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[Python] Segmentation fault when pyarrow is imported in exit handler #38626

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gusostow opened this issue Nov 7, 2023 · 8 comments · Fixed by #38637
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[Python] Segmentation fault when pyarrow is imported in exit handler #38626

gusostow opened this issue Nov 7, 2023 · 8 comments · Fixed by #38637
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Component: Python Critical Fix Bugfixes for security vulnerabilities, crashes, or invalid data. Type: bug
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@gusostow
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gusostow commented Nov 7, 2023

Describe the bug, including details regarding any error messages, version, and platform.

# example.py

import atexit

def exit(): import pyarrow

atexit.register(exit)
python example.py
[1]    2741781 segmentation fault (core dumped)  python example.py

Versions

libarrow                  13.0.0          h3b6bca8_14_cpu    conda-forge
pandas                    2.1.2                    pypi_0    pypi
pyarrow                   13.0.0                   pypi_0    pypi
python                    3.11.6          hab00c5b_0_cpython    conda-forge
python_abi                3.11                    4_cp311    conda-forge

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Python

@kou kou changed the title Segementation fault when pyarrow is imported in exit handler [Python] Segementation fault when pyarrow is imported in exit handler Nov 7, 2023
@kou
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kou commented Nov 7, 2023

Why do you want to do this...?

@gusostow
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gusostow commented Nov 8, 2023

Exit handlers in a complex codebase might incidentally import pyarrow especially via pandas.

@jorisvandenbossche
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I can confirm the segfault, both with pyarrow 13.0 and main from a few days ago. The gdb bactrace:

Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x0000555555737cdc in new_threadstate (interp=0x0, init=init@entry=1) at /usr/local/src/conda/python-3.10.6/Python/pystate.c:616
616	/usr/local/src/conda/python-3.10.6/Python/pystate.c: No such file or directory.
(gdb) bt
#0  0x0000555555737cdc in new_threadstate (interp=0x0, init=init@entry=1) at /usr/local/src/conda/python-3.10.6/Python/pystate.c:616
#1  0x00005555555fa7ce in PyThreadState_New (interp=<optimized out>) at /usr/local/src/conda/python-3.10.6/Python/pystate.c:684
#2  PyGILState_Ensure () at /usr/local/src/conda/python-3.10.6/Python/pystate.c:1504
#3  0x00007ffff6d183f7 in arrow::py::PyAcquireGIL::acquire (this=<synthetic pointer>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/common.h:115
#4  arrow::py::PyAcquireGIL::acquire (this=<synthetic pointer>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/common.h:113
#5  arrow::py::PyAcquireGIL::PyAcquireGIL (this=<synthetic pointer>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/common.h:109
#6  arrow::py::OwnedRefNoGIL::~OwnedRefNoGIL (this=0x555555e35b38, __in_chrg=<optimized out>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/common.h:233
#7  arrow::py::OwnedRefNoGIL::~OwnedRefNoGIL (this=0x555555e35b38, __in_chrg=<optimized out>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/common.h:227
#8  arrow::py::PyExtensionType::~PyExtensionType (this=0x555555e35ac0, __in_chrg=<optimized out>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/extension_type.h:31
#9  arrow::py::PyExtensionType::~PyExtensionType (this=0x555555e35ac0, __in_chrg=<optimized out>) at /home/joris/scipy/repos/arrow/python/pyarrow/src/arrow/python/extension_type.h:31
#10 0x00007ffff5684815 in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release (this=0x555555e79bc0)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr_base.h:158
#11 std::__shared_count<(__gnu_cxx::_Lock_policy)2>::~__shared_count (this=0x555555e62a20, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr_base.h:736
#12 std::__shared_ptr<arrow::ExtensionType, (__gnu_cxx::_Lock_policy)2>::~__shared_ptr (this=0x555555e62a18, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr_base.h:1188
#13 std::shared_ptr<arrow::ExtensionType>::~shared_ptr (this=0x555555e62a18, __in_chrg=<optimized out>) at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr.h:121
#14 std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >::~pair (this=0x555555e629f8, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/stl_pair.h:211
#15 __gnu_cxx::new_allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> >::destroy<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > > (__p=0x555555e629f8, this=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/ext/new_allocator.h:162
#16 std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> > >::destroy<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > > (__p=0x555555e629f8, __a=...)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/alloc_traits.h:531
#17 std::__detail::_Hashtable_alloc<std::allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> > >::_M_deallocate_node (__n=0x555555e629f0, this=<optimized out>) at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/hashtable_policy.h:2054
#18 std::__detail::_Hashtable_alloc<std::allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> > >::_M_deallocate_nodes (this=<optimized out>, __n=0x555555d68f00) at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/hashtable_policy.h:2076
#19 std::_Hashtable<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::clear (this=0x555555e58450)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/hashtable.h:2085
#20 std::_Hashtable<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::~_Hashtable (this=0x555555e58450, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/hashtable.h:1442
#21 std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::shared_ptr<arrow::ExtensionType>, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > > >::~unordered_map (this=0x555555e58450, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/unordered_map.h:102
#22 arrow::ExtensionTypeRegistryImpl::~ExtensionTypeRegistryImpl (this=0x555555e58420, __in_chrg=<optimized out>) at /home/joris/scipy/repos/arrow/cpp/src/arrow/extension_type.cc:97
#23 0x00007ffff5684a5a in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release (this=0x555555e58410)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr_base.h:158
#24 std::__shared_count<(__gnu_cxx::_Lock_policy)2>::~__shared_count (this=<optimized out>, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr_base.h:736
#25 std::__shared_ptr<arrow::ExtensionTypeRegistry, (__gnu_cxx::_Lock_policy)2>::~__shared_ptr (this=<optimized out>, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr_base.h:1188
#26 std::shared_ptr<arrow::ExtensionTypeRegistry>::~shared_ptr (this=<optimized out>, __in_chrg=<optimized out>)
    at /home/joris/miniconda3/envs/arrow-dev/x86_64-conda-linux-gnu/include/c++/10.4.0/bits/shared_ptr.h:121

