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Opened 4 years ago
Closed 4 years ago
#5124 closed defect (can't reproduce)
Crash loading OpenMM plugins
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tristan Croll | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.10.59-1-MANJARO-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007f943c58f740 (most recent call first):
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 4565 in loadPluginsFromDirectory
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/simtk/openmm/__init__.py", line 27 in
File "", line 219 in _call_with_frames_removed
File "", line 783 in exec_module
File "", line 671 in _load_unlocked
File "", line 975 in _find_and_load_unlocked
File "", line 991 in _find_and_load
File "/home/tati/.local/share/ChimeraX/1.2/site-packages/chimerax/isolde/constants.py", line 14 in
File "", line 219 in _call_with_frames_removed
File "", line 783 in exec_module
File "", line 671 in _load_unlocked
File "", line 975 in _find_and_load_unlocked
File "", line 991 in _find_and_load
File "/home/tati/.local/share/ChimeraX/1.2/site-packages/chimerax/isolde/manipulations/peptide_flip.py", line 11 in
File "", line 219 in _call_with_frames_removed
File "", line 783 in exec_module
File "", line 671 in _load_unlocked
File "", line 975 in _find_and_load_unlocked
File "", line 991 in _find_and_load
File "/home/tati/.local/share/ChimeraX/1.2/site-packages/chimerax/isolde/manipulations/__init__.py", line 11 in
File "", line 219 in _call_with_frames_removed
File "", line 783 in exec_module
File "", line 671 in _load_unlocked
File "", line 975 in _find_and_load_unlocked
File "", line 991 in _find_and_load
File "", line 219 in _call_with_frames_removed
File "", line 961 in _find_and_load_unlocked
File "", line 991 in _find_and_load
File "/home/tati/.local/share/ChimeraX/1.2/site-packages/chimerax/isolde/cmd/cmd.py", line 394 in register_isolde
File "/home/tati/.local/share/ChimeraX/1.2/site-packages/chimerax/isolde/__init__.py", line 148 in register_command
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/toolshed/__init__.py", line 1269 in register_command
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/toolshed/info.py", line 312 in _register_cmd
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/toolshed/info.py", line 302 in cb
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2105 in call
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2174 in lazy_register
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 3421 in find_aliases
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 3435 in list_aliases
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/session.py", line 392 in take_snapshot
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/session.py", line 281 in process
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/session.py", line 260 in discovery
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/session.py", line 607 in save
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/session.py", line 877 in save
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core_formats/__init__.py", line 79 in save
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 87 in provider_save
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 3404 in __call__
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2868 in run
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 280 in execute
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 117 in keyPressEvent
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/runpy.py", line 87 in _run_code
File "/media/Daten/Downloads/Software/chimerax-1.2.5/lib/python3.8/runpy.py", line 194 in _run_module_as_main
Log:
> mousemode shift leftMode "translate selected models"
> mousemode shift middleMode "rotate selected models"
> mousemode rightMode zoom
> mousemode control wheelMode "contour level"
> mousemode setting "contour level" speed 0.1
> mousemode shift wheelMode "rotate selected models"
> camera ortho
> set bgColor grey
> lighting soft
> lighting depthCue false
> lighting shadows false
> functionkey F1 cofr sel
> functionkey F2 mousemode rightMode 'mark surface'
> functionkey F3 mousemode rightMode 'move markers'
> functionkey F4 markercolour 3 1
> functionkey F5 view
> functionkey F6 view sel pad 0.92 clip false
> functionkey F7 mousemode rightMode 'delete markers'
> functionkey F8 mousemode rightMode zoom
> functionkey F9 sequence chain sel
> functionkey F10 transparency sel 65
> functionkey F11 transparency sel 0
> functionkey F12 tool show 'Fit in Map'
> color name f01graublau #BADBED
Color 'f01graublau' is opaque, 72.94% red, 85.88% green, and 92.94% blue
> color name f02silberblau #F6FAFC
Color 'f02silberblau' is opaque, 96.47% red, 98.04% green, and 98.82% blue
> color name f03muschel #FFFFE5
Color 'f03muschel' is opaque, 100% red, 100% green, and 89.8% blue
> color name f04beige #F3F3A9
Color 'f04beige' is opaque, 95.29% red, 95.29% green, and 66.27% blue
> color name f05blau #00AAFF
Color 'f05blau' is opaque, 0% red, 66.67% green, and 100% blue
> color name f06hellgrün #7EBE7E
Color 'f06hellgrün' is opaque, 49.41% red, 74.51% green, and 49.41% blue
> color name f07rot #FD625E
Color 'f07rot' is opaque, 99.22% red, 38.43% green, and 36.86% blue
> color name f08grün #349E34
Color 'f08grün' is opaque, 20.39% red, 61.96% green, and 20.39% blue
> color name f09flieder #D57AD5
Color 'f09flieder' is opaque, 83.53% red, 47.84% green, and 83.53% blue
> color name f10rotorange #FF6A25
Color 'f10rotorange' is opaque, 100% red, 41.57% green, and 14.51% blue
> color name f11cyan #8CEAEA
Color 'f11cyan' is opaque, 54.9% red, 91.76% green, and 91.76% blue
> color name f12grau #B2B2B2
Color 'f12grau' is opaque, 69.8% red, 69.8% green, and 69.8% blue
> color name f13gelb #FFFF00
Color 'f13gelb' is opaque, 100% red, 100% green, and 0% blue
> color name f14orange #FEB172
Color 'f14orange' is opaque, 99.61% red, 69.41% green, and 44.71% blue
> color name f15dunkelblau #0088CC
Color 'f15dunkelblau' is opaque, 0% red, 53.33% green, and 80% blue
> color name f16gold #FFBF34
Color 'f16gold' is opaque, 100% red, 74.9% green, and 20.39% blue
> color name f17lila #5B42CD
Color 'f17lila' is opaque, 35.69% red, 25.88% green, and 80.39% blue
> color name f18hellgrau #DCDCDC
Color 'f18hellgrau' is opaque, 86.27% red, 86.27% green, and 86.27% blue
> color name f19limette #32CD32
Color 'f19limette' is opaque, 19.61% red, 80.39% green, and 19.61% blue
> color name f20pink #E6ADE6
Color 'f20pink' is opaque, 90.2% red, 67.84% green, and 90.2% blue
> color name f21altrot #FF6B6B
Color 'f21altrot' is opaque, 100% red, 41.96% green, and 41.96% blue
