[CI][Python] test_plasma crashes

[asfimport]

test_plasma has started crashing on various CI configurations recently: Debian Python, Ubuntu Python but also macOS Python.

Example test log: https://dev.azure.com/ursacomputing/crossbow/_build/results?buildId=25782&view=logs&j=0da5d1d9-276d-5173-c4c4-9d4d4ed14fdb&t=d9b15392-e4ce-5e4c-0c8c-b69645229181&l=9148

Reporter: Antoine Pitrou / @pitrou

_{Note: This issue was originally created as ARROW-16593. Please see the migration documentation for further details.}

[asfimport]

Antoine Pitrou / @pitrou:
Here is the test log once pytest buffering is disabled:

/arrow/cpp/src/plasma/store.cc:1297: Starting object store with directory /dev/shm and huge page support disabled
/arrow/cpp/src/plasma/io.cc:177: Connection to IPC socket failed for pathname unknown-store-name, retrying 1 more times
Fatal Python error: Python memory allocator called without holding the GIL
Python runtime state: initialized

Current thread 0x00007fac00edb740 (most recent call first):
  File "/usr/local/lib/python3.8/dist-packages/pyarrow/tests/test_plasma.py", line 119 in test_connection_failure_raises_exception
  File "/usr/local/lib/python3.8/dist-packages/_pytest/python.py", line 192 in pytest_pyfunc_call
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/local/lib/python3.8/dist-packages/_pytest/python.py", line 1761 in runtest
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 166 in pytest_runtest_call
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 259 in <lambda>
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 338 in from_call
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 258 in call_runtest_hook
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 219 in call_and_report
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 130 in runtestprotocol
  File "/usr/local/lib/python3.8/dist-packages/_pytest/runner.py", line 111 in pytest_runtest_protocol
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/local/lib/python3.8/dist-packages/_pytest/main.py", line 347 in pytest_runtestloop
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/local/lib/python3.8/dist-packages/_pytest/main.py", line 322 in _main
  File "/usr/local/lib/python3.8/dist-packages/_pytest/main.py", line 268 in wrap_session
  File "/usr/local/lib/python3.8/dist-packages/_pytest/main.py", line 315 in pytest_cmdline_main
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_callers.py", line 39 in _multicall
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/usr/local/lib/python3.8/dist-packages/pluggy/_hooks.py", line 265 in __call__
  File "/usr/local/lib/python3.8/dist-packages/_pytest/config/__init__.py", line 164 in main
  File "/usr/local/lib/python3.8/dist-packages/_pytest/config/__init__.py", line 187 in console_main
  File "/usr/local/bin/pytest", line 8 in <module>
/arrow/cpp/src/plasma/store.cc:754: Disconnecting client on fd 7
/arrow/cpp/src/plasma/store.cc:754: Disconnecting client on fd 6
/arrow/ci/scripts/python_test.sh: line 55: 15097 Aborted                 (core dumped) pytest -r s -vs ${PYTEST_ARGS} --pyargs pyarrow.tests.test_plasma

[asfimport]

Antoine Pitrou / @pitrou:
Looks like a Cython bug appeared in 0.29.29 (0.29.28 is fine).

[asfimport]

Antoine Pitrou / @pitrou:
Filed cython/cython#4796

[asfimport]

Antoine Pitrou / @pitrou:
We may or may not want to pin Cython in the meantime. @raulcd @kou

(my experience is that the Cython developers are quite reactive)

[asfimport]

Raúl Cumplido / @raulcd:
I was able to reproduce locally and had a branch pinning the version ready but I saw it was being dealt with on the Cython repo already. I have tested now that the new Cython version with the fix 0.29.30 has been published:

#11 1.250 Collecting cython>=0.29
#11 1.351   Downloading Cython-0.29.30-py2.py3-none-any.whl (985 kB)

All tests are passing now, the issue is solved. I am not sure if I should manually Resolve or Close the issue on this case so I'll let someone else do it.

[asfimport]

Kouhei Sutou / @kou:
I don't think that we need to pin Cython.
I think that we should report a problem to Cython instead of pinning Cython like this case.

[asfimport]

Antoine Pitrou / @pitrou:

I have tested now that the new Cython version with the fix 0.29.30 has been published:
Wow, that was quick.