@jorisvandenbossche
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General cpython issue about issues with threads in finalization: python/cpython#80657 (cc @pitrou)

We do have some protection around acquiring the GIL here, but so that is not sufficient:

~OwnedRefNoGIL() {
// This destructor may be called after the Python interpreter is finalized.
// At least avoid spurious attempts to take the GIL when not necessary.
if (obj() == NULLPTR) {
return;
}
PyAcquireGIL lock;
reset();
}

@pitrou
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pitrou commented Nov 8, 2023

@jorisvandenbossche Is it the full backtrace? Are there other threads running?

@pitrou
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pitrou commented Nov 8, 2023

Ok, here is the full backtrace:

#0  0x0000555555724ded in new_threadstate (interp=0x0, init=init@entry=1) at /usr/local/src/conda/python-3.10.12/Python/pystate.c:624
#1  0x00005555555fc6d2 in PyThreadState_New (interp=<optimized out>) at /usr/local/src/conda/python-3.10.12/Python/pystate.c:692
#2  PyGILState_Ensure () at /usr/local/src/conda/python-3.10.12/Python/pystate.c:1512
#3  0x00007ffff66fa064 in arrow::py::PyAcquireGIL::acquire (this=0x7fffffffbaf0) at /home/antoine/arrow/dev/python/pyarrow/src/arrow/python/common.h:115
#4  0x00007ffff66fa025 in arrow::py::PyAcquireGIL::PyAcquireGIL (this=0x7fffffffbaf0) at /home/antoine/arrow/dev/python/pyarrow/src/arrow/python/common.h:109
#5  0x00007ffff66fa1e5 in arrow::py::OwnedRefNoGIL::~OwnedRefNoGIL (this=0x555555d905f8, __in_chrg=<optimized out>)
    at /home/antoine/arrow/dev/python/pyarrow/src/arrow/python/common.h:233
#6  0x00007ffff67b1c8b in arrow::py::PyExtensionType::~PyExtensionType (this=0x555555d90580, __in_chrg=<optimized out>)
    at /home/antoine/arrow/dev/python/pyarrow/src/arrow/python/extension_type.h:31
#7  0x00007ffff67b1cc4 in arrow::py::PyExtensionType::~PyExtensionType (this=0x555555d90580, __in_chrg=<optimized out>)
    at /home/antoine/arrow/dev/python/pyarrow/src/arrow/python/extension_type.h:31
#8  0x00007ffff67b23c8 in std::_Sp_counted_ptr<arrow::py::PyExtensionType*, (__gnu_cxx::_Lock_policy)2>::_M_dispose (this=0x555555e3c8c0)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:428
#9  0x00007ffff3a5f76b in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release_last_use (this=0x555555e3c8c0)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:175
#10 0x00007ffff3a5bfe0 in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release_last_use_cold (this=0x555555e3c8c0)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:199
#11 0x00007ffff3a57327 in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release (this=0x555555e3c8c0)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:353
#12 0x00007ffff3a5c291 in std::__shared_count<(__gnu_cxx::_Lock_policy)2>::~__shared_count (this=0x555555e489d0, __in_chrg=<optimized out>)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:1071
#13 0x00007ffff3e1e746 in std::__shared_ptr<arrow::ExtensionType, (__gnu_cxx::_Lock_policy)2>::~__shared_ptr (this=0x555555e489c8, __in_chrg=<optimized out>)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:1524
#14 0x00007ffff3e1e762 in std::shared_ptr<arrow::ExtensionType>::~shared_ptr (this=0x555555e489c8, __in_chrg=<optimized out>)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr.h:175
#15 0x00007ffff3e21b96 in std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >::~pair (this=0x555555e489a8, __in_chrg=<optimized out>) at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/stl_pair.h:185
#16 0x00007ffff3e21bc2 in std::__new_allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> >::destroy<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > > (this=0x555555bdf390, __p=0x555555e489a8)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/new_allocator.h:181
#17 0x00007ffff3e21453 in std::allocator_traits<std::allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> > >::destroy<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > > (__a=..., __p=0x555555e489a8)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/alloc_traits.h:535
