glibc invalid pointer error

David Huard david.huard at gmail.com
Mon Oct 30 08:26:39 CST 2006


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

Does this backtrace give enough info to track the problem or do the gurus
need more ?

Thanks,
David

*** glibc detected *** free(): invalid pointer: 0x00002aaaac1257e0 ***

Program received signal SIGABRT, Aborted.
[Switching to Thread 46912504440528 (LWP 25269)]
0x00002aaaab09011d in raise () from /lib/libc.so.6
(gdb) backtrace
#0  0x00002aaaab09011d in raise () from /lib/libc.so.6
#1  0x00002aaaab09184e in abort () from /lib/libc.so.6
#2  0x00002aaaab0c4e41 in __fsetlocking () from /lib/libc.so.6
#3  0x00002aaaab0ca90e in malloc_usable_size () from /lib/libc.so.6
#4  0x00002aaaab0cac56 in free () from /lib/libc.so.6
#5  0x00002aaaabff7770 in PyArray_FromArray (arr=0x1569500,
    newtype=0x2aaaac1257e0, flags=0) at arrayobject.c:7804
#6  0x00002aaaabfece56 in PyArray_FromAny (op=0x1569500, newtype=0x0,
    min_depth=0, max_depth=0, flags=0, context=0x0) at arrayobject.c:8257
#7  0x00002aaaabff40b1 in PyArray_MultiIterNew (n=2) at arrayobject.c:10253
#8  0x00002aaaabff44bc in _broadcast_cast (out=0x62b5, in=0x6,
    castfunc=0x2aaaabfbf5a0 <DOUBLE_to_FLOAT>, iswap=-1, oswap=6)
    at arrayobject.c:7445
#9  0x00002aaaabffe301 in PyArray_CastToType (mp=0x156dca0,
    at=<value optimized out>, fortran_=0) at arrayobject.c:7344
#10 0x00002aaaabffe785 in PyArray_FromScalar (scalar=0x1573b30,
    outcode=0x2aaaac1257e0) at scalartypes.inc.src:219
#11 0x00002aaaabfecff5 in PyArray_FromAny (op=0x1573b30,
    newtype=0x2aaaac1257e0, min_depth=0, max_depth=<value optimized out>,
    flags=0, context=0x0) at arrayobject.c:8260
#12 0x00002aaab6038b7b in array_from_pyobj (type_num=11,
dims=0x7fffff8f6200,
    rank=1, intent=<value optimized out>, obj=0x1573b30)
    at build/src.linux-x86_64-2.4/fortranobject.c:653
#13 0x00002aaab6034aa9 in f2py_rout_flib_beta (
    capi_self=<value optimized out>, capi_args=<value optimized out>,
    capi_keywds=<value optimized out>, f2py_func=0x2aaab603e830 <beta_>)
    at build/src.linux-x86_64-2.4/PyMC/flibmodule.c:2601
#14 0x0000000000414490 in PyObject_Call ()
#15 0x0000000000475de5 in PyEval_EvalFrame ()
#16 0x00000000004bdf69 in PyDescr_NewGetSet ()
#17 0x00000000004143eb in PyIter_Next ()
#18 0x000000000046ba53 in _PyUnicodeUCS4_IsNumeric ()
#19 0x0000000000477ab1 in PyEval_EvalFrame ()
#20 0x00000000004783ff in PyEval_EvalCodeEx ()
#21 0x000000000047699b in PyEval_EvalFrame ()
#22 0x0000000000476ab6 in PyEval_EvalFrame ()
#23 0x0000000000476ab6 in PyEval_EvalFrame ()
#24 0x00000000004783ff in PyEval_EvalCodeEx ()
#25 0x000000000047699b in PyEval_EvalFrame ()
#26 0x00000000004783ff in PyEval_EvalCodeEx ()
#27 0x000000000047699b in PyEval_EvalFrame ()
#28 0x00000000004783ff in PyEval_EvalCodeEx ()
#29 0x000000000047699b in PyEval_EvalFrame ()
#30 0x00000000004783ff in PyEval_EvalCodeEx ()
#31 0x0000000000478512 in PyEval_EvalCode ()
#32 0x000000000049c222 in PyRun_FileExFlags ()
#33 0x000000000049c4ae in PyRun_SimpleFileExFlags ()
#34 0x0000000000410a80 in Py_Main ()
#35 0x00002aaaab07d49b in __libc_start_main () from /lib/libc.so.6
#36 0x000000000040ffba in _start ()
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