right list for SIGABRT python binary question ?

Mon Oct 23 09:26:18 EDT 2017

On 2017-10-23 14:23, Karsten Hilbert wrote:
> On Sat, Oct 21, 2017 at 09:31:54AM +0200, dieter wrote:
> 
>> It points to a memory corruption.
> 
> While running valgrind and friends is beyond my capabilitis I
> have run the problem through gdb to at least obtain a stack
> trace to see what gives:

I wouldn't read too much into that. You know that somehow some memory
got corrupted. You know at which point Python trips over the error - but
that doesn't really tell you anything about how the memory initially got
corrupted.

> 
> 	...
> 	==> verifying target database schema ...
> 	==> checking migrated data for plausibility ...
> 	Done bootstrapping GNUmed database: We very likely succeeded.
> 	log: /home/ncq/Projekte/gm-git/gnumed/gnumed/server/bootstrap/bootstrap-latest.log
> 	Debug memory block at address p=0x6aab7c: API ''
> 	    0 bytes originally requested
> 	    The 3 pad bytes at p-3 are not all FORBIDDENBYTE (0xfb):
> 	        at p-3: 0x33 *** OUCH
> 	        at p-2: 0x47 *** OUCH
> 	        at p-1: 0x00 *** OUCH
> 	    Because memory is corrupted at the start, the count of bytes requested
> 	       may be bogus, and checking the trailing pad bytes may segfault.
> 	    The 4 pad bytes at tail=0x6aab7c are not all FORBIDDENBYTE (0xfb):
> 	        at tail+0: 0x00 *** OUCH
> 	        at tail+1: 0x00 *** OUCH
> 	        at tail+2: 0x00 *** OUCH
> 	        at tail+3: 0x00 *** OUCH
> 	    The block was made by call #0 to debug malloc/realloc.
> 	Fatal Python error: bad ID: Allocated using API '', verified using API 'o'
> 
> 	Program received signal SIGABRT, Aborted.
> 	0xb7fd9ce9 in __kernel_vsyscall ()
> 	(gdb) bt
> 	#0  0xb7fd9ce9 in __kernel_vsyscall ()
> 	#1  0xb7d6edd0 in __libc_signal_restore_set (set=0xbfffed40) at ../sysdeps/unix/sysv/linux/nptl-signals.h:79
> 	#2  __GI_raise (sig=6) at ../sysdeps/unix/sysv/linux/raise.c:48
> 	#3  0xb7d70297 in __GI_abort () at abort.c:89
> 	#4  0x0055fb74 in Py_FatalError (msg=0xbfffefec "bad ID: Allocated using API '\037', verified using API 'o'") at ../Python/pythonrun.c:1700
> 	#5  0x00499adb in _PyObject_DebugCheckAddressApi (api=111 'o', p=0x6aab7c <_Py_ZeroStruct>) at ../Objects/obmalloc.c:1640
> 	#6  0x004997a5 in _PyObject_DebugFreeApi (api=111 'o', p=0x6aab7c <_Py_ZeroStruct>) at ../Objects/obmalloc.c:1527
> 	#7  0x0049964f in _PyObject_DebugFree (p=0x6aab7c <_Py_ZeroStruct>) at ../Objects/obmalloc.c:1471
> 	#8  0x00471043 in int_dealloc (v=0x6aab7c <_Py_ZeroStruct>) at ../Objects/intobject.c:139
> 	#9  0x00497bee in _Py_Dealloc (op=False) at ../Objects/object.c:2262
> 	#10 0x00489bad in dict_dealloc (mp=0xb7888f34) at ../Objects/dictobject.c:1085
> 	Python Exception <class 'UnicodeDecodeError'> 'utf-8' codec can't decode bytes in position 1-2: unexpected end of data: 
> 	#11 0x00497bee in _Py_Dealloc (op=) at ../Objects/object.c:2262
> 	Python Exception <class 'UnicodeDecodeError'> 'utf-8' codec can't decode bytes in position 1-2: unexpected end of data: 
> 	#12 0x004b9ab7 in subtype_dealloc (self=) at ../Objects/typeobject.c:1035
> 	Python Exception <class 'UnicodeDecodeError'> 'utf-8' codec can't decode bytes in position 1-2: unexpected end of data: 
> 	#13 0x00497bee in _Py_Dealloc (op=) at ../Objects/object.c:2262
> 	#14 0x0044dc7a in instancemethod_dealloc (im=0xb78984b4) at ../Objects/classobject.c:2388
> 	#15 0x00497bee in _Py_Dealloc (op=<instancemethod at remote 0xb78984b4>) at ../Objects/object.c:2262
> 	#16 0x004885d7 in insertdict_by_entry (mp=0xb78880d4, key='_shutdown', hash=598970216, ep=0x88d6d4, value=None) at ../Objects/dictobject.c:519
> 	#17 0x00488857 in insertdict (mp=0xb78880d4, key='_shutdown', hash=598970216, value=None) at ../Objects/dictobject.c:556
> 	#18 0x0048910f in dict_set_item_by_hash_or_entry (
