[Biopython-dev] Bio.PDB.KDTree test for memory leak
Peter
biopython at maubp.freeserve.co.uk
Fri Feb 12 06:10:13 UTC 2010
On Thu, Feb 11, 2010 at 12:31 PM, Kristian Rother <krother at rubor.de> wrote:
>
> Hi,
>
> I've encountered a problem with running KDTree: it leaks memory.
> The code below fills 1GB memory within a minute.
>
> Running the GC doesn't help (it slows the process down, but only because
> the GC is much slower than KDTree.
You mean something like this?
import gc
from Bio.KDTree.KDTree import *
from numpy.random import random
nr_points=1000
dim=3
bucket_size=10
coords=(200*random((nr_points, dim)))
while True:
kdtree=KDTree(dim, bucket_size)
kdtree.set_coords(coords)
del kdtree #explicitly tell Python it can GC this object
gc.collect() #force Python to run GC
I agree, this does seem to gradually consume more and more RAM.
Could you open a bug on bugzilla to track this please?
> I think the problem might be in the C code. I'd like to get this bug
> sorted out, but I'm not very good in C. Is there anyone around who
> I could check ideas with?
Have you ever used valgrind on a C tool? I'm not sure if it is easy
to use via Python, but it is my tool of choice for checking memory
leaks in C.
Peter
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