#18 0x00007ffff3e208dd in std::__detail::_Hashtable_alloc<std::allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> > >::_M_deallocate_node (this=0x555555bdf390, __n=0x555555e489a0)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/hashtable_policy.h:1984
#19 0x00007ffff3e1ff70 in std::__detail::_Hashtable_alloc<std::allocator<std::__detail::_Hash_node<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, true> > >::_M_deallocate_nodes (this=0x555555bdf390, __n=0x555555e44120)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/hashtable_policy.h:2006
#20 0x00007ffff3e1f67b in std::_Hashtable<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::clear (
    this=0x555555bdf390) at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/hashtable.h:2500
#21 0x00007ffff3e1f145 in std::_Hashtable<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > >, std::__detail::_Select1st, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::~_Hashtable (
    this=0x555555bdf390, __in_chrg=<optimized out>) at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/hashtable.h:1584
#22 0x00007ffff3e1e45f in std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::shared_ptr<arrow::ExtensionType>, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::shared_ptr<arrow::ExtensionType> > > >::~unordered_map (this=0x555555bdf390, __in_chrg=<optimized out>)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/unordered_map.h:102
#23 0x00007ffff3e2237a in arrow::ExtensionTypeRegistryImpl::~ExtensionTypeRegistryImpl (this=0x555555bdf360, __in_chrg=<optimized out>)
    at /home/antoine/arrow/dev/cpp/src/arrow/extension_type.cc:97
#24 0x00007ffff3e22648 in std::_Destroy<arrow::ExtensionTypeRegistryImpl> (__pointer=0x555555bdf360)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/stl_construct.h:151
#25 0x00007ffff3e22626 in std::allocator_traits<std::allocator<void> >::destroy<arrow::ExtensionTypeRegistryImpl> (__p=0x555555bdf360)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/alloc_traits.h:648
#26 0x00007ffff3e224f5 in std::_Sp_counted_ptr_inplace<arrow::ExtensionTypeRegistryImpl, std::allocator<void>, (__gnu_cxx::_Lock_policy)2>::_M_dispose (
    this=0x555555bdf350) at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:613
#27 0x00007ffff3a5728b in std::_Sp_counted_base<(__gnu_cxx::_Lock_policy)2>::_M_release (this=0x555555bdf350)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:346
#28 0x00007ffff3a5c291 in std::__shared_count<(__gnu_cxx::_Lock_policy)2>::~__shared_count (this=0x7ffff63f7d98 <arrow::g_registry+8>, __in_chrg=<optimized out>)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:1071
#29 0x00007ffff3e1e8e0 in std::__shared_ptr<arrow::ExtensionTypeRegistry, (__gnu_cxx::_Lock_policy)2>::~__shared_ptr (this=0x7ffff63f7d90 <arrow::g_registry>, 
    __in_chrg=<optimized out>) at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr_base.h:1524
#30 0x00007ffff3e1ed76 in std::shared_ptr<arrow::ExtensionTypeRegistry>::~shared_ptr (this=0x7ffff63f7d90 <arrow::g_registry>, __in_chrg=<optimized out>)
    at /home/antoine/mambaforge/envs/pyarrow/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/shared_ptr.h:175
#31 0x00007ffff7cb5495 in __run_exit_handlers (status=0, listp=0x7ffff7e89838 <__exit_funcs>, run_list_atexit=run_list_atexit@entry=true, 
    run_dtors=run_dtors@entry=true) at ./stdlib/exit.c:113
#32 0x00007ffff7cb5610 in __GI_exit (status=<optimized out>) at ./stdlib/exit.c:143
#33 0x00007ffff7c99d97 in __libc_start_call_main (main=main@entry=0x55555571f4e0 <main>, argc=argc@entry=3, argv=argv@entry=0x7fffffffc0b8)
    at ../sysdeps/nptl/libc_start_call_main.h:74
#34 0x00007ffff7c99e40 in __libc_start_main_impl (main=0x55555571f4e0 <main>, argc=3, argv=0x7fffffffc0b8, init=<optimized out>, fini=<optimized out>, 
    rtld_fini=<optimized out>, stack_end=0x7fffffffc0a8) at ../csu/libc-start.c:392
#35 0x000055555571f421 in _start ()

