMol->read( $file );