Opened 4 years ago

Closed 4 years ago

#4913 closed defect (can't reproduce)

Crash in numpy.sum()

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.8.0-59-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202106260206 (2021-06-26 02:06:40 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f79417fa700 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/threading.py", line 306 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/threading.py", line 558 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/threading.py", line 1252 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/threading.py", line 890 in _bootstrap

Current thread 0x00007f79f4b76740 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 71 in _wrapreduction
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 2247 in sum
  File "", line 5 in sum
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/atomic/bond_geom.py", line 24 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/atomic/bond_geom.py", line 185 in tetra_pos
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/atomic/bond_geom.py", line 78 in bond_positions
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 210 in add_hydrogens
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170 in hbond_add_hydrogens
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63 in cmd_addh
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/coulombic/coulombic.py", line 79 in assign_charges
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/coulombic/cmd.py", line 90 in cmd_coulombic
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2854 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 280 in execute
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 117 in keyPressEvent
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/ChimeraX_main.py", line 879 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-packages/ChimeraX_main.py", line 1028 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.3.dev202106260206 (2021-06-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 460.80
OpenGL renderer: GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: 
Model: 
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       5.1Gi       5.0Gi       217Mi       5.5Gi        10Gi
	Swap:          15Gi       1.5Gi        13Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 710] [10de:128b] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. GK208B [GeForce GT 710] [19da:7326]	
	Kernel driver in use: nvidia
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.8
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.25.1
    ChimeraX-AtomicLibrary: 3.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    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-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202106260206
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.3
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.6
    ChimeraX-PDB: 2.4.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: chimera-programmers added
Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in numpy.sum()

comment:2 by Tom Goddard, 4 years ago

Owner: changed from Tom Goddard to Eric Pettersen

This crash in a basic numpy.sum() routine is very likely due to memory corruption. Code is in coulombic and addh. Will let Eric consider if that code might have corrupted memory in some way.

comment:3 by Eric Pettersen, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Unlikely to be due to coulombic. At the point of the crash it is still adding hydrogens which means it hasn't actually run the C++ coulombic calculation yet.

I suppose it could be due to copying the molecule in order to add the hydrogens, but I would need to know what structure it was to have any chance of tracking that down.

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