Pytest stall

[douglas-raillard-arm]

a detailed description of the bug or problem you are having

Pytest stalls in some specific conditions:

• running on GitHub action runner or Virtualbox (via vagrant)
• When not setting --log-cli-level
• On some test that uses subprocess to spawn some executable
  When connecting to the pytest process with gdb, I get this backtrace:

#0  futex_wait_cancelable (private=<optimized out>, expected=0, futex_word=0x7fc33a40a5f0) at ../sysdeps/nptl/futex-internal.h:183
#1  __pthread_cond_wait_common (abstime=0x0, clockid=0, mutex=0x7fc33a40a638, cond=0x7fc33a40a5c8) at pthread_cond_wait.c:508
#2  __pthread_cond_wait (cond=0x7fc33a40a5c8, mutex=0x7fc33a40a638) at pthread_cond_wait.c:638
#3  0x00007fc33b69c9a5 in background_thread_sleep (tsdn=<optimized out>, interval=<optimized out>, info=<optimized out>) at src/background_thread.c:232
#4  background_work_sleep_once (ind=0, info=<optimized out>, tsdn=<optimized out>) at src/background_thread.c:307
#5  background_thread0_work (tsd=<optimized out>) at src/background_thread.c:452
#6  background_work (ind=<optimized out>, tsd=<optimized out>) at src/background_thread.c:490
#7  background_thread_entry (ind_arg=<optimized out>) at src/background_thread.c:522
#8  0x00007fc34dfc0609 in start_thread (arg=<optimized out>) at pthread_create.c:477
#9  0x00007fc34e0fc293 in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95

