The package fails to build from source on arm64 and mips64el with
multiple test failures that look similar at first glance. For example,
on arm64:
Fatal Python error: Segmentation fault
Hello,
I tried to collect some more information.
I could just follow that far as a bogus pointer
gets written in NRT_MemInfo_new_varsize_dtor,
which gets later called in nrt_varsize_dtor.
Unfortunately I cannot see where this value originates from.
Below an example debugging session, after a failing build on arm64 hardware.
In below example the bogus pointer has a value of 0xf9000be0d10083ff.
Kind regards,
Bernhard
benutzer@chroot-13-trixie-arm64:~/source/numba/try1/numba-0.59.1+dfsg$ gdb -q
--args python3.12
Reading symbols from python3.12...
Reading symbols from
/usr/lib/debug/.build-id/d9/3d40f59d70863566375339beb0f380251a6436.debug...
(gdb) directory /home/benutzer/source/numba/try1/numba-0.59.1+dfsg
Source directories searched:
/home/benutzer/source/numba/try1/numba-0.59.1+dfsg:$cdir:$cwd
(gdb) set width 0
(gdb) set pagination off
(gdb) set environment
PYTHONPATH=/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/debian/python3-numba/usr/lib/python3.12/dist-packages:/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/.pybuild/cpython3_3.12_numba/build
(gdb) set environment NUMBA_DEBUGINFO=1
(gdb) set environment NUMBA_OPT=0
(gdb) b nrt.cpp:177
No source file named nrt.cpp.
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 1 (nrt.cpp:177) pending.
(gdb) b nrt_varsize_dtor
Function "nrt_varsize_dtor" not defined.
Make breakpoint pending on future shared library load? (y or [n]) y
Breakpoint 2 (nrt_varsize_dtor) pending.
(gdb) run numba/tests/test_array_iterators.py
Starting program: /usr/bin/python3.12 numba/tests/test_array_iterators.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/aarch64-linux-gnu/libthread_db.so.1".
Breakpoint 1.4, NRT_MemInfo_init (mi=0x2056870, data=0x18d2510, size=0,
dtor=0xfffff5901f28 <pyobject_dtor>, dtor_info=0xffffe93ae7f0,
external_allocator=0x0) at numba/core/runtime/nrt.cpp:177
177 if (TheMSys.stats.enabled)
(gdb) disa 1.1
(gdb) disa 1.2
(gdb) disa 1.3
(gdb) disa 1.4
(gdb) disa 1.5
(gdb) disa 1.6
(gdb) disa 1.7
(gdb) disa 1.9
(gdb) disa 1.10
(gdb) disa 1.11
(gdb) disa 1.12
(gdb) ignore 1 1
Will ignore next crossing of breakpoint 1.
(gdb) ignore 2 1
Will ignore next crossing of breakpoint 2.
(gdb) cont
Continuing.
......
Breakpoint 1.8, NRT_MemInfo_init (mi=0x29cdbd0, data=0x29bfd90, size=24,
dtor=<optimized out>, dtor_info=0x0, external_allocator=0x0) at
numba/core/runtime/nrt.cpp:177
177 if (TheMSys.stats.enabled)
(gdb) print mi
$1 = (NRT_MemInfo *) 0x29cdbd0
(gdb) print *mi
$2 = {refct = std::atomic<unsigned long> = { 1 }, dtor = 0xfffff5903580
<nrt_varsize_dtor(void*, size_t, void*)>, dtor_info = 0x0, data = 0x29bfd90, size =
24, external_allocator = 0x0}
(gdb) print &mi->dtor_info
$3 = (void **) 0x29cdbe0
(gdb) watch *(void **) 0x29cdbe0
Hardware watchpoint 3: *(void **) 0x29cdbe0
(gdb) display *(NRT_MemInfo *) 0x29cdbd0
1: *(NRT_MemInfo *) 0x29cdbd0 = {refct = std::atomic<unsigned long> = { 1 }, dtor =
0xfffff5903580 <nrt_varsize_dtor(void*, size_t, void*)>, dtor_info = 0x0, data =
0x29bfd90, size = 24, external_allocator = 0x0}
(gdb) cont
Continuing.
