Strange and hard to reproduce crash

David Goldsmith David.L.Goldsmith at noaa.gov
Mon Oct 23 18:46:31 CDT 2006


Hey, any chance it has something to do with running an up-to-date numpy 
with an "out-of-date" Python (2.3.4 is pretty old, isn't it?)

DG

Fernando Perez wrote:
> Hi all,
>
> two colleagues have been seeing occasional crashes from very
> long-running code which uses numpy.  We've now gotten a backtrace from
> one such crash, unfortunately it uses a build from a few days ago:
>
> In [3]: numpy.__version__
> Out[3]: '1.0b5.dev3097'
>
> In [4]: scipy.__version__
> Out[4]: '0.5.0.2180'
>
> Because it takes so long to get the code to crash (several days of
> 100%CPU usage), I can't make a new one right now, but I'll be happy to
> restart the same run with a current SVN build if necessary, and post
> the results in a few days.
>
> In the meantime, here's a gdb backtrace we were able to get by setting
> MALLOC_CHECK_ to 2 and running the python process from within gdb:
>
> Program received signal SIGABRT, Aborted.
> [Switching to Thread 1073880896 (LWP 26280)]
> 0x40000402 in __kernel_vsyscall ()
> (gdb) bt
> #0  0x40000402 in __kernel_vsyscall ()
> #1  0x0042c7d5 in raise () from /lib/tls/libc.so.6
> #2  0x0042e149 in abort () from /lib/tls/libc.so.6
> #3  0x0046b665 in free_check () from /lib/tls/libc.so.6
> #4  0x00466e65 in free () from /lib/tls/libc.so.6
> #5  0x005a4ab7 in PyObject_Free () from /usr/lib/libpython2.3.so.1.0
> #6  0x403f6336 in arraydescr_dealloc (self=0x40424020) at arrayobject.c:10455
> #7  0x403fab3e in PyArray_FromArray (arr=0xe081cb0, newtype=0x40424020, flags=0)
>     at arrayobject.c:7725
> #8  0x403facc3 in PyArray_FromAny (op=0xe081cb0, newtype=0x0, min_depth=0,
>     max_depth=0, flags=0, context=0x0) at arrayobject.c:8178
> #9  0x4043bc45 in PyUFunc_GenericFunction (self=0x943a660, args=0xa9dbf2c,
>     mps=0xbfc83730) at ufuncobject.c:906
> #10 0x40440a04 in ufunc_generic_call (self=0x943a660, args=0xa9dbf2c)
>     at ufuncobject.c:2742
> #11 0x0057d607 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
> #12 0x0057d6d4 in PyObject_CallFunction () from /usr/lib/libpython2.3.so.1.0
> #13 0x403eabb6 in PyArray_GenericBinaryFunction (m1=Variable "m1" is
> not available.
> ) at arrayobject.c:3296
> #14 0x0057b7e1 in PyNumber_Check () from /usr/lib/libpython2.3.so.1.0
> #15 0x0057c1e0 in PyNumber_Multiply () from /usr/lib/libpython2.3.so.1.0
> #16 0x005d16a3 in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #17 0x005d509e in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0
> #18 0x005d3d8f in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #19 0x005d509e in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0
> #20 0x00590e2e in PyFunction_SetClosure () from /usr/lib/libpython2.3.so.1.0
> #21 0x0057d607 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
> #22 0x00584d98 in PyMethod_New () from /usr/lib/libpython2.3.so.1.0
> #23 0x0057d607 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
> #24 0x005b584c in _PyObject_SlotCompare () from /usr/lib/libpython2.3.so.1.0
> #25 0x005aec2c in PyType_IsSubtype () from /usr/lib/libpython2.3.so.1.0
> #26 0x0057d607 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0
> #27 0x005d2b7f in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #28 0x005d509e in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0
> #29 0x005d3d8f in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #30 0x005d509e in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0
> #31 0x005d3d8f in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #32 0x005d497b in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #33 0x005d497b in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #34 0x005d497b in _PyEval_SliceIndex () from /usr/lib/libpython2.3.so.1.0
> #35 0x005d509e in PyEval_EvalCodeEx () from /usr/lib/libpython2.3.so.1.0
> #36 0x005d5362 in PyEval_EvalCode () from /usr/lib/libpython2.3.so.1.0
> #37 0x005ee817 in PyErr_Display () from /usr/lib/libpython2.3.so.1.0
> #38 0x005ef942 in PyRun_SimpleFileExFlags () from /usr/lib/libpython2.3.so.1.0
> #39 0x005f0994 in PyRun_AnyFileExFlags () from /usr/lib/libpython2.3.so.1.0
> #40 0x005f568e in Py_Main () from /usr/lib/libpython2.3.so.1.0
> #41 0x080485b2 in main ()
>
> # End of BT.
>
> This code is running on a Fedora Core 3 box, with python 2.3.4 and
> numpy/scipy compiled using gcc 3.4.4.
>
> I realize that it's extremely difficult to help with so little
> information, but unfortunately we have no small test that can
> reproduce the problem.  Only our large research codes, when running
> for multiple days on a single run, cause this.  Even very intensive
> uses of the same code but which last only a few hours never show this.
>
> This code is a long-runing iterative algorithm, so it's basically
> applying the same (complex) loop over and over until convergence,
> using numpy and scipy pretty extensively throughout.
>
> If super Travis (or anyone else) can have a Eureka moment from the
> above backtrace, that would be fantastic.  If there's any other
> information you think I may be able to provide, I'll be happy to do my
> best.
>
> Cheers,
>
> f
>
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