Opened 5 years ago
Closed 5 years ago
#4022 closed task (fixed)
Testing crash reporting on Linux
Reported by: | Owned by: | Tom Goddard | |
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Priority: | normal | Milestone: | |
Component: | Infrastructure | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-5.4.0-54-generic-x86_64-with-glibc2.14 ChimeraX Version: 1.2.dev202012030440 (2020-12-03 04:40:12 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Testing crash reporting on Linux. Fatal Python error: Segmentation fault Current thread 0x00007facb4edc740 (most recent call first): File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/stl/stl.py", line 294 in write_stl File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/stl/__init__.py", line 39 in save File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 78 in provider_save File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2837 in run File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 66 in cmd_save File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2837 in run File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 275 in execute File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 112 in keyPressEvent File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/chimerax/ui/gui.py", line 307 in event_loop File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/ChimeraX_main.py", line 782 in init File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/site-packages/ChimeraX_main.py", line 931 in File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/runpy.py", line 87 in _run_code File "/home/goddard/ucsf/chimerax/ChimeraX.app/lib/python3.8/runpy.py", line 194 in _run_module_as_main Log: Startup Messages --- warning | Unable to load numpy_formathandler accelerator from OpenGL_accelerate notes | OpenGL_accelerate module loaded Using accelerated ArrayDatatype Lock 140509252029696 acquired on /home/goddard/.cache/ChimeraX/1.2/toolshed/bundle_info.cache.lock Lock 140509252029696 released on /home/goddard/.cache/ChimeraX/1.2/toolshed/bundle_info.cache.lock UCSF ChimeraX version: 1.2.dev202012030440 (2020-12-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.6 (Core Profile) Mesa 20.0.8 OpenGL renderer: Mesa Intel(R) HD Graphics 6000 (BDW GT3) OpenGL vendor: Intel Manufacturer: unknown Model: unknown OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 4 Intel(R) Core(TM) i5-5250U CPU @ 1.60GHz Cache Size: 3072 KB Memory: total used free shared buff/cache available Mem: 15Gi 830Mi 13Gi 245Mi 1.3Gi 14Gi Swap: 2.0Gi 0B 2.0Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 6000 [8086:1626] (rev 09) Subsystem: Intel Corporation HD Graphics 6000 [8086:2057] Kernel driver in use: i915 Locale: ('en_US', 'UTF-8') PySide2 version: 5.15.1 Qt version: 5.15.1 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.11.8 cftime: 1.3.0 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.9.5 ChimeraX-AtomicLibrary: 1.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202012030440 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.1 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.3.1 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.2.2 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.3.1 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.0 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.5.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.1 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.7 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 20.3 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.8 psutil: 5.7.2 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PySide2: 5.15.1 python-dateutil: 2.8.1 pytz: 2020.4 pyzmq: 20.0.0 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 shiboken2: 5.15.1 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0
Change History (2)
comment:1 by , 5 years ago
Component: | Unassigned → Infrastructure |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Testing crash reporting on Linux |
Type: | defect → task |
comment:2 by , 5 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
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