output of pip list from the virtual environment you are using

Package                       Version    Location
----------------------------- ---------- -----------------------
alabaster                     0.7.12
anyio                         3.2.1
argon2-cffi                   20.1.0
async-generator               1.10
attrs                         21.2.0
Babel                         2.9.1
backcall                      0.2.0
bcrypt                        3.2.0
bisector                      1.0        /vagrant/tools/bisector
bleach                        3.3.1
bokeh                         2.3.3
build                         0.5.1
certifi                       2021.5.30
cffi                          1.14.6
charset-normalizer            2.0.3
click                         8.0.1
cloudpickle                   1.6.0
colorama                      0.4.4
colorcet                      2.0.6
cryptography                  3.4.7
cycler                        0.10.0
dask                          2021.7.0
datashader                    0.13.0
datashape                     0.5.2
debugpy                       1.3.0
decorator                     5.0.9
defusedxml                    0.7.1
devlib                        1.3.2.dev1
distributed                   2021.7.0
docutils                      0.16
entrypoints                   0.3
exekall                       1.0        /vagrant/tools/exekall
fsspec                        2021.7.0
future                        0.18.2
fuzzywuzzy                    0.18.0
HeapDict                      1.0.1
holoviews                     1.14.5
idna                          3.2
imagesize                     1.2.0
importlib-metadata            4.6.1
iniconfig                     1.1.1
ipykernel                     6.0.3
ipython                       7.25.0
ipython-genutils              0.2.0
ipywidgets                    7.6.3
jedi                          0.18.0
jeepney                       0.7.0
Jinja2                        3.0.1
json5                         0.9.6
jsonschema                    3.2.0
jupyter-client                6.1.12
jupyter-core                  4.7.1
jupyter-server                1.9.0
jupyterlab                    3.0.16
jupyterlab-pygments           0.1.2
jupyterlab-server             2.6.1
jupyterlab-widgets            1.0.0
keyring                       23.0.1
kiwisolver                    1.3.1
LISA                          2.0
lisa-linux                    2.0.0      /vagrant
llvmlite                      0.36.0
locket                        0.2.1
Louie-latest                  1.3.1
lxml                          4.6.3
Markdown                      3.3.4
MarkupSafe                    2.0.1
matplotlib                    3.4.2
matplotlib-inline             0.1.2
mistune                       0.8.4
msgpack                       1.0.2
multipledispatch              0.6.0
nbclassic                     0.3.1
nbclient                      0.5.3
nbconvert                     6.1.0
nbformat                      5.1.3
nbsphinx                      0.8.6
nest-asyncio                  1.5.1
nose                          1.3.7
notebook                      6.4.0
numba                         0.53.1
numpy                         1.21.1
packaging                     21.0
pandas                        1.3.0
pandocfilters                 1.4.3
panel                         0.12.0
param                         1.11.1
paramiko                      2.7.2
parso                         0.8.2
partd                         1.2.0
pep517                        0.11.0
pexpect                       4.8.0
phantomjs                     1.4.1
pickleshare                   0.7.5
Pillow                        8.3.1
pip                           21.1.3
pip-autoremove                0.9.1
pkg-resources                 0.0.0
pkginfo                       1.7.1
pluggy                        0.13.1
prometheus-client             0.11.0
prompt-toolkit                3.0.19
psutil                        5.8.0
ptyprocess                    0.7.0
py                            1.10.0
pyarrow                       4.0.1
pycparser                     2.20
pyct                          0.4.8
Pygments                      2.9.0
PyNaCl                        1.4.0
pyparsing                     2.4.7
pyrsistent                    0.18.0
pyserial                      3.5
pytest                        6.2.4
python-dateutil               2.8.2
pytz                          2021.1
pyviz-comms                   2.1.0
PyYAML                        5.4.1
pyzmq                         22.1.0
readme-renderer               29.0
requests                      2.26.0
requests-toolbelt             0.9.1
requests-unixsocket           0.2.0
rfc3986                       1.5.0
ruamel.yaml                   0.17.10
ruamel.yaml.clib              0.2.6
scipy                         1.7.0
scp                           0.13.6
SecretStorage                 3.3.1
selenium                      3.141.0
Send2Trash                    1.7.1
setuptools                    57.4.0
six                           1.16.0
sniffio                       1.2.0
snowballstemmer               2.1.0
sortedcontainers              2.4.0
Sphinx                        4.1.1
sphinx-rtd-theme              0.5.2
sphinxcontrib-applehelp       1.0.2
sphinxcontrib-devhelp         1.0.2
sphinxcontrib-htmlhelp        2.0.0
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-plantuml        0.21
sphinxcontrib-qthelp          1.0.3
sphinxcontrib-serializinghtml 1.1.5
sphobjinv                     2.1
tblib                         1.7.0
terminado                     0.10.1
testpath                      0.5.0
toml                          0.10.2
tomli                         1.0.4
toolz                         0.11.1
tornado                       6.1
tqdm                          4.61.2
traitlets                     5.0.5
twine                         3.4.2
typing-extensions             3.10.0.0
urllib3                       1.26.6
wcwidth                       0.2.5
webencodings                  0.5.1
websocket-client              1.1.0
wheel                         0.36.2
widgetsnbextension            3.5.1
wlauto                        3.3.1.dev1
wrapt                         1.12.1
xarray                        0.18.2
zict                          2.0.0
zipp                          3.5.0

pytest and operating system versions

pytest==6.2.4

Host: Archlinux, Linux 5.12.15-arch1-1 #1 SMP PREEMPT Wed, 07 Jul 2021 23:35:29 +0000
Guest: Ubuntu 20.04.2 LTS (Focal Fossa), Linux 5.4.0-77-generic #86-Ubuntu SMP Thu Jun 17 02:35:03 UTC 2021

minimal example if possible

Maybe this is related to that issue (at least the leaf C function matches):
https://forge.softwareheritage.org/D5048

I'll post the setup I'm currently using once I merged the (unrelated) fixes to my Vagrantfile. It's not so minimal but at least it can reproduce the issue (on my machine).

[douglas-raillard-arm]

It looks like passing -s "solves" the problem

[douglas-raillard-arm]

Closing as the issue seems to be coming from a threading.Lock in a library, that should be an RLock. I'm still unsure why it only triggers when capturing the output though ...