Opened 4 years ago

Closed 4 years ago

#6441 closed defect (can't reproduce)

Crash in self.graphics_window.mapFromGlobal(QCursor.pos())

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

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.
Fatal Python error: Bus error

Current thread 0x0000000203059e00 (most recent call first):
  File "/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mouse_modes/mousemodes.py", line 514 in _cursor_position
  File "/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mouse_modes/mousemodes.py", line 472 in mouse_pause_tracking
  File "/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 140 in _redraw_timer_callback
  File "/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py301event_loop/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py867init/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py1018/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py87_run_code/private/var/folders/4n/w8pqvfmn6k3g3yngkc79qj1c0000gn/T/AppTranslocation/BC9AD1C5-AE9E-439F-BBAD-A0F4F0A0C81B/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py197_run_module_as_main

Process:               ChimeraX [610]
Path:                  /Volumes/VOLUME/*/ChimeraX-1.3.app/Contents/MacOS/ChimeraX
Identifier:            edu.ucsf.cgl.ChimeraX
Version:               1.3.0 (1.3.0.0)
Code Type:             X86-64 (Translated)
Parent Process:        ??? [1]
Responsible:           ChimeraX [610]
User ID:               501

Date/Time:             2022-03-23 10:59:23.272 +0100
OS Version:            macOS 11.5.2 (20G95)
Report Version:        12
Anonymous UUID:        EE595A99-6D69-E7DC-EED0-546482C19A30


Time Awake Since Boot: 3700 seconds

System Integrity Protection: enabled

Crashed Thread:        0  CrBrowserMain  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGBUS)
Exception Codes:       KERN_MEMORY_ERROR at 0x000000010b359018
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Bus error: 10
Termination Reason:    Namespace SIGNAL, Code 0xa
Terminating Process:   exc handler [610]

VM Regions Near 0x10b359018:
    Rosetta Generic             10b358000-10b359000    [    4K] rw-/rwx SM=PRV  
--> mapped file                 10b359000-10b5be000    [ 2452K] r-x/rwx SM=COW  Object_id=c9046f0d
    mapped file                 10b5be000-10b5f8000    [  232K] rw-/rwx SM=COW  Object_id=c8e9450d

Thread 0 Crashed:: CrBrowserMain  Dispatch queue: com.apple.main-thread
0   dyld                          	0x0000000202f9da90 ImageLoaderMachO::usesTwoLevelNameSpace() const + 8
1   	0x0000000102ebd01c ???
2   dyld                          	0x0000000202fa92ad ImageLoaderMachOCompressed::doBindFastLazySymbol(unsigned int, ImageLoader::LinkContext const&, void (*)(), void (*)()) + 45
3   dyld                          	0x0000000202f8754b dyld::fastBindLazySymbol(ImageLoader**, unsigned long) + 86
4   libdyld.dylib                 	0x00007fff20474ce8 _dyld_fast_stub_entry(void*, long) + 65
5   libdyld.dylib                 	0x00007fff20474c26 dyld_stub_binder + 282
6   ???                           	0x000000010b5be1a8 ???
7   _multiarray_umath.cpython-39-darwin.so	000000000000000000 0 + 0
8   ???                           	0x0000000000000001 0 + 1

Thread 1:: com.apple.rosetta.exceptionserver
0   runtime                       	0x00007ffdffe28a28 0x7ffdffe24000 + 18984
1   runtime                       	0x00007ffdffe2deec 0x7ffdffe24000 + 40684
2   runtime                       	0x00007ffdffe2f2c0 0x7ffdffe24000 + 45760