Hardware watchpoint 3: *(void **) 0x29cdbe0
Old value = (void *) 0x0
New value = (void *) 0xf9000be0d10083ff
NRT_MemInfo_new_varsize_dtor (size=24, dtor=0xf9000be0d10083ff) at
numba/core/runtime/nrt.cpp:472
472 return mi;
1: *(NRT_MemInfo *) 0x29cdbd0 = {refct = std::atomic<unsigned long> = { 1 }, dtor =
0xfffff5903580 <nrt_varsize_dtor(void*, size_t, void*)>, dtor_info =
0xf9000be0d10083ff, data = 0x29bfd90, size = 24, external_allocator = 0x0}
(gdb) bt 6
#0 NRT_MemInfo_new_varsize_dtor (size=24, dtor=0xf9000be0d10083ff) at
numba/core/runtime/nrt.cpp:472
#1 0x0000fffff6dbd0f0 in
numba::cpython::listobj::list_constructor::_3clocals_3e::list_impl[abi:v39][abi:c8tJTC_2fWQI8IW1CiAAYKPM6RBFDjESZRVAJmaQIA](iter_28array_28int64_2c_201d_2c_20A_29_29)
() at listobj.py:469
#2 0x0000fffff6db91f4 in
__main__::array_iter_items[abi:v38][abi:c8tJTC_2fWwGaMLShh6CjAIxrKR0t9qKIYaQ0qDQwmMEsTAA_3d_3d](Array<long
long, 1, A, mutable, aligned>) (arr=...) at test_array_iterators.py:18
#3 0x0000fffff6db9540 in
cpython::__main__::array_iter_items[abi:v38][abi:c8tJTC_2fWwGaMLShh6CjAIxrKR0t9qKIYaQ0qDQwmMEsTAA_3d_3d](Array<long
long, 1, A, mutable, aligned>) ()
#4 0x0000ffffeb133e20 in call_cfunc (self=0xfffff6db9380
<cpython::__main__::array_iter_items[abi:v38][abi:c8tJTC_2fWwGaMLShh6CjAIxrKR0t9qKIYaQ0qDQwmMEsTAA_3d_3d](Array<long
long, 1, A, mutable, aligned>)>, locals=<optimized out>, cfunc=<built-in method array_iter_items of
_dynfunc._Closure object at remote 0xffffe79cfb20>, args=<optimized out>, kws=<optimized out>) at
numba/_dispatcher.cpp:745
#5 Dispatcher_call (self=self@entry=0xffffe7e9d090,
args=args@entry=(<numpy.ndarray at remote 0xffffe872ccf0>,), kws=kws@entry=0x0)
at numba/_dispatcher.cpp:1037
(More stack frames follow...)
(gdb) up
#1 0x0000fffff6dbd0f0 in
numba::cpython::listobj::list_constructor::_3clocals_3e::list_impl[abi:v39][abi:c8tJTC_2fWQI8IW1CiAAYKPM6RBFDjESZRVAJmaQIA](iter_28array_28int64_2c_201d_2c_20A_29_29)
() at listobj.py:469
469 res = []
(gdb) list
464
465 @lower_builtin(list, types.IterableType)
466 def list_constructor(context, builder, sig, args):
467
468 def list_impl(iterable):
469 res = []
470 res.extend(iterable)
471 return res
472
473 return context.compile_internal(builder, list_impl, sig, args)
(gdb) py-bt
Traceback (most recent call first):
File
"/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/numba/tests/test_array_iterators.py",
line 138, in check_array_iter_items
self.assertPreciseEqual(cfunc(arr), expected)
File
"/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/numba/tests/test_array_iterators.py",
line 175, in test_array_iter
self.check_array_iter_items(arr)
File "/usr/lib/python3.12/unittest/case.py", line 589, in _callTestMethod
if method() is not None:
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 690, in __call__
return self.run(*args, **kwds)
File "/usr/lib/python3.12/unittest/suite.py", line 122, in run
test(result)
File "/usr/lib/python3.12/unittest/suite.py", line 84, in __call__
return self.run(*args, **kwds)
File "/usr/lib/python3.12/unittest/suite.py", line 122, in run
test(result)
File "/usr/lib/python3.12/unittest/suite.py", line 84, in __call__
return self.run(*args, **kwds)
File "/usr/lib/python3.12/unittest/runner.py", line 240, in run
test(result)
File "/usr/lib/python3.12/unittest/main.py", line 281, in runTests
self.result = testRunner.run(self.test)
File "/usr/lib/python3.12/unittest/main.py", line 105, in __init__
self.runTests()
File
"/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/numba/tests/test_array_iterators.py",
line 555, in <module>
unittest.main()
(gdb) up
#2 0x0000fffff6db91f4 in
__main__::array_iter_items[abi:v38][abi:c8tJTC_2fWwGaMLShh6CjAIxrKR0t9qKIYaQ0qDQwmMEsTAA_3d_3d](Array<long
long, 1, A, mutable, aligned>) (arr=...) at test_array_iterators.py:18
18 return list(iter(arr))
(gdb) cont
Continuing.
