pyode-user

[Pyode-user] Global geom dictionary cause memory leak.

[Martin V. <vo...@na...>]

Hello

There seem to be a memory leak in PyODE due to
undeleted geom objects. I found the problem while working on a
simulator that need to create and delete many geom objects.
I used the Heapy memory profiler (part of Guppy-PE) to determine
the cause of the leak.
I'm running python-2.4.2 and PyODE 1.2.0.

The following program fills memory quickly:

import ode
while True:
    s = ode.Space()

The cause is due to a internal global lookup dictionary for
geom objects called _geom_c2py_lut.
When a geometry object is created it is added to the
global dictionary. This will prohibit the reference count
to reach zero and the object will not be removed.

I'm still quite new to Python and Pyrex and can unfortunately
not contribute much to any solution.
Currently I simply set ode._geom_c2py_lut = {} when deleting
an instance of my simulator. The same could be achieved by
placing a _geom_c2py_lut.clear() in CloseODE().
Neither is a solution.
One would like the geom objects to remove themselves from
the dictionary when deleted.

Why is the dictionary not removed when I do a reload(ode)?

/Martin

Re: [Pyode-user] Global geom dictionary cause memory leak.

[Chris B. <chr...@gm...>]

On 28/05/07, Martin Vopatek <vo...@na...> wrote:
> Hello
>
> There seem to be a memory leak in PyODE due to
> undeleted geom objects. I found the problem while working on a
> simulator that need to create and delete many geom objects.
> I used the Heapy memory profiler (part of Guppy-PE) to determine
> the cause of the leak.
> I'm running python-2.4.2 and PyODE 1.2.0.

Attached a reply from a thread in 2005 (since I can't find it archived
anywhere).

Matthias Baas <ba...@ir...> to pyode-user 04/08/05

Chris Bainbridge wrote:
> Hi, the following code appears to leak Body and dict objects. Memprof
> [...]
> I've looked at the pyode code. It appears that nothing is ever removed
> from the global dictionary _geom_c2py_lut. Should this be done in geom
> __dealloc__ ?

The _geom_c2py_lut is a dictionary that serves as a lookup table to
convert the geom pointer received from ODE into the appropriate Python
geom object (which has to be done during collisions).
So when a geom is created it adds itself to the dictionary and indeed,
it is never removed from there.
The geom cannot remove itself in __dealloc__() because as long as
there's a reference in the dictionary it is not destroyed and
__dealloc__() is never called. The solution would be weak references but
at the time I wrote the stuff Pyrex didn't support this. I contacted the
author, but I believe the current version of Pyrex still doesn't support
it (I haven't checked explicitly but at least I never noticed anything
in the changelogs).

Re: [Pyode-user] Global geom dictionary cause memory leak.

[Ethan Glasser-C. <gl...@cs...>]

Chris Bainbridge wrote:
> The _geom_c2py_lut is a dictionary that serves as a lookup table to
> convert the geom pointer received from ODE into the appropriate Python
> geom object (which has to be done during collisions).
> So when a geom is created it adds itself to the dictionary and indeed,
> it is never removed from there.
> The geom cannot remove itself in __dealloc__() because as long as
> there's a reference in the dictionary it is not destroyed and
> __dealloc__() is never called. The solution would be weak references but
> at the time I wrote the stuff Pyrex didn't support this. I contacted the
> author, but I believe the current version of Pyrex still doesn't support
> it (I haven't checked explicitly but at least I never noticed anything
> in the changelogs).

Pyrex seems to have weakref support:

http://www.sagemath.org:9002/sage_trac/ticket/165

Here's a simple patch that seems to run Martin Vopatek's test case
without running out of memory. I have no idea if it does anything
else, though! Please test carefully.

Ethan