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:
...
==> 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
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