Opened 15 months ago

Closed 15 months ago

Last modified 15 months ago

#15729 closed defect (fixed)

Crash under Rosetta emulation

Reported by: xiang.zhang@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x0000000204463240 (most recent call first):
  File "/private/var/folders/cn/89fp52rd0nlc70yqbgkh6glr0000gn/T/AppTranslocation/0FCD436F-40DB-4DD1-A2C4-57B5413CF187/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 525 in _cursor_position
  File "/private/var/folders/cn/89fp52rd0nlc70yqbgkh6glr0000gn/T/AppTranslocation/0FCD436F-40DB-4DD1-A2C4-57B5413CF187/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 483 in mouse_pause_tracking
  File "/private/var/folders/cn/89fp52rd0nlc70yqbgkh6glr0000gn/T/AppTranslocation/0FCD436F-40DB-4DD1-A2C4-57B5413CF187/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 151 in _redraw_timer_callback
  File "/private/var/folders/cn/89fp52rd0nlc70yqbgkh6glr0000gn/T/AppTranslocation/0FCD436F-40DB-4DD1-A2C4-57B5413CF187/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/private/var/folders/cn/89fp52rd0nlc70yqbgkh6glr0000gn/T/AppTranslocation/0FCD436F-40DB-4DD1-A2C4-57B5413CF187/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/private/var/folders/cn/89fp52rd0nlc70yqbgkh6glr0000gn/T/AppTranslocation/0FCD436F-40DB-4DD1-A2C4-57B5413CF187/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics (total: 49)


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  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,2",
  "coalitionID" : 12453,
  "osVersion" : {
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    "build" : "23F79",
    "releaseType" : "User"
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  "captureTime" : "2024-08-05 09:16:48.7602 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "01D8D53A-1AD5-4BCF-88B4-DD005DE2202A",
  "pid" : 19551,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-08-05 08:50:23.1620 -0400",
  "procStartAbsTime" : 252151282756,
  "procExitAbsTime" : 290203207576,
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3043CC1C-6A8F-8D05-4305-89A9110D377C",
  "codeSigningID" : "",
  "codeSigningTeamID" : "",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 0,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 2337,
  "sleepWakeUUID" : "0AF57137-8B48-4DA9-A3EE-95A67DB84C53",
  "sip" : "enabled",
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  "exception" : {"codes":"0x000000000000000a, 0x00000001356e0fd0","rawCodes":[10,5191372752],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x00000001356e0fd0"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":19551},
  "ktriageinfo" : "VM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/zhangxiang/Library/Mobile
> Documents/com~apple~CloudDocs/Lefko/Structures/cryosparc_P1_J269_003_volume_map_sharp.mrc"

Opened cryosparc_P1_J269_003_volume_map_sharp.mrc as #1, grid size 96,96,96,
pixel 2.2, shown at level 0.333, step 1, values float32  

> volume #1 level 0.2819

> ui tool show "Side View"


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1A3CH/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 2天18小时20分钟

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
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    ChimeraX-Crosslinks: 1.0
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    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
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    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
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    openvr: 1.26.701
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    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
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    webcolors: 1.13
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    widgetsnbextension: 4.0.11

Attachments (1)

PastedGraphic-1.png​ (22.9 KB ) - added by xiang.zhang@… 15 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (10)

comment:1 by Eric Pettersen, 15 months ago

Cc: Eric Pettersen added
Component: Unassigned → Platform
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash under Rosetta emulation

comment:2 by Tom Goddard, 15 months ago

You are running the Intel Mac ChimeraX on your Mac ARM computer. Did you get the Intel Mac ChimeraX from the ChimeraX download page? It should show you the Universal Mac ChimeraX on the download page. Can you check whether you have the Intel Mac ChimeraX by ctrl-clicking on its icon and choosing Get Info... and see whether the panel says "Kind: Application (Universal)" or "Kind: Application (Intel)". Let me know which you see. Thanks!

comment:3 by xiang.zhang@…, 15 months ago 

Thanks Tom,

It says (intel). I didn’t notice you have universal one available. Should I install the universal one instead?

Best,
Xiang

Xiang Zhang, PhD
Post-doc
Robert J. Lefkowitz Laboratory
Dept. of Medicine (Cardiology)
Duke University Medical Center
463 CARL Bldg, Research Drive
Durham, NC 27710
xiang.zhang@duke.edu




On Aug 5, 2024, at 15:56, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#15729: Crash under Rosetta emulation
------------------------------------+-------------------------
         Reporter:  xiang.zhang@…  |      Owner:  Tom Goddard
             Type:  defect         |     Status:  assigned
         Priority:  normal         |  Milestone:
        Component:  Platform       |    Version:
       Resolution:                 |   Keywords:
       Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
          Project:  ChimeraX       |
------------------------------------+-------------------------
Comment (by Tom Goddard):

