![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#6897 closed defect (nonchimerax)
Graphics driver crash, macOS 12.3.1, Radeon RX Vega 64
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
I asked CHIMERAX to use external GPU and then it was not working.
Fatal Python error: Aborted
Current thread 0x0000000116d28600 (most recent call first):
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1626 in set_multishadow_view
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 227 in _draw_scene
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 165 in draw
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2022-05-18 13:29:50.00 +0200","app_version":"1.3.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.3.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.3.1 (21E258)","incident_id":"B5DCBA47-D714-4B01-9257-43E702DD8532","name":"ChimeraX"}
{
"uptime" : 180000,
"procLaunch" : "2022-05-18 11:09:48.5418 +0200",
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookAir8,1",
"procStartAbsTime" : 171947025641674,
"coalitionID" : 15050,
"osVersion" : {
"train" : "macOS 12.3.1",
"build" : "21E258",
"releaseType" : "User"
},
"captureTime" : "2022-05-18 13:29:40.4033 +0200",
"incident" : "B5DCBA47-D714-4B01-9257-43E702DD8532",
"bug_type" : "309",
"pid" : 43600,
"procExitAbsTime" : 180338603826432,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EC590108-7EE4-5300-83B2-3392AB4761B4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "83C67B3E-A205-4F5D-C707-FF206C6208CC",
"wakeTime" : 9349,
"bridgeVersion" : {"build":"19P4243","train":"6.4"},
"sleepWakeUUID" : "4FD36150-1E39-4C46-8F23-5AAB04C927FC",
"sip" : "enabled",
"externalGPUInfo" : "ID Vend\/Dev\nb622 687f1002\nSeconds Ago ID Type\n 380.0 b622 Attach\n",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"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 =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb
Summary of feedback from opening
/Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb
---
warnings | Duplicate atom serial number found: 12179
Duplicate atom serial number found: 12180
Duplicate atom serial number found: 12181
Duplicate atom serial number found: 12182
Duplicate atom serial number found: 12183
24250 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 62 6262 ALA J 3 PHE J 8
0
Start residue of secondary structure not found: SHEET 63 6363 THR J 15 ASP J
18 0
Start residue of secondary structure not found: SHEET 64 6464 ALA J 33 HIS J
35 0
End residue of secondary structure not found: SHEET 68 6868 VAL J 271 ALA J
275 0
Chain information for gp56-gp17-coot-101.pdb #1
---
Chain | Description
A B C D E F H I | No description available
G | No description available
J | No description available
K | No description available
L | No description available
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
shweta.bhatt@cpr.ku.dk is subscribed to the ChimeraX announcements list
> set bgColor white
> save /Users/mvc581/Desktop/image12.png supersample 3
> open
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb
Summary of feedback from opening
/Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb
---
warnings | Duplicate atom serial number found: 12179
Duplicate atom serial number found: 12180
Duplicate atom serial number found: 12181
Duplicate atom serial number found: 12182
Duplicate atom serial number found: 12183
24250 messages similar to the above omitted
Start residue of secondary structure not found: SHEET 62 6262 ALA J 3 PHE J 8
0
Start residue of secondary structure not found: SHEET 63 6363 THR J 15 ASP J
18 0
Start residue of secondary structure not found: SHEET 64 6464 ALA J 33 HIS J
35 0
End residue of secondary structure not found: SHEET 68 6868 VAL J 271 ALA J
275 0
Chain information for gp56-gp17-coot-101.pdb #2
---
Chain | Description
A B C D E F H I | No description available
G | No description available
J | No description available
K | No description available
L | No description available
> close #2
> open
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/maps/Fullcapsid/FP_job403_700_300.mrc
Opened FP_job403_700_300.mrc as #2, grid size 401,401,401, pixel 1.11, shown
at level 0.0294, step 2, values float32
> open
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/maps/Fullcapsid/gp17_FP_700_300.mrc
Opened gp17_FP_700_300.mrc as #3, grid size 401,401,401, pixel 1.11, shown at
level 3.63e-06, step 2, values float32
> open
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/maps/Fullcapsid/FP_700_300_blur20.mrc
Opened FP_700_300_blur20.mrc as #4, grid size 540,540,540, pixel 0.823, shown
at level 0.0266, step 4, values float32
> close #3
> volume #4 step 1
> style stick
Changed 33148 atom styles
> style ball
Changed 33148 atom styles
> volume #4 color #0433ff
> show cartoons
> hide atoms
> volume #4 color #0433ff86
> volume #4 color #0433ff54
> volume #4 color black
> volume #4 color #d6d6d6
> volume #4 color #0433ff
> volume #4 color #0433ff2c
> volume #4 color #0433ff2b
> undo
> redo
> style sphere
Changed 33148 atom styles
> ui tool show Log
> save /Users/mvc581/Desktop/image13.png supersample 3
> volume #4 color #fffb00
> volume #4 color #fffb003c
> volume #4 color #fffb002c
> volume #4 color #fffb002b
> color bychain
> volume #4 color #ffd479
> volume #4 color #ffd4792a
> volume #4 color #ffd4793a
> volume #4 color #ffd4793b
> volume #4 color #00fdff
> volume #4 color #00fdff1b
> volume #4 color #d6d6d6
> volume #4 color #fffc79
> volume #4 color #fffb00
> volume #4 color #fffb001e
> save /Users/mvc581/Desktop/image14.png supersample 3
> save /Users/mvc581/Desktop/image15.png supersample 3
> volume #4 color #76d6ff
> volume #4 color #76d6ff94
