glibc invalid pointer error

Fernando Perez at
Mon Oct 30 13:18:52 CST 2006

On 10/30/06, David Huard <david.huard at> wrote:
> Hi,
> I have a script that crashes, but only if it runs over 9~10 hours, with the
> following backtrace from gdb. The script uses PyMC, and repeatedly calls (>
> 1000000) likelihood functions written in fortran and wrapped with f2py.
> Numpy: 1.0.dev3327
> Python: 2.4.3

This sounds awfully reminiscent of the bug I recently mentioned:

We left a fresh run over the weekend, but my office mate is currently
out of the office and his terminal is locked, so I don't know what the
result is.  I'll report shortly: we followed Travis' instructions and
ran with a fresh SVN build which includes the extra warnings he added
to the dealloc routines.  You may want to try the same advice, perhaps
with information from both of us the gurus may zero in on the problem,
if indeed it is the same.

Note that I'm not positive it's the same problem, and our backtraces
aren't quite the same.  But the rest of the scenario is similar:
low-level memory crash from glibc, very long run is needed to fire the
bug, potentially millions of calls to both numpy and to f2py-wrapped
in-house libraries.



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