[0.11] Segmentation fault on tests
olebole opened this issue · comments
Forwarding Debian#1026594:
Since a few weeks, the package produces a segmentation fault when running the tests:
autopkgtest [11:23:37]: test command1: cd $AUTOPKGTEST_TMP && python3 -m pytest --pyargs fast_histogram
autopkgtest [11:23:37]: test command1: [-----------------------
============================= test session starts ==============================
platform linux -- Python 3.11.1, pytest-7.2.0, pluggy-1.0.0+repack
rootdir: /tmp/autopkgtest-lxc.adqdcee1/downtmp/autopkgtest_tmp
plugins: hypothesis-6.61.0
collected 9 items
tests/test_histogram.py FFatal Python error: Segmentation fault
Current thread 0x00007f633c836040 (most recent call first):
Garbage-collecting
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/data.py", line 850 in __init__
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 891 in new_conjecture_data
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 1031 in cached_test_function
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 803 in generate_mutations_from
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 733 in generate_new_examples
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 880 in _run
File "/usr/lib/python3/dist-packages/hypothesis/internal/conjecture/engine.py", line 474 in run
File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 884 in run_engine
File "/usr/lib/python3/dist-packages/hypothesis/core.py", line 1292 in wrapped_test
File "/usr/lib/python3/dist-packages/fast_histogram/tests/test_histogram.py", line 78 in test_2d_compare_with_numpy
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 195 in pytest_pyfunc_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1789 in runtest
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 167 in pytest_runtest_call
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 260 in <lambda>
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 339 in from_call
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in call_runtest_hook
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 220 in call_and_report
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 131 in runtestprotocol
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 112 in pytest_runtest_protocol
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 349 in pytest_runtestloop
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 324 in _main
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 270 in wrap_session
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 317 in pytest_cmdline_main
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in __call__
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 167 in main
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 190 in console_main
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 in <module>
File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>", line 198 in _run_module_as_main
Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, fast_histogram._histogram_core, numpy.linalg.lapack_lite (total: 15)
Segmentation fault
This happens with both Python3.10.9 and 3.11.1. Other versions:
- hypothesis 6.60.0, 6.61.0 (6.36.0 works!)
- numpy 1.23.5, 1.24.1
- pytest 7.2.0,
- pluggy 1.0.0
This happens both when running during the build (log) and when testing with python3 -m pytest --pyargs fast_histogram on the installed package (log).
Any idea here? This seems to be a regression with newer "hypothesis" versions; however hypothesis itself is a pure Python package and therefore should not cause a segfault.
fast-histogram is used by quite a few packages; I'd like to keep it (and the packages that depend on it) in Debian. Shall I just pragmatically disable the tests?
Will try and investigate shortly - I am guessing this is a new hypothesis test case that is segfaulting
Running into a similar issue in spacetelescope/jdaviz#2498 when using the histogram viewer from glue-jupyter. If this isn't directly related, feel free to split into a separate issue.
Current thread 0x00007f4c96c5ec40 (most recent call first):
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/fast_histogram/histogram.py", line 58 in histogram1d
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue/core/data.py", line 2021 in compute_histogram
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue/viewers/histogram/state.py", line 254 in update_histogram
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue/viewers/histogram/state.py", line 217 in histogram
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue_jupyter/bqplot/histogram/layer_artist.py", line 51 in _calculate_histogram
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue_jupyter/bqplot/histogram/layer_artist.py", line 142 in _update_histogram
File "/home/runner/work/jdaviz/jdaviz/.tox/py311-test-alldeps-cov/lib/python3.11/site-packages/glue_jupyter/bqplot/histogram/layer_artist.py", line 153 in update
...
@kecnry would you be able to print out or save the arguments being passed to histogram1d that are causing the segfault?
It seems that it was caused (on our end) by passing arrays of length 1 to the histogram. We can just prevent passing these for now with a workaround, but it would be great if this could either be gracefully handled or raise an error instead of resulting in a segfault.