> volume #4 color #76d6ff6d
> volume #4 color #76d6ff41
> volume #4 color #76d6ff2e
> style ball
Changed 33148 atom styles
> volume #4 color #212121
> volume #4 color #2121215e
> volume #4 color #21212125
> volume #4 color #21212120
> volume #4 color #2121211d
> save /Users/mvc581/Desktop/image10.png supersample 3
> select /A
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel forest green
> color sel blue
> select /B
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /C
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /D
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /E
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /E
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> select /F
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /G
2919 atoms, 2977 bonds, 1 pseudobond, 383 residues, 2 models selected
> color (#!1 & sel) blue
> select /H
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /I
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> color sel blue
> select /I
3048 atoms, 3107 bonds, 401 residues, 1 model selected
> select /J
2052 atoms, 2089 bonds, 279 residues, 1 model selected
> color sel orange red
> select /J
2052 atoms, 2089 bonds, 279 residues, 1 model selected
> select /K
1902 atoms, 1933 bonds, 277 residues, 1 model selected
> color sel orange red
> select /L
1891 atoms, 1921 bonds, 1 pseudobond, 275 residues, 2 models selected
> color (#!1 & sel) orange red
> select clear
> save /Users/mvc581/Desktop/image10.png supersample 3
> save /Users/mvc581/Desktop/image11.png supersample 3
> ui tool show "Model Panel"
> show #!4 models
> hide #!4 models
> show #!2 models
> close #2
> show #!4 models
> hide #!4 models
> hide #!1 models
> open
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/FROM_COMPUTEROME/N4-FP_capsid/FP-
> job740_postprocess_masked.mrc
Opened FP-job740_postprocess_masked.mrc as #2, grid size 1350,1350,1350, pixel
1.11, shown at step 1, values float32
> volume #2 region 0,0,0,1349,1349,1349 step 8
> volume #2 step 1
/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log
h.show_data(log(counts + 1))
> lighting soft
> save
> /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/FROM_COMPUTEROME/N4_capsids_pdbs.cxs
> includeMaps true
Traceback (most recent call last):
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 624, in save
fserialize(stream, data)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large
ValueError: bytes object is too large
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 624, in save
fserialize(stream, data)
File
"/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 298, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 295, in msgpack._cmsgpack.Packer.pack
File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
ValueError: bytes object is too large
ValueError: bytes object is too large
File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status
r.draw_background()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1166, in draw_background
GL.glClear(flags)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/OpenGL/platform/baseplatform.py", line 415, in __call__
return self( *args, **named )
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status
r.draw_background()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1166, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/statusbar.py", line 150, in status
r.draw_background()
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1166, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.8.15
OpenGL renderer: AMD Radeon RX Vega 64 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir8,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1,6 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)
OS Loader Version: 540.100.7~23
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 8 days 19:30
Graphics/Displays:
Intel UHD Graphics 617:
Chipset Model: Intel UHD Graphics 617
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x87c0
Revision ID: 0x0002
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2719D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 9QF45R2
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple USB-C Digital AV Adapter
Adapter Firmware Version: 2,35
AMD Radeon RX Vega 64:
Chipset Model: AMD Radeon RX Vega 64
Type: External GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x687f
Revision ID: 0x00c1
Metal Family: Supported, Metal GPUFamily macOS 2
GPU is Removable: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → External GPU: Graphics hardware encountered an error and was reset |
comment:2 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | External GPU: Graphics hardware encountered an error and was reset → Graphics driver crash, macOS 12.3.1, Radeon RX Vega 64 |
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Apple graphics driver crash. Unfortunately Intel Mac OpenGL graphics drivers are unstable and Apple has no interest in fixing it. The M1 Mac OpenGL graphics is completely reliable. More details here
https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#maccrash
I see also in this bug report that saving a session file (*.cxs) failed because it tried to include maps larger than 4 Gbytes. We hope to fix that. The Google msgpack library used by ChimeraX to save sessions is limited to 4 GByte size objects, so we will need to add code to divide large maps into smaller pieces to save them. Saving without the "includeMaps" option avoids this problem, but then the session file includes a path to the map file on the local disk and if that map file is removed won't be restored when opening the session again unless you provide a new path to the missing map.