![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5709 closed defect (nonchimerax)
Graphics driver crash, macOS 12.0.1, Intel Iris Plus Graphics 640, VM - Fault hit memory shortage
| 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: 1.3rc202111292147 (2021-11-29 21:47:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x000070001b548000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001a545000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700019542000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001853f000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001753c000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700016539000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700015536000 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000010fe0a600 (most recent call first):
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.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":"2021-11-30 22:48:07.00 -0800","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 12.0.1 (21A559)","incident_id":"29D9CD0F-7B57-40A4-A304-42115F1FCDCC","name":"ChimeraX"}
{
"uptime" : 88000,
"procLaunch" : "2021-11-30 13:00:54.2163 -0800",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"procStartAbsTime" : 78115769201398,
"coalitionID" : 14990,
"osVersion" : {
"train" : "macOS 12.0.1",
"build" : "21A559",
"releaseType" : "User"
},
"captureTime" : "2021-11-30 22:47:40.5235 -0800",
"incident" : "29D9CD0F-7B57-40A4-A304-42115F1FCDCC",
"bug_type" : "309",
"pid" : 43865,
"procExitAbsTime" : 88062221966537,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.3-rc2021.11.29.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"CDA57E72-B4E5-5DF1-96E8-6823F7DDBA3F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "95028204-1289-77F6-0661-27B934961CB9",
"wakeTime" : 7081,
"sleepWakeUUID" : "9FC2219B-BF62-4EE2-9C92-69CC7D46DE9B",
"sip" : "enabled",
"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},
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"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.3-rc2021.11.29.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.6"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5429145600,
"size" : 8192,
"uuid" : "d6125191-ebf8-3e9e-aa83-52e897d6ea11",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.3-rc2021.11.29.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
"name" : "_queue.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4538998784,
"size" : 20480,
"uuid" : "96e817d5-7f44-3a56-9df2-c334b7dfaff9",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.3-rc2021.11.29.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
"name" : "select.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703510175744,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "3002b545-6841-3fc8-91a2-bcfbe5872465",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1855.105"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703554654208,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15257600,
"uuid" : "dd0028a3-78e3-3a8a-a51b-ddd68123adef",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5800939520,
"size" : 61087744,
"uuid" : "6286b1a0-1fc3-3620-a830-7af7902ead7f",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.3-rc2021.11.29.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4626857984,
"size" : 62603264,
"uuid" : "9112000d-375c-34f0-9a66-9d68f91a12cd",
"path" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.3-rc2021.11.29.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
}
],
"sharedCache" : {
"base" : 140703506632704,
"size" : 15213641728,
"uuid" : "3d05845f-3f65-358f-9ebf-2236e772ac01"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=4.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 1576K 49 \nColorSync 248K 29 \nCoreAnimation 5108K 82 \nCoreGraphics 12K 2 \nCoreServices 108K 1 \nCoreUI image data 5216K 44 \nFoundation 16K 1 \nKernel Alloc Once 32K 3 \nMALLOC 2.5G 630 \nMALLOC guard page 32K 7 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 5 \nSTACK GUARD 116K 29 \nStack 251.2M 30 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.2G 121 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__DATA 42.9M 707 \n__DATA_CONST 31.5M 342 \n__DATA_DIRTY 1641K 220 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 734.2M 171 \n__OBJC_RO 81.5M 1 \n__OBJC_RW 3120K 2 \n__TEXT 814.5M 695 \n__UNICODE 588K 1 \ndyld private memory 1024K 1 \nmapped file 514.0M 55 \nshared memory 2972K 23 \n=========== ======= ======= \nTOTAL 6.6G 3268 \nTOTAL, minus reserved VM space 6.2G 3268 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "6194416dea7ed64a7812a429"
},
"deploymentId" : 240000322
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
"deploymentId" : 240000162
},
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
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"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "614a34c5eae97a2111628dc5"
},
"deploymentId" : 240000271
},
{
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"factorPackIds" : {
},
"deploymentId" : 240000076
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.3rc202111292147 (2021-11-29)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nikolausflores/Downloads/Tbrucei_pp215fid.xyz
Install the SEQCROW bundle to open "XYZ file" format files.