You are running the Intel Mac ChimeraX on your Mac ARM computer.  Did you
get the Intel Mac ChimeraX from the ChimeraX download page?  It should
show you the Universal Mac ChimeraX on the download page.  Can you check
whether you have the Intel Mac ChimeraX by ctrl-clicking on its icon and
choosing Get Info... and see whether the panel says "Kind: Application
(Universal)" or "Kind: Application (Intel)".  Let me know which you see.
Thanks!
--
Ticket URL: <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15729%23comment%3A2&data=05%7C02%7Cxiang.zhang%40duke.edu%7C64cd971bfc4449ff0d6e08dcb588a973%7Ccb72c54e4a314d9eb14a1ea36dfac94c%7C0%7C0%7C638584845825277997%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=n%2B%2FlmhdhREzHCY8YRERt1Vwxr78x2RRk9Bcz5qgDEhI%3D&reserved=0>
ChimeraX <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cxiang.zhang%40duke.edu%7C64cd971bfc4449ff0d6e08dcb588a973%7Ccb72c54e4a314d9eb14a1ea36dfac94c%7C0%7C0%7C638584845825288227%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1uTd%2FAksD0jFlGlwvAozg%2BnBFyuF7yuZpWluC%2BY53Jw%3D&reserved=0>
ChimeraX Issue Tracker

comment:4 by Tom Goddard, 15 months ago

The ChimeraX download page should only show you one Mac ChimeraX version saying "macOS" under the Operating System column which is the universal version (includes both M1/M2/M3 and Intel). So I am puzzled how you got the Intel Mac ChimeraX. If you click the "Other releases" triangle on the download page it will show "macOS M1 or M2" and "macOS Intel" as other choices. Did you use the "Other release" and choose "macOS Intel"?

At any rate, you certainly want to use the universal or M1 ChimeraX since that is the native CPU type on your computer, so it will run faster.

Also this crash you reported came from running ChimeraX without first copying it from the distribution dmg file to your computer. That can work but it runs very slow. But then you force ejected the dmg disk image while ChimeraX was running and that crashed it. So first copy ChimeraX from the dmg by dragging to Applications or to your Desktop before running it.

comment:5 by xiang.zhang@…, 15 months ago 

I got the Intel Mac ChimeraX from the download page. I used link in universal one rather than other releases.

[PastedGraphic-1.png]

I will download the only for M1 release then. I actually dragged the icon and installed it. But I have problem in ejected the dmg after installation. I force ejected after several ejection. Thank you so much!
Best,
Xiang

Xiang Zhang, PhD
Post-doc
Robert J. Lefkowitz Laboratory
Dept. of Medicine (Cardiology)
Duke University Medical Center
463 CARL Bldg, Research Drive
Durham, NC 27710
xiang.zhang@duke.edu




On Aug 5, 2024, at 15:56, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#15729: Crash under Rosetta emulation
------------------------------------+-------------------------
         Reporter:  xiang.zhang@…  |      Owner:  Tom Goddard
             Type:  defect         |     Status:  assigned
         Priority:  normal         |  Milestone:
        Component:  Platform       |    Version:
       Resolution:                 |   Keywords:
       Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
          Project:  ChimeraX       |
------------------------------------+-------------------------
Comment (by Tom Goddard):

You are running the Intel Mac ChimeraX on your Mac ARM computer.  Did you
get the Intel Mac ChimeraX from the ChimeraX download page?  It should
show you the Universal Mac ChimeraX on the download page.  Can you check
whether you have the Intel Mac ChimeraX by ctrl-clicking on its icon and
choosing Get Info... and see whether the panel says "Kind: Application
(Universal)" or "Kind: Application (Intel)".  Let me know which you see.
Thanks!
--
Ticket URL: <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15729%23comment%3A2&data=05%7C02%7Cxiang.zhang%40duke.edu%7C64cd971bfc4449ff0d6e08dcb588a973%7Ccb72c54e4a314d9eb14a1ea36dfac94c%7C0%7C0%7C638584845825277997%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=n%2B%2FlmhdhREzHCY8YRERt1Vwxr78x2RRk9Bcz5qgDEhI%3D&reserved=0>
ChimeraX <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cxiang.zhang%40duke.edu%7C64cd971bfc4449ff0d6e08dcb588a973%7Ccb72c54e4a314d9eb14a1ea36dfac94c%7C0%7C0%7C638584845825288227%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1uTd%2FAksD0jFlGlwvAozg%2BnBFyuF7yuZpWluC%2BY53Jw%3D&reserved=0>
ChimeraX Issue Tracker

Added by email2trac

by xiang.zhang@…, 15 months ago

Attachment: PastedGraphic-1.png​ added

Added by email2trac

comment:6 by Tom Goddard, 15 months ago

Hi Xiang,

Thanks for the info. I am still confused. If you downloaded the ChimeraX that said "macOS" under operating system I think it would have to be the universal Mac ChimeraX, but you told me GetInfo showed it was the Intel ChimeraX. I'm trying to figure this out since I have seen a bunch of people accidentally get the Intel Mac ChimeraX on their Mac M1 machine. Could you try downloading the Universal Mac ChimeraX, and check Get Info on the ChimeraX in it to see if it says "Kind: Application (universal)"? If it says Intel then we have some bug we have to figure out.

Also I am curious what web browser you use to download ChimeraX as that could effect which Mac version it shows you in the download page. Do you use Safari, Chrome, or some other browser?

