[Biopython-dev] Bio.PDB.KDTree test for memory leak

[Kristian Rother]

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.

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?

Best Regards,
   Kristian



----

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 1:
    kdtree=KDTree(dim, bucket_size)
    kdtree.set_coords(coords)