Thread 2:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 3:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 4:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 5:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 6:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 7:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 8:
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000010cb4ba9f ???
3   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
4   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 9:: ThreadPoolServiceThread
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff2042e1d2 kevent64 + 10
2   ???                           	0x000000012d0b6cc7 ???
3   ???                           	0x000000012d03f62b ???
4   ???                           	0x000000012d0037cb ???
5   ???                           	0x000000012d04aa94 ???
6   ???                           	0x000000012d05ea7d ???
7   ???                           	0x000000012d0a7e07 ???
8   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
9   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 10:: ThreadPoolBackgroundWorker
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d054778 ???
4   ???                           	0x000000012d055150 ???
5   ???                           	0x000000012d054c44 ???
6   ???                           	0x000000012d0a7e07 ???
7   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
8   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 11:: Chrome_IOThread
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff2042e1d2 kevent64 + 10
2   ???                           	0x000000012d0b6cc7 ???
3   ???                           	0x000000012d03f62b ???
4   ???                           	0x000000012d0037cb ???
5   ???                           	0x0000000130f83f06 ???
6   ???                           	0x000000012d05ea7d ???
7   ???                           	0x000000012d0a7e07 ???
8   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
9   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 12:: NetworkConfigWatcher
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012cfd41db ???
5   ???                           	0x000000012d03f62b ???
6   ???                           	0x000000012d0037cb ???
7   ???                           	0x000000012d05ea7d ???
8   ???                           	0x000000012d0a7e07 ???
9   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
10  libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 13:: ThreadPoolForegroundWorker
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d054778 ???
4   ???                           	0x000000012d055150 ???
5   ???                           	0x000000012d054cd4 ???
6   ???                           	0x000000012d0a7e07 ???
7   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
8   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 14:: CompositorTileWorker1
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff20427cde __psynch_cvwait + 10
2   ???                           	0x000000012d0a3e18 ???
3   ???                           	0x000000012e35b5f8 ???
4   ???                           	0x000000012d0a7e07 ???
5   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
6   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 15:: Chrome_InProcGpuThread
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012cfd420f ???
4   ???                           	0x000000012d03f62b ???
5   ???                           	0x000000012d0037cb ???
6   ???                           	0x000000012d05ea7d ???
7   ???                           	0x000000012d0a7e07 ???
8   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
9   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 16:: Chrome_ChildIOThread
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff2042e1d2 kevent64 + 10
2   ???                           	0x000000012d0b6cc7 ???
3   ???                           	0x000000012d03f62b ???
4   ???                           	0x000000012d0037cb ???
5   ???                           	0x000000012d05ea7d ???
6   ???                           	0x000000012d0a7e07 ???
7   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
8   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 17:: VizCompositorThread
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012cfd41db ???
5   ???                           	0x000000012d03f62b ???
6   ???                           	0x000000012d0037cb ???
7   ???                           	0x000000012d05ea7d ???
8   ???                           	0x000000012d0a7e07 ???
9   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
10  libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 18:: NetworkConfigWatcher
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012cfd41db ???
5   ???                           	0x000000012d03f62b ???
6   ???                           	0x000000012d0037cb ???
7   ???                           	0x000000012d05ea7d ???
8   ???                           	0x000000012d0a7e07 ???
9   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
10  libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 19:: NetworkConfigWatcher
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012cfd41db ???
5   ???                           	0x000000012d03f62b ???
6   ???                           	0x000000012d0037cb ???
7   ???                           	0x000000012d05ea7d ???
8   ???                           	0x000000012d0a7e07 ???
9   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
10  libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 20:: ThreadPoolSingleThreadForegroundBlocking0
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012d05476a ???
5   ???                           	0x000000012d055150 ???
6   ???                           	0x000000012d054d34 ???
7   ???                           	0x000000012d0a7e07 ???
8   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
9   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 21:: MemoryInfra
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012cfd41db ???
5   ???                           	0x000000012d03f62b ???
6   ???                           	0x000000012d0037cb ???
7   ???                           	0x000000012d05ea7d ???
8   ???                           	0x000000012d0a7e07 ???
9   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
10  libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 22:: NetworkConfigWatcher
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012cfd41db ???
5   ???                           	0x000000012d03f62b ???
6   ???                           	0x000000012d0037cb ???
7   ???                           	0x000000012d05ea7d ???
8   ???                           	0x000000012d0a7e07 ???
9   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
10  libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 23:: com.apple.NSEventThread
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   com.apple.CoreFoundation      	0x00007fff20553855 __CFRunLoopServiceMachPort + 316
3   com.apple.CoreFoundation      	0x00007fff20551f0b __CFRunLoopRun + 1332
4   com.apple.CoreFoundation      	0x00007fff20551310 CFRunLoopRunSpecific + 567
5   ???                           	0x00007fff22e0923a ???
6   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
7   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 24:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d0ac2cf ???
4   ???                           	0x000000012d05476a ???
5   ???                           	0x000000012d054e3d ???
6   ???                           	0x000000012d054c74 ???
7   ???                           	0x000000012d0a7e07 ???
8   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
9   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 25:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 26:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 27:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 28:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 29:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 30:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 31:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 32:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 33:
0   runtime                       	0x00007ffdffe467c8 0x7ffdffe24000 + 141256