> 	    op={'current_thread': <function at remote 0xb78a28f4>, '_BoundedSemaphore': None, 'currentThread': <function at remote 0xb78a28f4>, '_Timer': None, '_format_exc': None, 'Semaphore': <function at remote 0xb789b6c4>, '_deque': None, 'activeCount': <function at remote 0xb78a2a34>, '_profile_hook': None, '_sleep': None, '_trace_hook': None, 'ThreadError': <type at remote 0xb784c034>, '_enumerate': None, '_start_new_thread': None, 'BoundedSemaphore': <function at remote 0xb789ba34>, '_shutdown': None, '__all__': ['activeCount', 'active_count', 'Condition', 'currentThread', 'current_thread', 'enumerate', 'Event', 'Lock', 'RLock', 'Semaphore', 'BoundedSemaphore', 'Thread', 'Timer', 'setprofile', 'settrace', 'local', 'stack_size'], '_Event': <type at remote 0xb789e034>, 'active_count': <function at remote 0xb78a2a34>, '__package__': None, '_Condition': <type at remote 0xb784c9e4>, '_RLock': <type at remote 0xb784c7f4>, '_test': <function at remote 0xb78a2b74>, 'local': <type at remote 0
>  x6fd420>, '__doc__': "Thread modul...(truncated), key='_shutdown', hash=598970216, ep=0x0, value=None) at ../Objects/dictobject.c:795
> 	#19 0x00489285 in PyDict_SetItem (
> 	    op={'current_thread': <function at remote 0xb78a28f4>, '_BoundedSemaphore': None, 'currentThread': <function at remote 0xb78a28f4>, '_Timer': None, '_format_exc': None, 'Semaphore': <function at remote 0xb789b6c4>, '_deque': None, 'activeCount': <function at remote 0xb78a2a34>, '_profile_hook': None, '_sleep': None, '_trace_hook': None, 'ThreadError': <type at remote 0xb784c034>, '_enumerate': None, '_start_new_thread': None, 'BoundedSemaphore': <function at remote 0xb789ba34>, '_shutdown': None, '__all__': ['activeCount', 'active_count', 'Condition', 'currentThread', 'current_thread', 'enumerate', 'Event', 'Lock', 'RLock', 'Semaphore', 'BoundedSemaphore', 'Thread', 'Timer', 'setprofile', 'settrace', 'local', 'stack_size'], '_Event': <type at remote 0xb789e034>, 'active_count': <function at remote 0xb78a2a34>, '__package__': None, '_Condition': <type at remote 0xb784c9e4>, '_RLock': <type at remote 0xb784c7f4>, '_test': <function at remote 0xb78a2b74>, 'local': <type at remote 0
>  x6fd420>, '__doc__': "Thread modul...(truncated), key='_shutdown', value=None) at ../Objects/dictobject.c:848
> 	#20 0x00492758 in _PyModule_Clear (m=<module at remote 0xb7892364>) at ../Objects/moduleobject.c:125
> 	#21 0x0054a33b in PyImport_Cleanup () at ../Python/import.c:530
> 	#22 0x0055c53c in Py_Finalize () at ../Python/pythonrun.c:458
> 	#23 0x0055fe9c in Py_Exit (sts=0) at ../Python/pythonrun.c:1783
> 	#24 0x0055e0fc in handle_system_exit () at ../Python/pythonrun.c:1151
> 	#25 0x0055e152 in PyErr_PrintEx (set_sys_last_vars=1) at ../Python/pythonrun.c:1161
> 	#26 0x0055dd5b in PyErr_Print () at ../Python/pythonrun.c:1064
> 	#27 0x0055d61f in PyRun_SimpleFileExFlags (fp=0x7ee010, filename=0xbffff7e6 "./bootstrap_gm_db_system.py", closeit=1, flags=0xbffff4f4) at ../Python/pythonrun.c:952
> 	#28 0x0055cc4e in PyRun_AnyFileExFlags (fp=0x7ee010, filename=0xbffff7e6 "./bootstrap_gm_db_system.py", closeit=1, flags=0xbffff4f4) at ../Python/pythonrun.c:752
> 	#29 0x00577cb0 in Py_Main (argc=5, argv=0xbffff684) at ../Modules/main.c:645
> 	#30 0x004259c8 in main (argc=5, argv=0xbffff684) at ../Modules/python.c:20
> 	(gdb) quit
> 	A debugging session is active.
> 
> 		Inferior 1 [process 32024] will be killed.
> 
> 	Quit anyway? (y or n) y
> 	Dropping obsoleted staging database gnumed_v2 ...
> 	(you may need to provide the password for root)
> 	Dropping obsoleted staging database gnumed_v3 ...
> 	...
> 
> Vague hints from the above might suggest that I go look for
> whether I do have a second thread and where improperly formed
> unicode data might come from.
> 
> Karsten
> 