[Biopython-dev] [Bug 3010] Bio.KDTree is leaking memory

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3010





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-09-18 12:25 EST -------
Created an attachment (id=1542)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1542&action=view)
C program to show the memory leak

C example written by Bartosz Telenczuk at the "Python and Friends" workshop
http://pythonfriends.blogspot.com

The idea of this was to determine if the memory leak was via the Python
binding, or in the KDTree C code - this showed it was in the C code.

We could then run this in valgrind which reveals the nature of the
memory leak which scales directly with the number of coordinates
(and a very big clue on how to fix this - commit to follow soon).

==5438== 16,000 bytes in 1 blocks are definitely lost in loss record 1 of 1
==5438==    at 0x4025016: realloc (vg_replace_malloc.c:525)
==5438==    by 0x8048F77: KDTree_add_point (in
/home/peterjc/repositories/biopython/Bio/KDTree/test)
==5438==    by 0x80495A3: KDTree_set_data (in
/home/peterjc/repositories/biopython/Bio/KDTree/test)
==5438==    by 0x8048618: main (in
/home/peterjc/repositories/biopython/Bio/KDTree/test)
==5438== 

(this was with 2000 points, one iteration)


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