> color name f22altgrün #60D89C
Color 'f22altgrün' is opaque, 37.65% red, 84.71% green, and 61.18% blue
> color name f23anthrazit #323F45
Color 'f23anthrazit' is opaque, 19.61% red, 24.71% green, and 27.06% blue
> color name f24altorange #D5A755
Color 'f24altorange' is opaque, 83.53% red, 65.49% green, and 33.33% blue
> color name f25altblau #0088CC
Color 'f25altblau' is opaque, 0% red, 53.33% green, and 80% blue
> color name f26dunkelgrün #39815D
Color 'f26dunkelgrün' is opaque, 22.35% red, 50.59% green, and 36.47% blue
> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4
> alias markercolour color zone #$2 near #$1 sharpEdges true distance 3; fun
> F4 'markercolour $1 $2'
> alias quickmarkercolour color zone #$2 near #$1 sharpEdges false distance 3;
> fun F4 'quickmarkercolour $1 $2'
> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3
> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3
> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow
> alias chaininfo preset custom chaininfo
> alias foto save browse format tiff width 4000 height 3000 supersample 4
> transparentBackground false
> alias durch save browse format tiff width 4000 height 3000 supersample 4
> transparentBackground true
> alias session save browse format session includeMaps true compress lz4
> alias nomapsession save browse format session includeMaps false compress lz4
> alias splitup color zone #$1 near sel sharpEdges true distance $2
> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.6 (Core Profile) Mesa 21.1.6
OpenGL renderer: Radeon RX 580 Series (POLARIS10, DRM 3.40.0, 5.10.59-1-MANJARO, LLVM 12.0.1)
OpenGL vendor: AMD
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B79
OS: Manjaro Linux 21.1.0 Pahvo
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 AMD Ryzen 5 2600X Six-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 2.1Gi 9.6Gi 88Mi 3.9Gi 13Gi
Swap: 17Gi 0B 17Gi
Graphics:
1d:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Ellesmere [Radeon RX 470/480/570/570X/580/580X/590] [1002:67df] (rev e7)
Subsystem: Sapphire Technology Limited Nitro+ Radeon RX 570/580/590 [1da2:e366]
Kernel driver in use: amdgpu
Locale: ('de_DE', 'UTF-8')
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: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
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-Clipper: 0.16.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
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: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
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: 2.0.1
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-SeqView: 2.3
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: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
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: 5.0.9
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
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: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
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
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
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
six: 1.15.0
snowballstemmer: 2.1.0
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: 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: 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 (8)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash loading OpenMM plugins |
comment:2 by , 4 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
comment:3 by , 4 years ago
That's a new one for me too, and a bit concerning. Is there any chance you could run this under gdb to get a better understanding of what's going on? Just do the following in a terminal window:
gdb ChimeraX
... do what you did before to get the segmentation fault, then in the terminal window type "bt" to get a stack trace and copy/paste the result into a reply.
follow-up: 4 comment:4 by , 4 years ago
I'd guess this crash is not reproducible. And I actually have one idea. We sometimes see a Python garbage collection crash where the Python traceback can be just about anything -- but what really happened was garbage collection was triggered and it crashed. We see this clearly on macOS where it provides the C++ stack trace. No way to know in this case on Linux if it was a garbage collection crash, but it seems very implausible that importing OpenMM caused the crash.
follow-up: 5 comment:5 by , 4 years ago
Hello, The crashes started happening yesterday, and it happened every time I tried to save a session that contained cryo-EM volumes (just loading some pdbs and saving those did not crash). I did not change anything in the ChimeraX folder and I had been using it without problems since I installed it, thats why I assumed it could come from my distro (which is rolling release and can break stuff). I updated my distro today and tried to reproduce the crash and I have to say that it still happened, but not every time I tried saving sessions. So I am also a bit puzzled, could it be faulty RAM or something? Am 30.08.21 um 21:19 schrieb ChimeraX:
comment:6 by , 4 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
Thanks for the info. I did not look closely enough at the traceback. It is initializing the "isolde" command but I see it is in a session save. It is somewhat bizarre that it would be initializing the "isolde" command while saving a session. I see this is because it is including all your command aliases in the session. I don't know why it is initializing the commands for aliases. Greg why is it doing that? But that is not a bug that would cause a crash.
So saving sessions with maps causes a crash often now, although in the past it did not. It does sound like something changed on your system. The most common cause of ChimeraX crashes is the system graphics driver crashes. But graphics should not be drawn when saving a session.
Can you try a simple test case that makes it crash, like open a single map and save a session?
comment:7 by , 4 years ago
If the simple test crashes, then submit it as a bug and say you opened one map and saved a session, or whatever steps were needed. I am curious if the crash is always in initializing isolde. Have you used ISOLDE since it started crashing -- does that work? Maybe it really does crash just importing OpenMM which ISOLDE uses because some system library OpenMM uses (e.g CUDA) is corrupted.
comment:8 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Reporter did not respond to request to do simple test opening a map and saving a session.
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Looks like ISOLDE is importing OpenMM and it crashes. I don't have any idea what might cause this.