Opener for format 'XYZ file' is not installed; see log for more info
> open /Users/nikolausflores/Downloads/Tbrucei_pp215.3dmod
Unrecognized file suffix '.3dmod'
Downloading bundle SEQCROW-1.3-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
WARNING: Value for scheme.platlib does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application
Support/ChimeraX/1.3/site-packages
sysconfig: /Users/nikolausflores/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.purelib does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application
Support/ChimeraX/1.3/site-packages
sysconfig: /Users/nikolausflores/Library/Python/3.9/lib/python/site-packages
WARNING: Value for scheme.headers does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application
Support/ChimeraX/include/python3.9/Send2Trash
sysconfig: /Users/nikolausflores/Library/Python/3.9/include/Send2Trash
WARNING: Value for scheme.scripts does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application Support/ChimeraX/bin
sysconfig: /Users/nikolausflores/Library/Python/3.9/bin
WARNING: Value for scheme.data does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application Support/ChimeraX
sysconfig: /Users/nikolausflores/Library/Python/3.9
WARNING: Additional context:
user = True
home = None
root = None
prefix = None
WARNING: Value for scheme.headers does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application
Support/ChimeraX/include/python3.9/SEQCROW
sysconfig: /Users/nikolausflores/Library/Python/3.9/include/SEQCROW
WARNING: Value for scheme.headers does not match. Please report this to
distutils: /Users/nikolausflores/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /Users/nikolausflores/Library/Python/3.9/include/UNKNOWN
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.
You should consider upgrading via the
'/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip' command.
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/nikolausflores/Downloads/SEQCROW-1.3-py3-none-any.whl
Requirement already satisfied: psutil in
/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.3) (5.8.0)
Requirement already satisfied: ChimeraX-Core=1.2 in
/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.3) (1.3rc202111292147)
Collecting Send2Trash
Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB)
Requirement already satisfied: scipy in
/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.3) (1.7.1)
Requirement already satisfied: numpy=1.16.5 in
/private/var/folders/79/9bpth0t959q66ym0dygfygh00000gn/T/AppTranslocation/1D3D22A0-39CC-4B3D-B80A-3892846E9389/d/ChimeraX-1.3-rc2021.11.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from scipy->SEQCROW==1.3) (1.21.2)
Installing collected packages: Send2Trash, SEQCROW
Successfully installed SEQCROW-1.3 Send2Trash-1.8.0
\---
Successfully installed SEQCROW-1.3 Send2Trash-1.8.0
Installed SEQCROW (1.3)
> open /Users/nikolausflores/Downloads/Tbrucei_pp215.3dmod
Unrecognized file suffix '.3dmod'
> open /Users/nikolausflores/Downloads/Tbrucei_pp215fid.xyz
Install the SEQCROW bundle to open "XYZ file" format files.
Opener for format 'XYZ file' is not installed; see log for more info
> help help:quickstart
> open /Users/nikolausflores/Downloads/Tbrucei_pp215_full_rec.mrc
Opened Tbrucei_pp215_full_rec.mrc as #1, grid size 960,364,928, pixel
10.2,10.2,10.2, shown at step 1, values float32
> set bgColor white
> set bgColor black
> volume #1 region 0,0,0,959,363,927 step 4
> set bgColor white
> volume #1 change image level 0.2071,0 level 1.201,0.8 level 1.743,1
> volume #1 level 0.1766
> volume #1 level 0.8578
> volume #1 level 1.098
> volume #1 level 0.6174
> volume #1 level 0.8778
> volume #1 step 2
> volume #1 level 1.221
> volume #1 level 1.367
> volume #1 level -0.3464
> volume #1 level -3.137
> volume #1 level 0.6819
> lighting soft
> lighting full
> lighting soft
> volume #1 level 0.7554
> volume #1 level 0.9023
> style stick
Changed 0 atom styles
> ui tool show "Side View"
> lighting shadows true intensity 0.5
> volume #1 step 16
> volume #1 step 4
> volume #1 step 2
> volume #1 step 4
> view
> graphics silhouettes true
> select #1
3 models selected
> ~select #1
Nothing selected
> set bgColor gray
> set bgColor black
> set bgColor white
> ui tool show "Color Actions"
> ui tool show "Surface Color"
> color cylindrical #1.2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff
> center 4878.8,-20.424,4715.4
> volume #1 step 2
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3rc202111292147 (2021-11-29)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.2.10
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 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: 8 GB
System Firmware Version: 447.40.12.0.0
OS Loader Version: 540.40.4~45
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 13 days 1:22
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
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)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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: 2.0.8
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: 1.3rc202111292147
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: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
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: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
Send2Trash: 1.8.0
SEQCROW: 1.3
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 , 4 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset: VM - Fault hit memory shortage |
comment:2 by , 4 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset: VM - Fault hit memory shortage → Graphics driver crash, macOS 12.0.1, Intel Iris Plus Graphics 640, VM - Fault hit memory shortage |
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Mac driver crash.