@pitrou pitrou self-assigned this Nov 8, 2023
@pitrou pitrou changed the title [Python] Segementation fault when pyarrow is imported in exit handler [Python] Segmentation fault when pyarrow is imported in exit handler Nov 8, 2023
pitrou added a commit to pitrou/arrow that referenced this issue Nov 8, 2023
…tdown

Some C++ destructors may be called after the Python interpreter has ceased to exist.
pitrou added a commit to pitrou/arrow that referenced this issue Nov 8, 2023
…tdown

Some C++ destructors may be called after the Python interpreter has ceased to exist.
jorisvandenbossche pushed a commit that referenced this issue Nov 14, 2023
…38637)

### Rationale for this change

Some C++ destructors may be called after the Python interpreter has ceased to exist.
If such a destructor tries to call back in the Python interpreter, for example by calling `Py_DECREF`, we get a crash.

### What changes are included in this PR?

Protect `OwnedRef` and `OwneRefNoGIL` destructors against decref'ing a Python object after Python finalization.

### Are these changes tested?

Yes.

### Are there any user-facing changes?

No.
* Closes: #38626

Authored-by: Antoine Pitrou <[email protected]>
Signed-off-by: Joris Van den Bossche <[email protected]>
@jorisvandenbossche jorisvandenbossche added this to the 15.0.0 milestone Nov 14, 2023
@raulcd raulcd modified the milestones: 15.0.0, 14.0.2 Nov 28, 2023
raulcd pushed a commit that referenced this issue Nov 28, 2023
…38637)

### Rationale for this change

Some C++ destructors may be called after the Python interpreter has ceased to exist.
If such a destructor tries to call back in the Python interpreter, for example by calling `Py_DECREF`, we get a crash.

### What changes are included in this PR?

Protect `OwnedRef` and `OwneRefNoGIL` destructors against decref'ing a Python object after Python finalization.

### Are these changes tested?

Yes.

### Are there any user-facing changes?

No.
* Closes: #38626

Authored-by: Antoine Pitrou <[email protected]>
Signed-off-by: Joris Van den Bossche <[email protected]>
@amoeba amoeba added the Critical Fix Bugfixes for security vulnerabilities, crashes, or invalid data. label Dec 7, 2023
dgreiss pushed a commit to dgreiss/arrow that referenced this issue Feb 19, 2024
…tdown (apache#38637)

### Rationale for this change

Some C++ destructors may be called after the Python interpreter has ceased to exist.
If such a destructor tries to call back in the Python interpreter, for example by calling `Py_DECREF`, we get a crash.

### What changes are included in this PR?

Protect `OwnedRef` and `OwneRefNoGIL` destructors against decref'ing a Python object after Python finalization.

