![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15875 closed defect (nonchimerax)
Graphics crash, macOS 14.5, Mac M1 Max GPU
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| 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: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x000000045cf07000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000204865240 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2744 in update_buffer_data
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1912 in update_buffers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1924 in activate_bindings
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 814 in _draw_geometry
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1579 in draw_depth
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 254 in _draw_scene
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, lxml._elementpath, lxml.etree, 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.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 (total: 54)
{"app_name":"ChimeraX","timestamp":"2024-09-04 10:17:51.00 +0200","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","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":"A78AE4CC-C930-460D-842D-4E0345A80023"}
{
"uptime" : 7600,
"procRole" : "Background",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,4",
"coalitionID" : 2021,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-09-04 10:17:49.8230 +0200",
"codeSigningMonitor" : 1,
"incident" : "A78AE4CC-C930-460D-842D-4E0345A80023",
"pid" : 5889,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-04 09:50:40.3915 +0200",
"procStartAbsTime" : 143968436474,
"procExitAbsTime" : 183074714991,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D491EDF1-B66C-5C98-A3E6-A9EEF98E481E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AFC4ABDE-7FF3-DE90-05C8-6E2510F3789E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 7338,
"sleepWakeUUID" : "39385610-D634-437E-A72B-E7011AF4AFB8",
"sip" : "enabled",
"vmRegionInfo" : "0x1304d0000 is in 0x1304d0000-0x1304f4000; bytes after start: 0 bytes before end: 147455\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 13049f000-1304a0000 [ 4K] r--\/rwx SM=COW Object_id=97a810d3\n GAP OF 0x30000 BYTES\n---> mapped file 1304d0000-1304f4000 [ 144K] r--\/r-- SM=ALI Object_id=aa8c81f4\n Rosetta Generic 1304f4000-1304f5000 [ 4K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x00000001304d0000","rawCodes":[2,5105319936],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x00000001304d0000"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":5889},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x1304d0000 is in 0x1304d0000-0x1304f4000; bytes after start: 0 bytes before end: 147455\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 13049f000-1304a0000 [ 4K] r--\/rwx SM=COW Object_id=97a810d3\n GAP OF 0x30000 BYTES\n---> mapped file 1304d0000-1304f4000 [ 144K] r--\/r-- SM=ALI Object_id=aa8c81f4\n Rosetta Generic 1304f4000-1304f5000 [ 4K] rw-\/rwx SM=PRV ",
"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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"uuid" : "a32f4005-d666-32c2-8e52-f67fc64616e0",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2503.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703405060096,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21164019,
"uuid" : "33ecd3dc-c895-35e2-a1fd-c1761b155964",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.60.105"
}
],
"sharedCache" : {
"base" : 140703343542272,
"size" : 25769803776,
"uuid" : "6f51a82c-c96c-3bc8-82ca-9c109185bd3c"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "98becd95eeba870ea53e92ae2545f897dfd3e03d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000570
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF89D3D6A78)"
]
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/lfu/Work/experiment/cargos/HIV-1 capsid/HIV-1 capsid and FG
> interaction/information/HIV-1 capsid/3J3Y/3j3y.cif" format mmcif
3j3y.cif title:
Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12
pentamers) [more info...]
