woutdenolf
commented
1 year ago The data being send to the dialog in ErrorReporting.handle_exception looks like this (see below). When I create an exception and replace the data with that dictionary, the dialog pops up as expected. So the segfault does not seem to be caused by the data send to the dialog.
data = OrderedDict(
[
(
"Exception",
"ValueError: Array passed to NMF (input W) is full of zeros.",
),
("Module", "sklearn.decomposition._nmf:67"),
("Version", "3.36.0.dev"),
(
"Environment",
"Python 3.8.5 on Linux 5.4.0-155-generic #172-Ubuntu SMP Fri Jul 7 16:10:02 UTC 2023 x86_64",
),
(
"Installed Packages",
"AnyQt==0.2.0, Automat==22.10.0, Babel==2.10.3, Bottleneck==1.3.5, CacheControl==0.12.11, CoilMQ==1.0.1, Cython==0.29.32, Deprecated==1.2.13, Flask-Cors==3.0.10, Flask-RESTful==0.3.9, Flask-SocketIO==5.2.0, Flask==2.2.5, Glymur==0.12.0, HeapDict==1.0.1, Jinja2==3.1.2, JsonForm==0.0.2, JsonSir==0.0.2, Mako==1.2.3, MarkupSafe==2.1.1, Orange3==3.36.0.dev0+92d84ee, PeakUtils==1.3.4, Pillow==9.2.0, Pint==0.19.2, PyCifRW==4.4.3, PyMca5==5.8.7, PyOpenGL==3.1.6, PyQt5-Qt5==5.15.2, PyQt5-sip==12.11.0, PyQt5==5.15.9, PyQtWebEngine-Qt5==5.15.2, PyQtWebEngine==5.15.6, PyWavelets==1.4.1, PyYAML==5.4.1, Pygments==2.13.0, Python-EasyConfig==0.1.7, QtPy==2.2.1, Resource==0.2.1, SQLAlchemy==1.4.41, SecretStorage==3.3.3, Send2Trash==1.8.0, StrEnum==0.4.9, Twisted==22.10.0, Werkzeug==2.2.3, XlsxWriter==3.0.3, accessible-pygments==0.0.4, alabaster==0.7.12, algopy==0.5.7, amqp==5.1.1, aniso8601==9.0.1, ansiwrap==0.8.4, anyio==3.6.1, apispec==5.2.2, appdirs==1.4.4, argon2-cffi-bindings==21.2.0, argon2-cffi==21.3.0, arrow==1.2.3, asteval==0.9.27, asttokens==2.0.8, async-lru==2.0.3, async-timeout==4.0.2, attrs==23.1.0, backcall==0.2.0, backports.zoneinfo==0.2.1, baycomp==1.0.2, beautifulsoup4==4.11.1, bes==1.0.0rc1, bidict==0.22.0, billiard==4.0.2, black==23.1.0, bleach==5.0.1, blinker==1.6.2, blissdata==0.3.2, blissdemo==0.1.0, blissoda==0.0.1a0, bokeh==2.4.3, cattrs==23.1.2, celery==5.3.0b1, certifi==2022.9.24, cffi==1.15.1, chardet==5.0.0, charset-normalizer==2.1.1, circle-fit==0.1.3, click-didyoumean==0.3.0, click-plugins==1.1.1, click-repl==0.2.0, click==8.1.3, cloudpickle==2.2.0, colorama==0.4.5, commonmark==0.9.1, conda-souschef==2.2.3, constantly==15.1.0, contourpy==1.0.5, cryptography==38.0.1, cycler==0.11.0, darfix==0.10.0, dask-jobqueue==0.8.1, dask==2023.3.1, debugpy==1.6.3, decorator==5.1.1, defusedxml==0.7.1, dictdiffer==0.9.0, dicttoxml==1.7.16, distributed==2023.3.1, distro==1.8.0, docopt==0.6.2, docutils==0.19, easistrain==0.0.6, edna2==1.0.0rc1, edna==1.0rc1, emmet-core==0.38.6, entrypoints==0.4, est==0.5.1, et-xmlfile==1.1.0, ewoks==0.3.0, ewokscore==0.7.0, ewoksdask==0.1.0rc2, ewoksdata==0.2.7, ewoksfluo==0.0.1a0, ewoksid11==0.0.1a0, ewoksid22==0.0.2rc0, ewoksid31==0.0.1a0, ewoksixs==0.0.1a0, ewoksjob==0.2.5, ewoksndreg==0.0.1a1, ewoksorange==0.1.4, ewoksorangetemplate==0.0.1a0, ewoksppf==0.1.3, ewokspr==0.0.1, ewoksserver==0.2.0, ewoksutils==0.1.2, ewoksweb==0.1.0rc4, ewoksxrpd==0.3.0, exceptiongroup==1.1.2, executing==1.1.0, fabio==0.11.0, fastjsonschema==2.16.2, fisx==1.3.0, flake8-nb==0.5.2, flake8==5.0.4, flask-apispec==0.11.4, flower==1.2.0, fonttools==4.37.4, fqdn==1.5.1, fsspec==2022.8.2, future==0.18.2, geometricopticssimulation==0.0.1a0, gevent==22.10.2, graphviz==0.20.1, graypy==2.1.0, grayskull==1.8.3, greenlet==2.0.0, gunicorn==20.1.0, h11==0.12.0, h5grove==1.3.0, h5py==3.7.0, hdf5plugin==3.3.1, httpcore==0.15.0, httpx==0.23.0, humanize==4.4.0, hyperlink==21.0.0, idna==3.4, imageio==2.22.1, imagesize==1.4.1, importlib-metadata==5.0.0, importlib-resources==5.10.0, incremental==22.10.0, iniconfig==1.1.1, ipykernel==6.16.0, ipython-genutils==0.2.0, ipython==8.5.0, ipywidgets==8.0.2, isoduration==20.11.0, isort==5.10.1, itsdangerous==2.1.2, ixstools==2021a0, jaraco.classes==3.2.3, jedi==0.18.1, jeepney==0.8.0, joblib==1.2.0, json-rpc==1.13.0, json5==0.9.10, jsonpickle==2.2.0, jsonpointer==2.4, jsonrpc==3.0.1, jsonschema-specifications==2023.7.1, jsonschema==4.18.4, jupyter-client==8.3.0, jupyter-contrib-core==0.4.2, jupyter-contrib-nbextensions==0.7.0, jupyter-core==5.3.1, jupyter-events==0.6.3, jupyter-highlight-selected-word==0.2.0, jupyter-lsp==2.2.0, jupyter-nbextensions-configurator==0.6.1, jupyter-server-terminals==0.4.4, jupyter-server==2.7.0, jupyterlab-h5web==10.0.0, jupyterlab-pygments==0.2.2, jupyterlab-server==2.23.0, jupyterlab-spellchecker==0.7.3, jupyterlab-widgets==3.0.3, jupyterlab==4.0.3, keyring==23.9.3, keyrings.alt==4.2.0, kiwisolver==1.4.4, kombu==5.3.1, latexcodec==2.0.1, lazy-loader==0.2, livereload==2.6.3, lmfit==1.0.3, locket==1.0.0, lockfile==0.12.2, lxml==4.9.1, markdown-it-py==3.0.0, marshmallow==3.18.0, matplotlib-inline==0.1.6, matplotlib==3.5.0, mccabe==0.7.0, mdit-py-plugins==0.4.0, mdurl==0.1.2, memory-profiler==0.61.0, memray==1.5.0, mirakuru==2.4.2, mistune==2.0.4, mock==5.0.1, mongita==1.1.1, monty==2022.9.9, more-itertools==9.0.0, mp-api==0.29.3, mpmath==1.2.1, msgpack==1.0.4, multianalyzer==0.4.0, mypy-extensions==0.4.3, mypy==0.982, myst-parser==2.0.0, nabu==2022.2.0rc5, nbclassic==0.4.5, nbclient==0.7.0, nbconvert==7.2.10, nbformat==5.6.1, nbsphinx-link==1.3.0, nbsphinx==0.8.9, nest-asyncio==1.5.6, networkx==2.8.7, notebook-shim==0.2.0, notebook==6.5.1, numdifftools==0.9.40, numexpr==2.8.3, numpy==1.24.3, nxtomomill==0.12.3, objgraph==3.5.0, openTSNE==0.6.2, opencv-python==4.3.0.36, openpyxl==3.0.10, orange-canvas-core==0.1.32.dev0, orange-widget-base==4.22.0.dev0+ebc5230, orjson==3.9.2, overrides==7.3.1, packaging==23.0, palettable==3.3.0, pandas==1.4.4, pandoc==2.2, pandocfilters==1.5.0, papermill==2.4.0, parso==0.8.3, partd==1.3.0, pathspec==0.10.1, patsy==0.5.3, pexpect==4.8.0, pickleshare==0.7.5, pid==3.0.4, pip==23.1.2, pkginfo==1.8.3, pkgutil-resolve-name==1.3.10, platformdirs==2.5.2, plotly==5.11.0, pluggy==1.0.0, plumbum==1.8.0, ply==3.11, port-for==0.6.2, processview==1.2.0, progressbar2==4.0.0, prometheus-client==0.15.0, prompt-toolkit==3.0.31, psutil==5.9.2, ptyprocess==0.7.0, pure-eval==0.2.2, py==1.11.0, pyOpenSSL==22.1.0, pyaml==21.10.1, pyasn1-modules==0.2.8, pyasn1==0.4.8, pybtex==0.24.0, pycodestyle==2.9.1, pycparser==2.21, pydantic==1.10.2, pydata-sphinx-theme==0.13.3, pyee==8.2.2, pyfai==2023.5.0, pyflakes==2.5.0, pyicat-plus==0.1.5, pymatgen==2022.10.22, pymca==5.8.7, pymongo==3.10.1, pyopencl==2022.2.3, pyparsing==3.0.9, pyppeteer==1.0.2, pypushflow==0.5.0, pyqtgraph==0.13.1, pyrsistent==0.18.1, pyshortcuts==1.8.2, pyslurmutils==0.0.6b0, pytango==9.4.1, pytest-asyncio==0.20.1, pytest-celery==0.0.0, pytest-mock==3.10.0, pytest-redis==2.4.0, pytest-subtests==0.8.0, pytest-timeout==2.1.0, pytest==7.1.3, python-daemon==3.0.1, python-dateutil==2.8.2, python-engineio==4.3.4, python-json-logger==2.0.7, python-louvain==0.16, python-socketio==5.7.1, python-utils==3.3.3, pytools==2022.1.12, pytz==2022.4, pyzmq==24.0.1, qasync==0.23.0, qtconsole==5.3.2, rapidfuzz==2.11.1, readme-renderer==37.2, recommonmark==0.7.1, redis==4.5.4, referencing==0.30.0, requests-cache==1.1.0, requests-toolbelt==0.10.0, requests==2.28.1, rfc3339-validator==0.1.4, rfc3986-validator==0.1.1, rfc3986==1.5.0, rich==12.6.0, rpds-py==0.9.2, rsyncmanager==0.1.2, ruamel.yaml.clib==0.2.6, ruamel.yaml.jinja2==0.2.7, ruamel.yaml==0.17.21, scikit-image==0.20.0, scikit-learn==1.1.2, scipy==1.9.1, serverfiles==0.3.1, service-identity==21.1.0, setuptools-scm==7.0.5, setuptools==67.8.0, silx==1.1.2, simple-websocket==0.8.1, six==1.16.0, sluurp==0.2.0, sniffio==1.3.0, snowballstemmer==2.2.0, sortedcontainers==2.4.0, soupsieve==2.3.2.post1, spglib==2.0.1, sphinx-autobuild==2021.3.14, sphinx-autodoc-typehints==1.19.4, sphinx-book-theme==1.0.1, sphinx-design==0.4.1, sphinx==6.1.1, sphinxcontrib-applehelp==1.0.2, sphinxcontrib-devhelp==1.0.2, sphinxcontrib-htmlhelp==2.0.0, sphinxcontrib-jsmath==1.0.1, sphinxcontrib-mermaid==0.7.1, sphinxcontrib-qthelp==1.0.3, sphinxcontrib-serializinghtml==1.1.5, srxraylib==1.0.39, stack-data==0.5.1, statsmodels==0.13.2, stdlib-list==0.8.0, stomp.py==8.1.0, stompest==2.3.0, streamline-changer==0.0.1a0, suds==1.1.2, sympy==1.11.1, syned==1.0.27, tabulate==0.9.0, tblib==1.7.0, tenacity==8.1.0, termcolor==2.0.1, terminado==0.16.0, testbook==0.4.2, textwrap3==0.9.2, threadpoolctl==3.1.0, tifffile==2022.10.10, tinycss2==1.1.1, tokenize-rt==5.0.0, toml==0.10.2, tomli-w==1.0.0, tomli==2.0.1, tomoscan==1.1.5, tomwer==1.1.2, toolz==0.12.0, tornado==6.2, tqdm==4.64.1, traitlets==5.9.0, twine==4.0.2, typing-extensions==4.4.0, tzdata==2023.3, uncertainties==3.1.7, uri-template==1.3.0, url-normalize==1.4.3, urllib3==1.26.12, vine==5.0.0, wcwidth==0.2.5, webargs==8.2.0, webcolors==1.13, webencodings==0.5.1, websocket-client==1.4.1, websockets==10.4, wheel==0.38.4, widgetsnbextension==4.0.3, wofry==1.0.31, wrapt==1.14.1, wsproto==1.2.0, xlrd==2.0.1, xmltodict==0.13.0, xraydb==4.4.7, xraylarch==0.9.65, xyzservices==2023.2.0, zict==2.2.0, zipp==3.8.1, zope.event==4.5.0, zope.interface==5.4.0",
),
("Machine ID", "f5978952-26af-4d35-86c5-b44aaa96886f"),
(
"Stack Trace",
'Traceback (most recent call last):\n File "/home/denolf/dev/darfix/src/darfix/gui/operationThread.py", line 32, in run\n self.data = self.func(*self.args, **self.kwargs)\n File "/home/denolf/dev/darfix/src/darfix/core/dataset.py", line 1632, in nica_nmf\n return self.nmf(\n File "/home/denolf/dev/darfix/src/darfix/core/dataset.py", line 1591, in nmf\n W = model.fit_transform(X, W=W, H=H)\n File "/users/denolf/virtualenvs/ewoks/ubuntu_20_04/py38/lib/python3.8/site-packages/sklearn/decomposition/_nmf.py", line 1593, in fit_transform\n W, H, n_iter = self._fit_transform(X, W=W, H=H)\n File "/users/denolf/virtualenvs/ewoks/ubuntu_20_04/py38/lib/python3.8/site-packages/sklearn/decomposition/_nmf.py", line 1652, in _fit_transform\n W, H = self._check_w_h(X, W, H, update_H)\n File "/users/denolf/virtualenvs/ewoks/ubuntu_20_04/py38/lib/python3.8/site-packages/sklearn/decomposition/_nmf.py", line 1518, in _check_w_h\n _check_init(W, (n_samples, self._n_components), "NMF (input W)")\n File "/users/denolf/virtualenvs/ewoks/ubuntu_20_04/py38/lib/python3.8/site-packages/sklearn/decomposition/_nmf.py", line 67, in _check_init\n raise ValueError("Array passed to %s is full of zeros." % whom)\nValueError: Array passed to NMF (input W) is full of zeros.\n',
),
(
"Local Variables",
"OrderedDict([('A',\n array([[0, 0, 0, ..., 0, 0, 0],\n [0, 0, 0, ..., 0, 0, 0],\n [0, 0, 0, ..., 0, 0, 0],\n ...,\n [0, 0, 0, ..., 0, 0, 0],\n [0, 0, 0, ..., 0, 0, 0],\n [0, 0, 0, ..., 0, 0, 0]], dtype=uint16)),\n ('shape', (180, 27)),\n ('whom', 'NMF (input W)')])",
),
]
)
Orange version
Qt related packages
It also happens in our production environment which has
OS: Ubuntu 20.04
Issue description
I have a particular case where an error in
qt.ThreadcausesErrorReporting.handle_exceptionto segfault.If I replace this
with this I don't get the segfault (i.e. the exception gets printed and the app keeps running)
This is the traceback I got from the core dump:
Steps to reproduce the behavior
I can upload the workflow and the data (~1GB) somewhere if you want a way to reproduce the problem.