### Are these changes tested?

Yes.

### Are there any user-facing changes?

No.
* Closes: apache#38626

Authored-by: Antoine Pitrou <[email protected]>
Signed-off-by: Joris Van den Bossche <[email protected]>
@asda10
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asda10 commented Sep 5, 2024

please, I am having problems, I have tried many time find a solution and failed miserably:

Fatal Python error: Segmentation fault
Current thread 0x00000001053fee00 (most recent call first):
File "", line 488 in _call_with_frames_removed
File "", line 1289 in create_module
File "", line 813 in module_from_spec
File "", line 921 in _load_unlocked
File "", line 1331 in _find_and_load_unlocked
File "", line 1360 in _find_and_load
File "/Users/pong/Library/Python/3.12/lib/python/site-packages/pyarrow/init.py", line 65 in
File "", line 488 in _call_with_frames_removed
File "", line 995 in exec_module
File "", line 935 in _load_unlocked
File "", line 1331 in _find_and_load_unlocked
File "", line 1360 in _find_and_load
File "/Users/pong/Library/Python/3.12/lib/python/site-packages/pandas/compat/pyarrow.py", line 8 in
File "", line 488 in _call_with_frames_removed
File "", line 995 in exec_module
File "", line 935 in _load_unlocked
File "", line 1331 in _find_and_load_unlocked
File "", line 1360 in _find_and_load
File "/Users/pong/Library/Python/3.12/lib/python/site-packages/pandas/compat/init.py", line 27 in
File "", line 488 in _call_with_frames_removed
File "", line 995 in exec_module
File "", line 935 in _load_unlocked
File "", line 1331 in _find_and_load_unlocked
File "", line 1360 in _find_and_load
File "/Users/pong/Library/Python/3.12/lib/python/site-packages/pandas/init.py", line 26 in
File "", line 488 in _call_with_frames_removed
File "", line 995 in exec_module
File "", line 935 in _load_unlocked
File "", line 1331 in _find_and_load_unlocked
File "", line 1360 in _find_and_load
File "/Users/pong/Documents/Study/University/visu/forum_modulo_2.py", line 3 in
Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, PIL._imaging, kiwisolver._cext (total: 4)

Process:               Python [94096]
Path:                  /opt/local/Library/Frameworks/Python.framework/Versions/3.12/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.12.5 (3.12.5)
Code Type:             X86-64 (Native)
Parent Process:        zsh [41124]
Responsible:           Terminal [409]
User ID:               502

Date/Time:             2024-09-05 22:03:29.283 +0700
OS Version:            macOS 11.7.10 (20G1427)
Report Version:        12
Anonymous UUID:        2CFC1131-0466-5E47-269C-67E4356A145B

Sleep/Wake UUID:       1A5221B5-3E73-4275-8B00-A6571F9BF66B

Time Awake Since Boot: 130000 seconds
Time Since Wake:       47000 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x00000000020a9b54
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0x20a9b54:
--> 
    __TEXT                      107c99000-107c9d000    [   16K] r-x/r-x SM=COW  /opt/local/Library/Frameworks/Python.framework/Versions/3.12/Resources/Python.app/Contents/MacOS/Python

Application Specific Information:
/Users/pong/Library/Python/3.12/lib/python/site-packages/pyarrow/libarrow.1700.dylib