Chain information for 3j3y.cif #1
---
Chain | Description | UniProt
0 1 10 11 12 13 14 15 16 17 18 19 1A 1B 1C 1D 1E 1F 1G 1H 1I 1J 1K 1L 1M 1N 1O
1P 1Q 1R 1S 1T 1U 1V 1W 1X 1Y 1Z 1a 1b 1c 1d 1e 1f 1g 1h 1i 1j 1k 1l 1m 1n 1o
1p 1q 1r 1s 1t 1u 1v 1w 1x 1y 1z 2 20 21 22 23 24 25 26 27 28 29 2A 2B 2C 2D
2E 2F 2G 2H 2I 2J 2K 2L 2M 2N 2O 2P 2Q 2R 2S 2T 2U 2V 2W 2X 2Y 2Z 2a 2b 2c 2d
2e 2f 2g 2h 2i 2j 2k 2l 2m 2n 2o 2p 2q 2r 2s 2t 2u 2v 2w 2x 2y 2z 3 30 31 32
33 34 35 36 37 38 39 3A 3B 3C 3D 3E 3F 3G 3H 3I 3J 3K 3L 3M 3N 3O 3P 3Q 3R 3S
3T 3U 3V 3W 3X 3Y 3Z 3a 3b 3c 3d 3e 3f 3g 3h 3i 3j 3k 3l 3m 3n 3o 3p 3q 3r 3s
3t 3u 3v 3w 3x 3y 3z 4 40 41 42 43 44 45 46 47 48 49 4A 4B 4C 4D 4E 4F 4G 4H
4I 4J 4K 4L 4M 4N 4O 4P 4Q 4R 4S 4T 4U 4V 4W 4X 4Y 4Z 4a 4b 4c 4d 4e 4f 4g 4h
4i 4j 4k 4l 4m 4n 4o 4p 4q 4r 4s 4t 4u 4v 4w 4x 4y 4z 5 50 51 52 53 54 55 56
57 58 59 5A 5B 5C 5D 5E 5F 5G 5H 5I 5J 5K 5L 5M 5N 5O 5P 5Q 5R 5S 5T 5U 5V 5W
5X 5Y 5Z 5a 5b 5c 5d 5e 5f 5g 5h 5i 5j 5k 5l 5m 5n 5o 5p 5q 5r 5s 5t 5u 5v 5w
5x 5y 5z 6 60 61 62 63 64 65 66 67 68 69 6A 6B 6C 6D 6E 6F 6G 6H 6I 6J 6K 6L
6M 6N 6O 6P 6Q 6R 6S 6T 6U 6V 6W 6X 6Y 6Z 6a 6b 6c 6d 6e 6f 6g 6h 6i 6j 6k 6l
6m 6n 6o 6p 6q 6r 6s 6t 6u 6v 6w 6x 6y 6z 7 70 71 72 73 74 75 76 77 78 79 7A
7B 7C 7D 7E 7F 7G 7H 7I 7J 7K 7L 7M 7N 7O 7P 7Q 7R 7S 7T 7U 7V 7W 7X 7Y 7Z 7a
7b 7c 7d 7e 7f 7g 7h 7i 7j 7k 7l 7m 7n 7o 7p 7q 7r 7s 7t 7u 7v 7w 7x 7y 7z 8
80 81 82 83 84 85 86 87 88 89 8A 8B 8C 8D 8E 8F 8G 8H 8I 8J 8K 8L 8M 8N 8O 8P
8Q 8R 8S 8T 8U 8V 8W 8X 8Y 8Z 8a 8b 8c 8d 8e 8f 8g 8h 8i 8j 8k 8l 8m 8n 8o 8p
8q 8r 8s 8t 8u 8v 8w 8x 8y 8z 9 90 91 92 93 94 95 96 97 98 99 9A 9B 9C 9D 9E
9F 9G 9H 9I 9J 9K 9L 9M 9N 9O 9P 9Q 9R 9S 9T 9U 9V 9W 9X 9Y 9Z 9a 9b 9c 9d 9e
9f 9g 9h 9i 9j 9k 9l 9m 9n 9o 9p 9q 9r 9s 9t 9u 9v 9w 9x 9y 9z A B C D E F G H
I J K L M N O P Q R S T U V W X Y Z a a0 a1 a2 a3 a4 a5 a6 a7 a8 a9 aA aB aC
aD aE aF aG aH aI aJ aK aL aM aN aO aP aQ aR aS aT aU aV aW aX aY aZ aa ab ac
ad ae af ag ah ai aj ak al am an ao ap aq ar as at au av aw ax ay az b b0 b1
b2 b3 b4 b5 b6 b7 b8 b9 bA bB bC bD bE bF bG bH bI bJ bK bL bM bN bO bP bQ bR
bS bT bU bV bW bX bY bZ ba bb bc bd be bf bg bh bi bj bk bl bm bn bo bp bq br
bs bt bu bv bw bx by bz c c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 cA cB cC cD cE cF cG
cH cI cJ cK cL cM cN cO cP cQ cR cS cT cU cV cW cX cY cZ ca cb cc cd ce cf cg
ch ci cj ck cl cm cn co cp cq cr cs ct cu cv cw cx cy cz d d0 d1 d2 d3 d4 d5
d6 d7 d8 d9 dA dB dC dD dE dF dG dH dI dJ dK dL dM dN dO dP dQ dR dS dT dU dV
dW dX dY dZ da db dc dd de df dg dh di dj dk dl dm dn do dp dq dr ds dt du dv
dw dx dy dz e e0 e1 e2 e3 e4 e5 e6 e7 e8 e9 eA eB eC eD eE eF eG eH eI eJ eK
eL eM eN eO eP eQ eR eS eT eU eV eW eX eY eZ ea eb ec ed ee ef eg eh ei ej ek
el em en eo ep eq er es et eu ev ew ex ey ez f f0 f1 f2 f3 f4 f5 f6 f7 f8 f9
fA fB fC fD fE fF fG fH fI fJ fK fL fM fN fO fP fQ fR fS fT fU fV fW fX fY fZ
fa fb fc fd fe ff fg fh fi fj fk fl fm fn fo fp fq fr fs ft fu fv fw fx fy fz
g g0 g1 g2 g3 g4 g5 g6 g7 g8 g9 gA gB gC gD gE gF gG gH gI gJ gK gL gM gN gO
gP gQ gR gS gT gU gV gW gX gY gZ ga gb gc gd ge gf gg gh gi gj gk gl gm gn go
gp gq gr gs gt gu gv gw gx gy gz h h0 h1 h2 h3 h4 h5 h6 h7 h8 h9 hA hB hC hD
hE hF hG hH hI hJ hK hL hM hN hO hP hQ hR hS hT hU hV hW hX hY hZ ha hb hc hd
he hf hg hh hi hj hk hl hm hn ho hp hq hr hs ht hu hv hw hx hy hz i i0 i1 i2
i3 i4 i5 i6 i7 i8 i9 iA iB iC iD iE iF iG iH iI iJ iK iL iM iN iO iP iQ iR iS