Tom

comment:7 by xiang.zhang@…, 15 months ago 

I checked the application from the dmg installation windows as you suggested (that I downloaded just now). It said universal. I used Safari to download the package. Thank you for helping me get the right version!

Best,
Xiang

Xiang Zhang, PhD
Post-doc
Robert J. Lefkowitz Laboratory
Dept. of Medicine (Cardiology)
Duke University Medical Center
463 CARL Bldg, Research Drive
Durham, NC 27710
xiang.zhang@duke.edu




On Aug 5, 2024, at 16:47, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#15729: Crash under Rosetta emulation
------------------------------------+-------------------------
         Reporter:  xiang.zhang@…  |      Owner:  Tom Goddard
             Type:  defect         |     Status:  assigned
         Priority:  normal         |  Milestone:
        Component:  Platform       |    Version:
       Resolution:                 |   Keywords:
       Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
          Project:  ChimeraX       |
------------------------------------+-------------------------
Comment (by Tom Goddard):

Hi Xiang,

  Thanks for the info.  I am still confused.  If you downloaded the
ChimeraX that said "macOS" under operating system I think it would have to
be the universal Mac ChimeraX, but you told me GetInfo showed it was the
Intel ChimeraX.  I'm trying to figure this out since I have seen a bunch
of people accidentally get the Intel Mac ChimeraX on their Mac M1 machine.
Could you try downloading the Universal Mac ChimeraX, and check Get Info
on the ChimeraX in it to see if it says "Kind: Application (universal)"?
If it says Intel then we have some bug we have to figure out.

  Also I am curious what web browser you use to download ChimeraX as that
could effect which Mac version it shows you in the download page.  Do you
use Safari, Chrome, or some other browser?

   Tom
--
Ticket URL: <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15729%23comment%3A6&data=05%7C02%7Cxiang.zhang%40duke.edu%7C7b8cf2cf797d4950742208dcb58fe5b6%7Ccb72c54e4a314d9eb14a1ea36dfac94c%7C0%7C0%7C638584876897295366%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=64ZJvotz3SkHxfp2y%2FbBAnimaQUVdXCQwQbHbDpaoM8%3D&reserved=0>
ChimeraX <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cxiang.zhang%40duke.edu%7C7b8cf2cf797d4950742208dcb58fe5b6%7Ccb72c54e4a314d9eb14a1ea36dfac94c%7C0%7C0%7C638584876897310347%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=L4%2BBjwegtNIQaQ01OIxEKWlzTmijUIA8njnuZfp0Doo%3D&reserved=0>
ChimeraX Issue Tracker

comment:8 by Tom Goddard, 15 months ago

Resolution: → fixed
Status: assigned → closed

Glad you got the M1 ChimeraX. It will be much faster.

The crash report shows the that ChimeraX was definitely run from the .dmg file and then the dmg was force ejected which crashed ChimeraX. Maybe you accidentally double clicked it while dragging it. Not likely to run into that again.

I think I figured out how you might have ended up with the Intel Mac ChimeraX. It turns out that the ChimeraX "New version available" dialog that pops up gives a link to the Intel Mac ChimeraX even when your machine is an M1 Mac. We will fix that bug soon. Your help allowed me to find that and led to 100 downloads of the wrong version in the last 4 days and probably tens of thousands over the last few years. So thanks a lot for helping me find that bug. People get a faster native Mac M1/M2/M3 ChimeraX after we fix that.

comment:9 by xiang.zhang@…, 15 months ago 

Thank you and I am so glad to help you fix it. I got the M1 ChimeraX and it runs much faster!
Xiang

获取 Outlook for iOS<https://aka.ms/o0ukef>
________________________________
发件人: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
发送时间: Monday, August 5, 2024 10:22:11 PM
收件人: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Xiang Zhang, Ph.D. <xiang.zhang@duke.edu>
抄送: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
主题: Re: [ChimeraX] #15729: Crash under Rosetta emulation

#15729: Crash under Rosetta emulation
------------------------------------+-------------------------
          Reporter:  xiang.zhang@…  |      Owner:  Tom Goddard
              Type:  defect         |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Platform       |    Version:
        Resolution:  fixed          |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------
Changes (by Tom Goddard):

 * resolution:   => fixed
 * status:  assigned => closed

Comment:

 Glad you got the M1 ChimeraX.  It will be much faster.

 The crash report shows the that ChimeraX was definitely run from the .dmg
 file and then the dmg was force ejected which crashed ChimeraX.  Maybe you
 accidentally double clicked it while dragging it.  Not likely to run into
 that again.

 I think I figured out how you might have ended up with the Intel Mac
 ChimeraX.  It turns out that the ChimeraX "New version available" dialog
 that pops up gives a link to the Intel Mac ChimeraX even when your machine
 is an M1 Mac.  We will fix that bug soon.  Your help allowed me to find
 that and led to 100 downloads of the wrong version in the last 4 days and
 probably tens of thousands over the last few years.  So thanks a lot for
 helping me find that bug.  People get a faster native Mac M1/M2/M3
 ChimeraX after we fix that.
--
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