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	0x00007fff202e490e __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff203135bd pthread_kill + 263
2   libsystem_c.dylib             	0x00007fff201f7bd5 raise + 26
3   org.python.python             	0x0000000107ec0f4c faulthandler_fatal_error + 395
4   libsystem_platform.dylib      	0x00007fff20358d7d _sigtramp + 29
5   ???                           	000000000000000000 0 + 0
6   libc++.1.dylib                	0x00007fff202aa3d9 std::__1::mutex::lock() + 9
7   libc++.1.dylib                	0x00007fff202ab2d9 std::__1::__shared_mutex_base::lock() + 31
8   libarrow.1700.dylib           	0x0000000115c3a212 arrow::fs::FileSystemFactoryRegistry::RegisterFactory(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, arrow::fs::FileSystemFactory, std::__1::function<void ()>, bool) + 82
9   libarrow.1700.dylib           	0x0000000115c3a72d arrow::fs::FileSystemRegistrar::FileSystemRegistrar(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, arrow::fs::FileSystemFactory, std::__1::function<void ()>) + 285
10  libarrow.1700.dylib           	0x0000000115c817ca _GLOBAL__sub_I_unity_0_cxx.cxx + 154
11  dyld                          	0x0000000113426b47 ImageLoaderMachO::doModInitFunctions(ImageLoader::LinkContext const&) + 535
12  dyld                          	0x0000000113426f52 ImageLoaderMachO::doInitialization(ImageLoader::LinkContext const&) + 40
13  dyld                          	0x0000000113421ae6 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 492
14  dyld                          	0x0000000113421a51 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 343
15  dyld                          	0x0000000113421a51 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 343
16  dyld                          	0x0000000113421a51 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 343
17  dyld                          	0x0000000113421a51 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 343
18  dyld                          	0x0000000113421a51 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 343
19  dyld                          	0x000000011341f89f ImageLoader::processInitializers(ImageLoader::LinkContext const&, unsigned int, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 191
20  dyld                          	0x000000011341f940 ImageLoader::runInitializers(ImageLoader::LinkContext const&, ImageLoader::InitializerTimingList&) + 82
21  dyld                          	0x000000011340fa12 dyld::runInitializers(ImageLoader*) + 82
22  dyld                          	0x000000011341b11a dlopen_internal + 616
23  libdyld.dylib                 	0x00007fff20330c94 dlopen_internal(char const*, int, void*) + 185
24  libdyld.dylib                 	0x00007fff2031f07e dlopen + 28
25  org.python.python             	0x0000000107ebb026 _PyImport_FindSharedFuncptr + 139
26  org.python.python             	0x0000000107e76d62 _PyImport_LoadDynamicModuleWithSpec + 500
27  org.python.python             	0x0000000107e76171 _imp_create_dynamic + 171
28  org.python.python             	0x0000000107d742aa cfunction_vectorcall_FASTCALL + 98
29  org.python.python             	0x0000000107e2f7b0 _PyEval_EvalFrameDefault + 60594
30  org.python.python             	0x0000000107d1df45 object_vacall + 269
31  org.python.python             	0x0000000107d1dde9 PyObject_CallMethodObjArgs + 230
32  org.python.python             	0x0000000107e731ff PyImport_ImportModuleLevelObject + 1097
33  org.python.python             	0x0000000107e2a4c8 _PyEval_EvalFrameDefault + 39370
34  org.python.python             	0x0000000107e20929 PyEval_EvalCode + 304
35  org.python.python             	0x0000000107e1c9b8 builtin_exec + 470
36  org.python.python             	0x0000000107d74380 cfunction_vectorcall_FASTCALL_KEYWORDS + 90
37  org.python.python             	0x0000000107e2f7b0 _PyEval_EvalFrameDefault + 60594
38  org.python.python             	0x0000000107d1df45 object_vacall + 269
39  org.python.python             	0x0000000107d1dde9 PyObject_CallMethodObjArgs + 230
40  org.python.python             	0x0000000107e731ff PyImport_ImportModuleLevelObject + 1097
41  org.python.python             	0x0000000107e2a4c8 _PyEval_EvalFrameDefault + 39370
42  org.python.python             	0x0000000107e20929 PyEval_EvalCode + 304
43  org.python.python             	0x0000000107e1c9b8 builtin_exec + 470
44  org.python.python             	0x0000000107d74380 cfunction_vectorcall_FASTCALL_KEYWORDS + 90
45  org.python.python             	0x0000000107e2f7b0 _PyEval_EvalFrameDefault + 60594
46  org.python.python             	0x0000000107d1df45 object_vacall + 269
47  org.python.python             	0x0000000107d1dde9 PyObject_CallMethodObjArgs + 230
48  org.python.python             	0x0000000107e731ff PyImport_ImportModuleLevelObject + 1097
49  org.python.python             	0x0000000107e2a4c8 _PyEval_EvalFrameDefault + 39370
50  org.python.python             	0x0000000107e20929 PyEval_EvalCode + 304
51  org.python.python             	0x0000000107e1c9b8 builtin_exec + 470
52  org.python.python             	0x0000000107d74380 cfunction_vectorcall_FASTCALL_KEYWORDS + 90
53  org.python.python             	0x0000000107e2f7b0 _PyEval_EvalFrameDefault + 60594
54  org.python.python             	0x0000000107d1df45 object_vacall + 269
55  org.python.python             	0x0000000107d1dde9 PyObject_CallMethodObjArgs + 230
56  org.python.python             	0x0000000107e731ff PyImport_ImportModuleLevelObject + 1097
57  org.python.python             	0x0000000107e2a4c8 _PyEval_EvalFrameDefault + 39370
58  org.python.python             	0x0000000107e20929 PyEval_EvalCode + 304
59  org.python.python             	0x0000000107e1c9b8 builtin_exec + 470
60  org.python.python             	0x0000000107d74380 cfunction_vectorcall_FASTCALL_KEYWORDS + 90
61  org.python.python             	0x0000000107e2f7b0 _PyEval_EvalFrameDefault + 60594
62  org.python.python             	0x0000000107d1df45 object_vacall + 269
63  org.python.python             	0x0000000107d1dde9 PyObject_CallMethodObjArgs + 230
64  org.python.python             	0x0000000107e731ff PyImport_ImportModuleLevelObject + 1097
65  org.python.python             	0x0000000107e2a4c8 _PyEval_EvalFrameDefault + 39370
66  org.python.python             	0x0000000107e20929 PyEval_EvalCode + 304
67  org.python.python             	0x0000000107e98465 run_eval_code_obj + 83
68  org.python.python             	0x0000000107e9643f run_mod + 107
69  org.python.python             	0x0000000107e9581f pyrun_file + 147
70  org.python.python             	0x0000000107e94b1a _PyRun_SimpleFileObject + 291
71  org.python.python             	0x0000000107e9471c _PyRun_AnyFileObject + 66
72  org.python.python             	0x0000000107ebc2ba pymain_run_file_obj + 187
73  org.python.python             	0x0000000107ebc073 pymain_run_file + 89
74  org.python.python             	0x0000000107ebb529 Py_RunMain + 912
75  org.python.python             	0x0000000107ebbb76 pymain_main + 411
76  org.python.python             	0x0000000107ebbc1e Py_BytesMain + 42
77  libdyld.dylib                 	0x00007fff2032ef3d start + 1