iT iU iV iW iX ia ib ic id ie if ig ih ii ij ik il im in io ip iq ir is it iu
iv iw ix iy iz j k l m n o p q r s t u v w x y z | capsid protein |
Q79791_9HIV1 1-231
> hide atoms
> select /0
1800 atoms, 1841 bonds, 231 residues, 1 model selected
> show sel target ab
> measure sasa protein 0 & protein sum :gly,pro
Expected a keyword
> measure sasa protein /0 & protein sum :gly,pro
Expected a keyword
> measure sasa /0 & protein sum :phe,tyr,trp
Solvent accessible area for /0 & protein (1800 atoms) = 13926
Solvent accessible area for :phe,tyr,trp (190512 atoms) of /0 & protein (1800
atoms) = 425.04
> measure sasa /0 select ::area>25
Expected a keyword
> surface protein enclose protein
> color sel magenta
> select /0:1-231
1800 atoms, 1841 bonds, 231 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 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: 3.11.2
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: MacBook Pro
Model Identifier: MacBookPro18,4
Model Number: Z15K00059D/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 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 hours, 24 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U4021QW:
Resolution: 7680 x 3240
UI Looks like: 3840 x 1620 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
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: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.3.2
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: 1.7.1
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: 1.1.3
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: 1.1.8
ChimeraX-ListInfo: 1.2.2
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: 2.6.1
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: 1.5.14
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: 1.13.1
ChimeraX-PDB: 2.7.3
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
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: 1.12.4
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: 1.33.3
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-vrml: 1.0
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: 0.2.1
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: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
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: 25.1.2
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
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: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (4)
comment:1 by , 14 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash drawing frame |
comment:2 by , 14 months ago
comment:3 by , 14 months ago
| Summary: | Crash drawing frame → Graphics crash, macOS 14.5, Mac M1 Max GPU |
|---|
comment:4 by , 14 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
While this is reproducible it seems almost certainly a graphics driver limitation caused by making an extremely large surface, probably on the order of 700 million triangles judging from ChimeraX using 24 Gbytes, and each triangle taking about 28 bytes.
Note:
See TracTickets
for help on using tickets.
Duplicate of #15877.
I tried repeating the exact same steps as in the log on my MacBook Pro M1 Max laptop (MacBookPro18,2 with 32 GB memory). The surface calculation took 6 minutes, got up to peak memory use of 24 Gbytes. And it crashed exactly the same way at the command "select /0:1-231". So it is reproducible.