Segmentation Fault when using GUI

[heaton-ox-physics]

Hi, I was trying to use LiquidDiffract in GUI mode (ubuntu platform). When changing stoichmetry and charge, the program crashes with a segfault. Using gdb, I traced this back to the PyQt6. I tried downgrading versions (of both LiquidDiffract and PyQt6) but it continued to crash. I've switched to PyQt5 and the seg fault no longer causes a crash. Just wanted to point this out.

[bjheinen]

Thanks for letting me know. This could be a bug upstream in Qt but I will check if we can do anything about it in LiquidDiffract. I can't reproduce this with PyQt6 on my system so it might be platform dependent or something in a very recent package version. Could you post the output of pip freeze?

[heaton-ox-physics]

Hi, thanks for getting back.

So this run failed. I started by setting the QT env variable to PyQt6:
$ export QT_API=PyQt6
$ gdb python3
$ run /path/to/LiquidDiffract

This failed when trying to change the charge state. gdb backtrace (first 5 lines):

Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
0x00007ffff3a3d78b in ?? () from /pathtominiconda/miniconda3/lib/python3.11/site-packages/PyQt6/Qt6/lib/libQt6Widgets.so.6
(gdb) bt
#0 0x00007ffff3a3d78b in ?? () from /pathtominiconda/miniconda3/lib/python3.11/site-packages/PyQt6/Qt6/lib/libQt6Widgets.so.6
#1 0x00007ffff3a424d2 in ?? () from /pathtominiconda/miniconda3/lib/python3.11/site-packages/PyQt6/Qt6/lib/libQt6Widgets.so.6
#2 0x00007ffff3a4427e in ?? () from /pathtominiconda/miniconda3/lib/python3.11/site-packages/PyQt6/Qt6/lib/libQt6Widgets.so.6
#3 0x00007ffff3a2a93b in QApplication::notify(QObject*, QEvent*) () from /pathtominiconda/miniconda3/lib/python3.11/site-packages/PyQt6/Qt6/lib/libQt6Widgets.so.6
#4 0x00007ffff43a265e in sipQApplication::notify(QObject*, QEvent*) () from /pathtominiconda/miniconda3/lib/python3.11/site-packages/PyQt6/QtWidgets.abi3.so

Pip freeze is exhaustive for completeness but the main ones are:

scipy==1.16.0
numpy==2.3.1
lmfit==1.3.3
LiquidDiffract==1.2.5
PyQt6==6.9.1
PyQt6-Qt6==6.9.1
PyQt6_sip==13.10.2
QtPy==2.4.3
pyqtgraph==0.13.7

$python3 -m pip freeze

archspec==0.2.5
ase @ file:///home/conda/feedstock_root/build_artifacts/ase_1744459813439/work
asteval==1.0.6
bibtexparser==1.4.3
blinker @ file:///croot/blinker_1737448726027/work
boltons==25.0.0
Bottleneck==1.5.0
Brotli==1.1.0
castepxbin==0.3.0
certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1749972191589/work/certifi
cffi==1.17.1
charset-normalizer==3.4.2
click==8.2.1
colormath @ file:///home/conda/feedstock_root/build_artifacts/colormath_1735759840625/work
conda @ file:///home/conda/feedstock_root/build_artifacts/conda_1736947889204/work
conda-content-trust @ file:///croot/conda-content-trust_1693490622020/work
conda-libmamba-solver @ file:///croot/conda-libmamba-solver_1702997573971/work/src
conda-package-handling==2.4.0
conda_package_streaming==0.12.0
contourpy==1.3.2
cryptography==45.0.5
cycler==0.12.1
dill==0.4.0
distro==1.9.0
Flask==3.1.1
fonttools==4.58.5
frozendict==2.4.6
future @ file:///croot/future_1730902796226/work
gmpy2 @ file:///croot/gmpy2_1738085463648/work
gpaw @ file:///home/conda/feedstock_root/build_artifacts/gpaw_1717499103727/work
h5py==3.14.0
idna==3.10
importlib_resources==6.5.2
itsdangerous @ file:///croot/itsdangerous_1716533337253/work
Jinja2 @ file:///croot/jinja2_1741710844255/work
joblib==1.5.1
jsonpatch==1.33
jsonpointer==3.0.0
kiwisolver @ file:///croot/kiwisolver_1737039087198/work
latexcodec==3.0.1
libmambapy @ file:///croot/mamba-split_1698782620632/work/libmambapy
LiquidDiffract==1.2.5
lmfit==1.3.3
MarkupSafe @ file:///croot/markupsafe_1738584038848/work
matplotlib==3.10.3
menuinst @ file:///croot/menuinst_1702390294373/work
monty @ file:///home/conda/feedstock_root/build_artifacts/monty_1741071865066/work
mpmath @ file:///croot/mpmath_1690848262763/work
narwhals==1.45.0
networkx==3.5
numexpr==2.11.0
numpy==2.3.1
orjson==3.10.18
packaging==25.0
palettable==3.3.3
pandas==2.3.0
phonopy==2.41.1
pillow==11.3.0
pip-review==1.3.0
platformdirs==4.3.8
plotly==6.2.0
pluggy==1.6.0
pybtex==0.25.1
pycosat @ file:///croot/pycosat_1696536503704/work
pycparser==2.22
pymatgen==2025.6.14
pyOpenSSL==25.1.0
pyparsing==3.2.3
PyQt5==5.15.11
PyQt5-Qt5==5.15.17
PyQt5_sip==12.17.0
PyQt6==6.9.1
PyQt6-Qt6==6.9.1
PyQt6_sip==13.10.2
pyqtgraph==0.13.7
PySocks @ file:///work/ci_py311/pysocks_1676822712504/work
python-dateutil @ file:///croot/python-dateutil_1716495738603/work
pytz==2025.2
PyYAML @ file:///croot/pyyaml_1728657952215/work
QtPy==2.4.3
requests==2.32.4
ruamel.yaml==0.18.14
ruamel.yaml.clib==0.2.12
scipy==1.16.0
seekpath @ file:///home/conda/feedstock_root/build_artifacts/seekpath_1734291626863/work
sif-parser==0.3.5
six @ file:///croot/six_1744271502820/work
spglib @ file:///home/conda/feedstock_root/build_artifacts/spglib_1741599968635/work
sumo @ file:///home/conda/feedstock_root/build_artifacts/sumo_1746667759564/work
symfc==1.5.0
sympy==1.14.0
tabulate @ file:///croot/tabulate_1701354810597/work
tqdm==4.67.1
truststore==0.10.1
typing_extensions==4.14.1
tzdata @ file:///croot/python-tzdata_1746123641790/work
uncertainties @ file:///home/conda/feedstock_root/build_artifacts/uncertainties_1745274325800/work
unicodedata2==16.0.0
urllib3==2.5.0
Werkzeug @ file:///croot/werkzeug_1737448706492/work
zstandard==0.23.0

[bjheinen]

Thanks for the extra info. I can't reproduce this on my machine using that pip-freeze so it might be something specific to your machine/config. If you have the time for more debugging then running valgrind might give a bit more info ('valgrind --track-origins=yes --leak-check=full --show-leak-kinds=all LiquidDiffract' - it will run v slow!).

I'll add some more safeguards in that bit of the gui in case there's something in there that's causing the segfault. I'll leave the issue open for now.