Thread 1:
0   libsystem_kernel.dylib        	0x00007fff202e0cbe __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff20313e49 _pthread_cond_wait + 1298
2   libscipy_openblas64_.dylib    	0x000000010963c6ee blas_thread_server + 222
3   libsystem_pthread.dylib       	0x00007fff203138fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff2030f443 thread_start + 15

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x00000001134e0e00  rcx: 0x00007fb2a495f9e8  rdx: 0x0000000000000000
  rdi: 0x0000000000000103  rsi: 0x000000000000000b  rbp: 0x00007fb2a495fa10  rsp: 0x00007fb2a495f9e8
   r8: 0x0000000000000001   r9: 0xcccccccccccccccd  r10: 0x00000001134e0e00  r11: 0x0000000000000246
  r12: 0x0000000000000103  r13: 0x0000000108186c70  r14: 0x000000000000000b  r15: 0x0000000000000016
  rip: 0x00007fff202e490e  rfl: 0x0000000000000246  cr2: 0x0000000107eab6e9
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133

Thread 0 instruction stream:
  48 89 f3 49 89 fe 48 8d-3d 51 ee 2f 60 be 00 00  H..I..H.=Q./`...
  05 00 e8 3d 7e 00 00 b8-00 01 00 00 48 8d 0d 47  ...=~.......H..G
  ee 2f 60 48 83 3c c1 00-74 12 48 ff c0 48 3d 00  ./`H.<..t.H..H=.
  03 00 00 75 ee bb 23 00-00 00 eb 0c 48 f7 d3 48  ...u..#.....H..H
  89 1c c1 49 89 06 31 db-48 8d 3d 0f ee 2f 60 e8  ...I..1.H.=../`.
  06 7e 00 00 89 d8 5b 41-5e 5d c3 90 55 48 89 e5  .~....[A^]..UH..
 [48]81 3f 5a 54 55 4d 75-73 8b 47 0c 89 c1 81 e1  H.?ZTUMus.G.....	<==
  c0 01 00 00 83 f9 40 74-6b 0f ba e0 0e 72 6d 48  [email protected]
  8d 57 27 48 83 e2 f8 48-8b 0a f6 c1 02 75 45 4c  .W'H...H.....uEL
  8d 57 1f 49 83 e2 f8 65-4c 8b 04 25 f8 ff ff ff  .W.I...eL..%....
  49 b9 00 00 00 00 ff ff-ff ff 48 89 ce f6 c1 02  I.........H.....
  75 22 4c 21 ce 89 c8 48-09 f0 83 c9 02 48 09 f1  u"L!...H.....H..
  