Breakpoint 2, nrt_varsize_dtor (ptr=0x29bfd90, size=96,
info=0xf9000be0d10083ff) at numba/core/runtime/nrt.cpp:444
444 if (info) {
1: *(NRT_MemInfo *) 0x29cdbd0 = {refct = std::atomic<unsigned long> = { 0 }, dtor =
0xfffff5903580 <nrt_varsize_dtor(void*, size_t, void*)>, dtor_info =
0xf9000be0d10083ff, data = 0x29bfd90, size = 96, external_allocator = 0x0}
(gdb) up
#1 0x0000fffff5903da0 in NRT_MemInfo_call_dtor (mi=0x29cdbd0) at
numba/core/runtime/nrt.cpp:401
401 mi->dtor(mi->data, mi->size, mi->dtor_info);
(gdb) print mi
$4 = (NRT_MemInfo *) 0x29cdbd0
(gdb) bt 6
#0 nrt_varsize_dtor (ptr=0x29bfd90, size=96, info=0xf9000be0d10083ff) at
numba/core/runtime/nrt.cpp:444
#1 0x0000fffff5903da0 in NRT_MemInfo_call_dtor (mi=0x29cdbd0) at
numba/core/runtime/nrt.cpp:401
#2 0x0000fffff7fbb1f8 in NRT_decref ()
#3 0x0000fffff6db9638 in
cpython::__main__::array_iter_items[abi:v38][abi:c8tJTC_2fWwGaMLShh6CjAIxrKR0t9qKIYaQ0qDQwmMEsTAA_3d_3d](Array<long
long, 1, A, mutable, aligned>) ()
#4 0x0000ffffeb133e20 in call_cfunc (self=0xfffff6db9380
<cpython::__main__::array_iter_items[abi:v38][abi:c8tJTC_2fWwGaMLShh6CjAIxrKR0t9qKIYaQ0qDQwmMEsTAA_3d_3d](Array<long
long, 1, A, mutable, aligned>)>, locals=<optimized out>, cfunc=<built-in method array_iter_items of
_dynfunc._Closure object at remote 0xffffe79cfb20>, args=<optimized out>, kws=<optimized out>) at
numba/_dispatcher.cpp:745
#5 Dispatcher_call (self=self@entry=0xffffe7e9d090,
args=args@entry=(<numpy.ndarray at remote 0xffffe872ccf0>,), kws=kws@entry=0x0)
at numba/_dispatcher.cpp:1037
(More stack frames follow...)
(gdb) py-bt
Traceback (most recent call first):
File
"/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/numba/tests/test_array_iterators.py",
line 138, in check_array_iter_items
self.assertPreciseEqual(cfunc(arr), expected)
File
"/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/numba/tests/test_array_iterators.py",
line 175, in test_array_iter
self.check_array_iter_items(arr)
File "/usr/lib/python3.12/unittest/case.py", line 589, in _callTestMethod
if method() is not None:
File "/usr/lib/python3.12/unittest/case.py", line 634, in run
self._callTestMethod(testMethod)
File "/usr/lib/python3.12/unittest/case.py", line 690, in __call__
return self.run(*args, **kwds)
File "/usr/lib/python3.12/unittest/suite.py", line 122, in run
test(result)
File "/usr/lib/python3.12/unittest/suite.py", line 84, in __call__
return self.run(*args, **kwds)
File "/usr/lib/python3.12/unittest/suite.py", line 122, in run
test(result)
File "/usr/lib/python3.12/unittest/suite.py", line 84, in __call__
return self.run(*args, **kwds)
File "/usr/lib/python3.12/unittest/runner.py", line 240, in run
test(result)
File "/usr/lib/python3.12/unittest/main.py", line 281, in runTests
self.result = testRunner.run(self.test)
File "/usr/lib/python3.12/unittest/main.py", line 105, in __init__
self.runTests()
File
"/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/numba/tests/test_array_iterators.py",
line 555, in <module>
unittest.main()
(gdb) next
448 dtor(ptr);
1: *(NRT_MemInfo *) 0x29cdbd0 = {refct = std::atomic<unsigned long> = { 0 }, dtor =
0xfffff5903580 <nrt_varsize_dtor(void*, size_t, void*)>, dtor_info =
0xf9000be0d10083ff, data = 0x29bfd90, size = 96, external_allocator = 0x0}
(gdb)
Program received signal SIGBUS, Bus error.
0x00000be0d10083ff in ?? ()
1: *(NRT_MemInfo *) 0x29cdbd0 = {refct = std::atomic<unsigned long> = { 0 }, dtor =
0xfffff5903580 <nrt_varsize_dtor(void*, size_t, void*)>, dtor_info =
0xf9000be0d10083ff, data = 0x29bfd90, size = 96, external_allocator = 0x0}
(gdb) kill
Kill the program being debugged? (y or n) y
[Inferior 1 (process 584) killed]
(gdb) q
benutzer@chroot-13-trixie-arm64:~/source/numba/try1/numba-0.59.1+dfsg$
gdb -q --args python3.12
directory /home/benutzer/source/numba/try1/numba-0.59.1+dfsg
set width 0
set pagination off
set environment
PYTHONPATH=/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/debian/python3-numba/usr/lib/python3.12/dist-packages:/home/benutzer/source/numba/try1/numba-0.59.1+dfsg/.pybuild/cpython3_3.12_numba/build
set environment NUMBA_DEBUGINFO=1
set environment NUMBA_OPT=0
b nrt.cpp:177
y
b nrt_varsize_dtor
y
run numba/tests/test_array_iterators.py
disa 1.1
disa 1.2
disa 1.3
disa 1.4
disa 1.5
disa 1.6
disa 1.7
disa 1.9
disa 1.10
disa 1.11
disa 1.12
ignore 1 1
ignore 2 1
cont
