[BUG-REPORT] Hitting `pybind11::handle::inc_ref()` when using NumPy 1.26 with vaex 4.18.0

[setu4993]

Description

All our unit tests and validations which worked fine on v4.17.1 started failing upon updating to v4.18.0. Curiously, this is occurring only on GitHub Actions so far (ubuntu-latest images) and not reproducible on M-series MacBooks. I suspect this is limited to some instruction sets.

I don't have a great sample right now (but can get one tomorrow) to reproduce this, but the CI run here might be helpful to compare the diff. This is occurring across repos but this public one was the easiest to link to.

Software information

• Vaex version (import vaex; vaex.__version__): 4.18.0
• Vaex was installed via: pip / conda-forge / from source: pip
• OS: GitHub Actions, ubuntu-latest

[iisakkirotko]

I think we're running into the same issue in this run at widgetti/solara. We also see an error on windows: Windows fatal exception: access violation resulting in a seg fault.

The full log for Windows

```bash Thread 0x00000694 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\hash.py", line 171 in add File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\cpu.py", line 344 in process File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\execution.py", line 564 in process_tasks File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\execution.py", line 500 in process_part File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\multithreading.py", line 80 in wrapped File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\concurrent\futures\thread.py", line 58 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\concurrent\futures\thread.py", line 83 in _worker File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 917 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Current thread 0x00000b14 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\hash.py", line 171 in add File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\cpu.py", line 344 in process File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\execution.py", line 564 in process_tasks File "Windows fatal exception: C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\execution.pyaccess violation" , line 500 in process_part File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\vaex\multithreading.py", line 80 in wrapped File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\concurrent\futures\thread.py", line 58 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\concurrent\futures\thread.py", line 83 in _worker File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 917 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00001810 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 316 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 581 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 1304 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00001468 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x000004cc (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line [38](https://github.com/widgetti/solara/actions/runs/11138736498/job/30955789237#step:9:39)0 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00000a44 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x000019ec (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x0000130c (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00000798 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00000b18 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00001ff0 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00001074 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00000958 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00001a84 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00000f34 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x000018e4 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00001b6c (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 67 in _read_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\read_directory_changes.py", line 70 in queue_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 158 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x000013e4 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 312 in wait File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\queue.py", line 171 in get File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 379 in dispatch_events File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\api.py", line 213 in run File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 980 in _bootstrap_inner File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\threading.py", line 937 in _bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 306 in _WidgetContextAwareThread__bootstrap File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\solara\server\patch.py", line 284 in WidgetContextAwareThread__bootstrap Thread 0x00000e08 (most recent call first): File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 326 in read_directory_changes File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\watchdog\observers\winapi.py", line 380 in read_events File 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File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\_pytest\main.py", line 330 in pytest_cmdline_main File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\pluggy\_callers.py", line 103 in _multicall File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\pluggy\_manager.py", line 120 in _hookexec File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\pluggy\_hooks.py", line 513 in __call__ File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\_pytest\config\__init__.py", line 175 in main File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\site-packages\_pytest\config\__init__.py", line 201 in console_main File "C:\hostedtoolcache\windows\Python\3.9.13\x64\Scripts\pytest.exe\__main__.py", line 7 in File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\runpy.py", line 87 in _run_code File "C:\hostedtoolcache\windows\Python\3.9.13\x64\lib\runpy.py", line 197 in _run_module_as_main D:\a\_temp\691c007b-3684-4dbd-aff5-fd213c6997ea.sh: line 3: 9[56](https://github.com/widgetti/solara/actions/runs/11138736498/job/30955789237#step:9:57) Segmentation fault pytest tests/unit --doctest-modules --timeout=60 ```

• Vaex version: 4.18.0
• Vaex was installed via: pip / conda-forge / from source: pip
• OS: GitHub Actions, ubuntu-latest and windows-latest

[maartenbreddels]

The relevant part of the logs:

self = <vaex.hash.HashMapUnique object at 0x7fe128022ee0>

    def flatten(self):
        if self.dtype == object:
            return self # already flat
>       keys = self._internal.key_array()
E       RuntimeError: pybind11::handle::inc_ref() PyGILState_Check() failure.

/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/vaex/hash.py:78: RuntimeError
----------------------------- Captured stderr call -----------------------------
pybind11::handle::inc_ref() is being called while the GIL is either not held or invalid. Please see https://pybind11.readthedocs.io/en/stable/advanced/misc.html#common-sources-of-global-interpreter-lock-errors for debugging advice.
The failing pybind11::handle::inc_ref() call was triggered on a numpy.ndarray object.

I think this is a bug in vaex-core which only gets exposed now due to upgrading pybind11. We should write a test to expose this, and see if we can reproduce this in CI. I think we should yank the vaex-core release to avoid other people hitting this.

[setu4993]

+1, yanking seems like a good idea if this is arising from vaex-core.

[maartenbreddels]

it's yanked

[maartenbreddels]

I could not reproduce this on a local ubuntu machine with Python 3.11, but i'll continue to see if I can reproduce it (help is welcome)

[ddelange]

I googled RuntimeError: pybind11::handle::inc_ref() PyGILState_Check() failure and blamed it onto the following release from 2022 (3rd bullet point):

https://github.com/pybind/pybind11/releases/tag/v2.10.2

looks like the end-user can disable these checks using environment variables although it does look like a valid point made in the PR description

[maartenbreddels]

Update: We do not build with -DNDEBUG when we use cibuildwheel, but in a regular build we do pass this to the compiler. This causes our release to be shipped with this check, while in our CI we do not have this check. This is the exact opposite of what we want.

I'm not sure why this is, and who sets this (layers of abstraction are not always great...)

[maartenbreddels]

See https://github.com/vaexio/vaex/pull/2440

[ddelange]

https://pypi.org/project/vaex-core/4.18.1/

[setu4993]

Thank you!