[Biopython-dev] [Bug 2666] New: Bio.PDB.NeighborSearch self test often fails with MemoryError

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2666

           Summary: Bio.PDB.NeighborSearch self test often fails with
                    MemoryError
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


>From the Biopython source code (from CVS), in the Bio/PDB folder, running
NeighborSearch.py does a quick self test.

This is a random test, and sometimes this is fine:

$ python NeighborSearch.py 
Found  1
Found  4
Found  3
Found  2
Found  2
Found  2
Found  3
Found  3
Found  1
Found  5
Found  2
Found  3
Found  2
Found  2
Found  2
Found  6
Found  3
Found  2
Found  3
Found  1

However, about 50% of the time I get something like this:

$ python NeighborSearch.py 
Found  2
Found  1
Found  2
Found  1
Found  1
Found  1
Found  4
Found 
Traceback (most recent call last):
  File "NeighborSearch.py", line 139, in <module>
    print "Found ", len(ns.search_all(5.0))
  File "NeighborSearch.py", line 104, in search_all
    self.kdt.all_search(radius)
  File
"/Users/pjcock/repositories/biopython/build/lib.macosx-10.3-i386-2.5/Bio/KDTree/KDTree.py",
line 198, in all_search
    self.neighbors = self.kdt.neighbor_search(radius)
MemoryError: calculation failed due to lack of memory

I've tried this on a MAC which had over 4GB or RAM free at the time, so I don't
believe this really is a MemoryError.

I've also tried this on a less powerful Windows machine, which fails in the
same way (it can finish the test, but possibly with a lower success rate).

[As an aside, I'm planning to use this self test to create an actual Biopython
unit test for the Bio.PDB.NeighborSearch module.]


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