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bluesky / ophyd

hardware abstraction in Python with an emphasis on EPICS
https://blueskyproject.io/ophyd
BSD 3-Clause "New" or "Revised" License
51 stars 79 forks source link

Segfault observed in GitHub Action executing pytest #937

Open danielballan opened 3 years ago

danielballan commented 3 years ago

This might be a one-off, just leaving this here for later reference. Will close if it doesn't come up again in the near future.

Run coverage run --concurrency=thread --parallel-mode -m pytest -v -k "${TEST_CL}"
============================= test session starts ==============================
platform linux -- Python 3.8.6, pytest-6.1.2, py-1.9.0, pluggy-0.13.1 -- /opt/hostedtoolcache/Python/3.8.6/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/ophyd/ophyd, configfile: pytest.ini
collecting ... collected 3604 items / 1802 deselected / 1802 selected

Fatal Python error: Segmentation fault

Thread 0x00007f2ef3fff700 (most recent call first):
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 146 in _debug_monitor
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 870 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Current thread 0x00007f2f10ff9700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/ca.py", line 1132 in write_access
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/ca.py", line 579 in wrapper
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/ca.py", line 1170 in access
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/pv.py", line 275 in force_read_access_rights
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/pv.py", line 48 in wrapped
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/pv.py", line 738 in get_ctrlvars
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/pv.py", line 48 in wrapped
  File "/home/runner/work/ophyd/ophyd/ophyd/_pyepics_shim.py", line 98 in get_all_metadata_blocking
  File "/home/runner/work/ophyd/ophyd/ophyd/_pyepics_shim.py", line 105 in get_metadata_thread
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 45 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f117fa700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 306 in wait
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/queue.py", line 179 in get
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 37 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f11ffb700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 306 in wait
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/queue.py", line 179 in get
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 37 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f127fc700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 306 in wait
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/queue.py", line 179 in get
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 37 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f12ffd700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 306 in wait
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/queue.py", line 179 in get
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 37 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f137fe700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 306 in wait
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/queue.py", line 179 in get
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 37 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f13fff700 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 306 in wait
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/queue.py", line 179 in get
  File "/home/runner/work/ophyd/ophyd/ophyd/_dispatch.py", line 37 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f2f28e1e740 (most recent call first):
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/ca.py", line 999 in create_channel
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/ca.py", line 549 in wrapper
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/pv.py", line 250 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/_pyepics_shim.py", line 56 in __init__
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/epics/pv.py", line 125 in get_pv
  File "/home/runner/work/ophyd/ophyd/ophyd/signal.py", line 801 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/signal.py", line 1308 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 176 in create_component
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 1218 in _instantiate_component
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 225 in __get__
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 759 in <listcomp>
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 759 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/areadetector/plugins.py", line 99 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 176 in create_component
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 1218 in _instantiate_component
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 225 in __get__
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 759 in <listcomp>
  File "/home/runner/work/ophyd/ophyd/ophyd/device.py", line 759 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/areadetector/trigger_mixins.py", line 87 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/areadetector/trigger_mixins.py", line 116 in __init__
  File "/home/runner/work/ophyd/ophyd/ophyd/tests/test_areadetector.py", line 94 in test_basic
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/python.py", line 184 in pytest_pyfunc_call
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/python.py", line 1627 in runtest
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 163 in pytest_runtest_call
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 256 in <lambda>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 310 in from_call
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 255 in call_runtest_hook
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 216 in call_and_report
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 127 in runtestprotocol
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/runner.py", line 110 in pytest_runtest_protocol
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/main.py", line 338 in pytest_runtestloop
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/main.py", line 313 in _main
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/main.py", line 257 in wrap_session
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/main.py", line 306 in pytest_cmdline_main
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/config/__init__.py", line 164 in main
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/_pytest/config/__init__.py", line 187 in console_main
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/pytest/__main__.py", line 5 in <module>
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/coverage/execfile.py", line 247 in run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/coverage/cmdline.py", line 740 in do_run
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/coverage/cmdline.py", line 582 in command_line
  File "/opt/hostedtoolcache/Python/3.8.6/x64/lib/python3.8/site-packages/coverage/cmdline.py", line 865 in main
  File "/opt/hostedtoolcache/Python/3.8.6/x64/bin/coverage", line 8 in <module>
/home/runner/work/_temp/23a3f2c3-5d34-446e-a17f-8e61724051ee.sh: line 1:  4121 Segmentation fault      (core dumped) coverage run --concurrency=thread --parallel-mode -m pytest -v -k "${TEST_CL}"
ophyd/tests/test_areadetector.py::test_basic[pyepics] 
Error: Process completed with exit code 139.
danielballan commented 3 years ago

Not seeing this again after ~10 more runs.