Thread 34:: ThreadPoolForegroundWorker
0   ???                           	0x00007ffe946928f4 ???
1   libsystem_kernel.dylib        	0x00007fff204252ba mach_msg_trap + 10
2   ???                           	0x000000012d0ac492 ???
3   ???                           	0x000000012d054778 ???
4   ???                           	0x000000012d054e3d ???
5   ???                           	0x000000012d054cd4 ???
6   ???                           	0x000000012d0a7e07 ???
7   libsystem_pthread.dylib       	0x00007fff2045a8fc _pthread_start + 224
8   libsystem_pthread.dylib       	0x00007fff20456443 thread_start + 15

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x000000010b359000  rbx: 0x00007fff20474d1a  rcx: 0x00007fff20474d1a  rdx: 0x0000000203026298
  rdi: 0x000000020302e3b0  rsi: 0x0000000000000e87  rbp: 0x00007f80d815fd20  rsp: 0x00007f80d815fd20
   r8: 0x00007fff20474d33   r9: 0x88f87a276f6ffcb2  r10: 0x0000000203059eac  r11: 0x000000010b5be1a8
  r12: 0x88f87a276f6ffcb2  r13: 0x000000020302e3b0  r14: 0x0000000000000e87  r15: 0x0000000203026298
  rip: 0x0000000202f9da90  rfl: 0x0000000000000202