Thread 0 last branch register state not available.


Binary Images:
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    0x7fff2accf000 -     0x7fff2acd9fff  libChineseTokenizer.dylib (37.1) <62BC78D3-1400-3366-A04E-C8BEE6AC00B5> /usr/lib/libChineseTokenizer.dylib
    0x7fff2acda000 -     0x7fff2ad97fff  libvMisc.dylib (760.100.3) <560739C2-D16B-36CA-89F4-BD4DD2192333> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
    0x7fff2d8f8000 -     0x7fff2d8f8fff  liblaunch.dylib (2038.120.1.701.2) <B79B00B1-954F-3EC4-9E22-A24E25CAE88D> /usr/lib/system/liblaunch.dylib
    0x7fff2fd94000 -     0x7fff2fd94fff  libsystem_product_info_filter.dylib (8.40.1) <BB06C92C-6BD7-310C-A176-DC0DCE8D9F2B> /usr/lib/system/libsystem_product_info_filter.dylib
    0x7fff2fe6c000 -     0x7fff2fe6cfff  com.apple.Accelerate.vecLib (3.11 - vecLib 3.11) <F46E0ACF-7524-3CA3-A64A-5DDF6081EB67> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
    0x7fff2fe92000 -     0x7fff2fe92fff  com.apple.CoreServices (1122.45 - 1122.45) <05DA2462-9BFC-38D9-820A-8842710471D6> /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices
    0x7fff3004e000 -     0x7fff3004efff  com.apple.Accelerate (1.11 - Accelerate 1.11) <3D8DECC6-19B3-3A32-98CF-EB07536D1635> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
    0x7fff6b81f000 -     0x7fff6b825fff  libCoreFSCache.dylib (200.12) <B6360761-3B05-35AE-8E0C-F819414FD093> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=749.7M resident=0K(0%) swapped_out_or_unallocated=749.7M(100%)
Writable regions: Total=151.2M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=151.2M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Kernel Alloc Once                    8K        1 
MALLOC                            44.1M       37 
MALLOC guard page                   16K        3 
MALLOC_LARGE (reserved)            384K        2         reserved VM address space (unallocated)
STACK GUARD                          4K        1 
Stack                             16.5M        2 
Stack Guard                          4K        1 
VM_ALLOCATE                       55.0M       27 
VM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)
__DATA                            8039K      209 
__DATA_CONST                      9062K      138 
__DATA_DIRTY                       289K       61 
__LINKEDIT                       530.9M      109 
__OBJC_RO                         70.3M        1 
__OBJC_RW                         2496K        2 
__TEXT                           219.2M      206 
__UNICODE                          588K        1 
shared memory                        8K        2 
===========                     =======  ======= 
TOTAL                            988.3M      804 
TOTAL, minus reserved VM space   956.0M      804 

Model: MacBookAir6,2, BootROM 478.0.0.0.0, 2 processors, Dual-Core Intel Core i5, 1,4 GHz, 4 GB, SMC 2.13f15
Graphics: kHW_IntelHD5000Item, Intel HD Graphics 5000, spdisplays_builtin
Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3230554638454455302D474E2D4620
Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1600 MHz, 0x02FE, 0x45424A3230554638454455302D474E2D4620
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x117), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1680.11)
Bluetooth: Version 8.0.5d7, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SD0128F, 121,33 GB
USB Device: USB 3.0 Bus
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Air, Apple Inc., 23.6

@pitrou
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pitrou commented Sep 5, 2024

@asda10 This does not seem related to this issue, can you open a new issue for it? Also please include a reproducer so that we can try it out ourselves.

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Component: Python Critical Fix Bugfixes for security vulnerabilities, crashes, or invalid data. Type: bug
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