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Opened 15 months ago
Closed 15 months ago
#15646 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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: 1.7rc202311100232 (2023-11-10 02:32:35 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070001056e000 (most recent call first):
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff85c7bffc0 (most recent call first):
Garbage-collecting
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 243 in set_c_pointer
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 108 in __init__
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2403 in
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py", line 164 in add_bond
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py", line 108 in add_atom
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 949 in new_hydrogen
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 910 in add_altloc_hyds
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 909 in _attach_hydrogens
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 225 in add_hydrogens
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 184 in hbond_add_hydrogens
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 95 in assign_charges
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/private/var/folders/ql/27r944jd44scvb7yd88571rhyc8z14/T/AppTranslocation/9115FC5A-32F6-4FBF-8D7C-40CD81532C14/d/ChimeraX-1.7-rc2023.11.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 58)
{"app_name":"ChimeraX","timestamp":"2024-07-21 21:13:42.00 -0500","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"E0E12260-D305-4CD5-B43D-01A8135F00AC"}
{
"uptime" : 570000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1019509796,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 18325,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-07-21 21:13:42.0811 -0500",
"codeSigningMonitor" : 0,
"incident" : "E0E12260-D305-4CD5-B43D-01A8135F00AC",
"pid" : 56755,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-21 20:43:42.8727 -0500",
"procStartAbsTime" : 574995451773618,
"procExitAbsTime" : 576794564495332,
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.7-rc2023.11.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"BB8F601C-4C57-552E-9FE6-13CCD1FAA87B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "534E2971-3E00-0E0B-D1E3-DDAE6765C493",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4357050199\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103b35000-103b39000 [ 16K] r-x\/r-x SM=COW \/var\/folders\/*\/ChimeraX-1.7-rc2023.11.10.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":56755},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4357050199\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 103b35000-103b39000 [ 16K] r-x\/r-x SM=COW \/var\/folders\/*\/ChimeraX-1.7-rc2023.11.10.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7rc202311100232 (2023-11-10)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/suj/Downloads/fold_2024_07_21_20_47_rice_dimer/fold_2024_07_21_20_47_rice_dimer_model_0.cif
Chain information for fold_2024_07_21_20_47_rice_dimer_model_0.cif #1
---
Chain | Description
A B | .
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2024_07_21_20_47_rice_dimer_model_0.cif_A SES
surface #1.1: minimum, -14.14, mean -1.99, maximum 10.03
Coulombic values for fold_2024_07_21_20_47_rice_dimer_model_0.cif_B SES
surface #1.2: minimum, -14.42, mean -1.99, maximum 10.07
To also show corresponding color key, enter the above coulombic command and
add key true
> close
> open
> /Users/suj/Downloads/fold_2024_07_21_20_53_soybean_dimer/fold_2024_07_21_20_53_soybean_dimer_model_0.cif
Chain information for fold_2024_07_21_20_53_soybean_dimer_model_0.cif #1
---
Chain | Description
A B | .
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2024_07_21_20_53_soybean_dimer_model_0.cif_A SES
surface #1.1: minimum, -11.98, mean 0.22, maximum 11.23
Coulombic values for fold_2024_07_21_20_53_soybean_dimer_model_0.cif_B SES
surface #1.2: minimum, -12.17, mean 0.21, maximum 12.50
To also show corresponding color key, enter the above coulombic command and
add key true
> close
> open
> /Users/suj/Downloads/fold_2024_07_21_21_06_liverworts/fold_2024_07_21_21_06_liverworts_model_0.cif
Chain information for fold_2024_07_21_21_06_liverworts_model_0.cif #1
---
Chain | Description
A B | .
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_A SES
surface #1.1: minimum, -12.03, mean 0.17, maximum 14.54
Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_B SES
surface #1.2: minimum, -11.86, mean 0.16, maximum 14.97
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> show atoms
> mlp
Map values for surface "fold_2024_07_21_21_06_liverworts_model_0.cif_A SES
surface": minimum -25.74, mean -3.189, maximum 21.66
Map values for surface "fold_2024_07_21_21_06_liverworts_model_0.cif_B SES
surface": minimum -25.9, mean -3.159, maximum 21.5
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_A SES
surface #1.1: minimum, -12.03, mean 0.17, maximum 14.54
Coulombic values for fold_2024_07_21_21_06_liverworts_model_0.cif_B SES
surface #1.2: minimum, -11.86, mean 0.16, maximum 14.97
To also show corresponding color key, enter the above coulombic command and
add key true
> close
> open
> /Users/suj/Downloads/fold_2024_07_21_21_09_amoeba/fold_2024_07_21_21_09_amoeba_model_0.cif
Chain information for fold_2024_07_21_21_09_amoeba_model_0.cif #1
---
Chain | Description
A B | .
> coulombic
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7rc202311100232 (2023-11-10)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 6 days, 16 hours, 13 minutes
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-011
Option ROM Version: 113-D322A1XL-011
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7rc202311100232
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
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: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.44.0
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.11.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.7
wcwidth: 0.2.9
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 15 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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