Binary Images:
                 0 - 0xffffffffffffffff +_multiarray_umath.cpython-39-darwin.so (???) /Volumes/VOLUME/*/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_multiarray_umath.cpython-39-darwin.so
       0x10ae47000 -        0x10ae96fff +libRosettaRuntime (203.58)  /Library/Apple/*/libRosettaRuntime
       0x202f82000 -        0x20301dfff  dyld (852.2)  /usr/lib/dyld
    0x7ffdffe24000 -     0x7ffdffe53fff  runtime (203.58)  /usr/libexec/rosetta/runtime
    0x7fff20192000 -     0x7fff20193fff  libsystem_blocks.dylib (79)  /usr/lib/system/libsystem_blocks.dylib
    0x7fff20194000 -     0x7fff201c9fff  libxpc.dylib (2038.120.1)  /usr/lib/system/libxpc.dylib
    0x7fff201ca000 -     0x7fff201e1fff  libsystem_trace.dylib (1277.120.1)  /usr/lib/system/libsystem_trace.dylib
    0x7fff201e2000 -     0x7fff2027ffff  libcorecrypto.dylib (1000.140.4)  /usr/lib/system/libcorecrypto.dylib
    0x7fff20280000 -     0x7fff202acfff  libsystem_malloc.dylib (317.140.5)  /usr/lib/system/libsystem_malloc.dylib
    0x7fff202ad000 -     0x7fff202f1fff  libdispatch.dylib (1271.120.2)  /usr/lib/system/libdispatch.dylib
    0x7fff202f2000 -     0x7fff2032bfff  libobjc.A.dylib (824)  /usr/lib/libobjc.A.dylib
    0x7fff2032c000 -     0x7fff2032efff  libsystem_featureflags.dylib (28.60.1)  /usr/lib/system/libsystem_featureflags.dylib
    0x7fff2032f000 -     0x7fff203b7fff  libsystem_c.dylib (1439.141.1)  /usr/lib/system/libsystem_c.dylib
    0x7fff203b8000 -     0x7fff2040dfff  libc++.1.dylib (905.6)  /usr/lib/libc++.1.dylib
    0x7fff2040e000 -     0x7fff20423fff  libc++abi.dylib (905.6)  /usr/lib/libc++abi.dylib
    0x7fff20424000 -     0x7fff20453fff  libsystem_kernel.dylib (7195.141.2)  /usr/lib/system/libsystem_kernel.dylib
    0x7fff20454000 -     0x7fff2045ffff  libsystem_pthread.dylib (454.120.2)  /usr/lib/system/libsystem_pthread.dylib
    0x7fff20460000 -     0x7fff2049bfff  libdyld.dylib (852.2)  /usr/lib/system/libdyld.dylib
    0x7fff2049c000 -     0x7fff204a5fff  libsystem_platform.dylib (254.80.2)  /usr/lib/system/libsystem_platform.dylib
    0x7fff204a6000 -     0x7fff204d1fff  libsystem_info.dylib (542.40.3)  /usr/lib/system/libsystem_info.dylib
    0x7fff204d2000 -     0x7fff2096ffff  com.apple.CoreFoundation (6.9 - 1777.103)  /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
    0x7fff2256b000 -     0x7fff227cafff  libicucore.A.dylib (66112)  /usr/lib/libicucore.A.dylib
    0x7fff227cb000 -     0x7fff227d4fff  libsystem_darwin.dylib (1439.141.1)  /usr/lib/system/libsystem_darwin.dylib
    0x7fff22bea000 -     0x7fff22bf5fff  libsystem_notify.dylib (279.40.4)  /usr/lib/system/libsystem_notify.dylib
    0x7fff24b82000 -     0x7fff24b90fff  libsystem_networkextension.dylib (1295.140.3)  /usr/lib/system/libsystem_networkextension.dylib
    0x7fff24bef000 -     0x7fff24c05fff  libsystem_asl.dylib (385)  /usr/lib/system/libsystem_asl.dylib
    0x7fff26300000 -     0x7fff26307fff  libsystem_symptoms.dylib (1431.140.1)  /usr/lib/system/libsystem_symptoms.dylib
    0x7fff28613000 -     0x7fff28623fff  libsystem_containermanager.dylib (318.100.4)  /usr/lib/system/libsystem_containermanager.dylib
    0x7fff2932b000 -     0x7fff2932efff  libsystem_configuration.dylib (1109.140.1)  /usr/lib/system/libsystem_configuration.dylib
    0x7fff2932f000 -     0x7fff29333fff  libsystem_sandbox.dylib (1441.141.1)  /usr/lib/system/libsystem_sandbox.dylib
    0x7fff29f33000 -     0x7fff29f35fff  libquarantine.dylib (119.40.2)  /usr/lib/system/libquarantine.dylib
    0x7fff2a4d1000 -     0x7fff2a4ddfff  libbz2.1.0.dylib (44)  /usr/lib/libbz2.1.0.dylib
    0x7fff2a4de000 -     0x7fff2a4e2fff  libsystem_coreservices.dylib (127.1)  /usr/lib/system/libsystem_coreservices.dylib
    0x7fff2a6df000 -     0x7fff2a6f1fff  libz.1.dylib (76)  /usr/lib/libz.1.dylib
    0x7fff2a6f2000 -     0x7fff2a73dfff  libsystem_m.dylib (3186.100.3)  /usr/lib/system/libsystem_m.dylib
    0x7fff2a73f000 -     0x7fff2a744fff  libmacho.dylib (980)  /usr/lib/system/libmacho.dylib
    0x7fff2a761000 -     0x7fff2a76cfff  libcommonCrypto.dylib (60178.120.3)  /usr/lib/system/libcommonCrypto.dylib
    0x7fff2a76d000 -     0x7fff2a777fff  libunwind.dylib (201)  /usr/lib/system/libunwind.dylib
    0x7fff2a778000 -     0x7fff2a77ffff  liboah.dylib (203.58)  /usr/lib/liboah.dylib
    0x7fff2a780000 -     0x7fff2a78afff  libcopyfile.dylib (173.40.2)  /usr/lib/system/libcopyfile.dylib
    0x7fff2a78b000 -     0x7fff2a792fff  libcompiler_rt.dylib (102.2)  /usr/lib/system/libcompiler_rt.dylib
    0x7fff2a793000 -     0x7fff2a795fff  libsystem_collections.dylib (1439.141.1)  /usr/lib/system/libsystem_collections.dylib
    0x7fff2a796000 -     0x7fff2a798fff  libsystem_secinit.dylib (87.60.1)  /usr/lib/system/libsystem_secinit.dylib
    0x7fff2a799000 -     0x7fff2a79bfff  libremovefile.dylib (49.120.1)  /usr/lib/system/libremovefile.dylib
    0x7fff2a79c000 -     0x7fff2a79cfff  libkeymgr.dylib (31)  /usr/lib/system/libkeymgr.dylib
    0x7fff2a79d000 -     0x7fff2a7a4fff  libsystem_dnssd.dylib (1310.140.1)  /usr/lib/system/libsystem_dnssd.dylib
    0x7fff2a7a5000 -     0x7fff2a7aafff  libcache.dylib (83)  /usr/lib/system/libcache.dylib
    0x7fff2a7ab000 -     0x7fff2a7acfff  libSystem.B.dylib (1292.120.1)  /usr/lib/libSystem.B.dylib
    0x7fff2a7ad000 -     0x7fff2a7b0fff  libfakelink.dylib (3)  /usr/lib/libfakelink.dylib
    0x7fff2a7b1000 -     0x7fff2a7b1fff  com.apple.SoftLinking (1.0 - 1)  /System/Library/PrivateFrameworks/SoftLinking.framework/Versions/A/SoftLinking
    0x7fff2dd09000 -     0x7fff2dd09fff  liblaunch.dylib (2038.120.1)  /usr/lib/system/liblaunch.dylib
    0x7fff301a0000 -     0x7fff301a0fff  libsystem_product_info_filter.dylib (8.40.1)  /usr/lib/system/libsystem_product_info_filter.dylib
    0x7fff5d246000 -     0x7fff5d255fff  libSimplifiedChineseConverter.dylib (90)  /System/Library/CoreServices/Encodings/libSimplifiedChineseConverter.dylib

Translated Code Information:
  tmp0: 0x0000000102ebd880 tmp1: 0x0000000202fa92ad tmp2: 0x0000000102ebd01c


External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=517.7M resident=0K(0%) swapped_out_or_unallocated=517.7M(100%)
Writable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               128K        1 
Activity Tracing                   256K        1 
CG backing stores                 5760K        6 
CG image                           112K       15 
CoreAnimation                       96K       10 
CoreGraphics                        12K        2 
CoreUI image data                 2220K       17 
Foundation                          16K        1 
Kernel Alloc Once                    8K        1 
MALLOC                           339.2M       69 
MALLOC guard page                  192K        8 
MALLOC_MEDIUM (reserved)         656.0M        6         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
Mach message                        24K        6 
OpenGL GLSL                        384K        5 
Rosetta Arena                     4096K        2 
Rosetta Generic                   1492K      370 
Rosetta IndirectBranch            1024K        1 
Rosetta JIT                      128.0M        1 
Rosetta Return Stack               680K       68 
Rosetta Thread Context             680K       68 
STACK GUARD                         36K        9 
Stack                            144.6M       34 
Stack Guard                       56.1M       25 
VM_ALLOCATE                       98.6M      156 
VM_ALLOCATE (reserved)           160.1M       11         reserved VM address space (unallocated)
__DATA                             532K       53 
__DATA_CONST                      2984K       42 
__DATA_DIRTY                        95K       24 
__LINKEDIT                       505.2M        7 
__OBJC_RO                         70.3M        1 
__OBJC_RW                         2480K        2 
__TEXT                            12.6M       52 
__UNICODE                          588K        1 
dylib                             1932K       19 
dylib (reserved)                   120K       12         reserved VM address space (unallocated)
mapped file                        5.3G      835 
shared memory                     7396K       35 
unshared pmap                      9.9M        5 
===========                     =======  ======= 
TOTAL                              7.8G     1982 
TOTAL, minus reserved VM space     6.6G     1982 

===== 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  


===== 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  




OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 4 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 11.5.2 (20G95)
      Kernel Version: Darwin 20.6.0
      Time since boot: 3:29

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        DELL U3219Q:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: 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 Eric Pettersen, 4 years ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in self.graphics_window.mapFromGlobal(QCursor.pos())

comment:2 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Log has no commands, so appears to have crashed on startup. But memory use of 7.8 Gbytes suggests data had been loaded.

Similar to mac crash #6426, also #4835 and a few others, all on Apple M1. Also about 20 Windows crashes in this cursor position routine.

Python traceback suggests it was trying to get the mouse position with Qt.

        p = self.graphics_window.mapFromGlobal(QCursor.pos())

But C traceback says the crash was in loading a dynamic library maybe related to numpy

Thread 0 Crashed:: CrBrowserMain  Dispatch queue: com.apple.main-thread
0   dyld                          	0x0000000202f9da90 ImageLoaderMachO::usesTwoLevelNameSpace() const + 8
1   	0x0000000102ebd01c ???
2   dyld                          	0x0000000202fa92ad ImageLoaderMachOCompressed::doBindFastLazySymbol(unsigned int, ImageLoader::LinkContext const&, void (*)(), void (*)()) + 45
3   dyld                          	0x0000000202f8754b dyld::fastBindLazySymbol(ImageLoader**, unsigned long) + 86
4   libdyld.dylib                 	0x00007fff20474ce8 _dyld_fast_stub_entry(void*, long) + 65
5   libdyld.dylib                 	0x00007fff20474c26 dyld_stub_binder + 282
6   ???                           	0x000000010b5be1a8 ???
7   _multiarray_umath.cpython-39-darwin.so	000000000000000000 0 + 0

On an Apple M1 CPU using Rosetta emulation.

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