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Opened 3 years ago
Closed 3 years ago
#6876 closed defect (fixed)
Nogui save crash with labels / ensure exported graphics is up to date
| Reported by: | Eric Pettersen | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202205120056 (2022-05-12 00:56:21 UTC)
Description
Running attached file. The problem is that the save-command machinery does a session.update_loop.update_graphics_now() to ensure that graphics data structures are up to date before they get exported/save -- but with a label in the scene in nogui mode that call causes a crash.
Fatal Python error: Segmentation fault
Current thread 0x000000010fd27dc0 (most recent call first):
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 2201 in text_image_rgba
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/label/label3d.py", line 803 in _label_image
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/label/label3d.py", line 544 in
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/label/label3d.py", line 544 in _packed_texture
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/label/label3d.py", line 513 in _rebuild_label_graphics
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/label/label3d.py", line 503 in _update_graphics_if_needed
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 271 in check_for_drawing_change
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 86 in provider_save
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 173 in _run_commands
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 160 in open_command_script
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 428 in remember_data_format
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 440 in collated_open
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 193 in provider_open
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 846 in init
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [8081]
Path: /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.4.0 (1.4.0.0)
Code Type: X86-64 (Native)
Parent Process: tcsh [605]
Responsible: Terminal [501]
User ID: 501
Date/Time: 2022-05-16 15:27:05.276 -0700
OS Version: Mac OS X 10.15.7 (19H1824)
Report Version: 12
Anonymous UUID: 1001EC17-01AB-23EF-FBAF-2E1668FB0851
Time Awake Since Boot: 27000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0:
-->
__TEXT 00000001070b6000-00000001070ba000 [ 16K] r-x/r-x SM=COW /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff7373532a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff737f1e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff7364c93e raise + 26
3 libsystem_platform.dylib 0x00007fff737e65fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 QtGui 0x0000000118721415 QFontPrivate::engineForScript(int) const + 261
6 QtGui 0x00000001187a9a11 QTextEngine::fontEngine(QScriptItem const&, QFixed*, QFixed*, QFixed*) const + 385
7 QtGui 0x00000001187a8789 QTextEngine::shapeText(int) const + 697
8 QtGui 0x00000001187b03a7 QTextEngine::boundingBox(int, int) const + 279
9 QtGui 0x000000011874d547 QFontMetrics::boundingRect(QString const&) const + 103
10 QtGui.abi3.so 0x000000010f8f969e meth_QFontMetrics_boundingRect(_object*, _object*, _object*) + 158
11 org.python.python 0x00000001071466db cfunction_call + 59
12 org.python.python 0x00000001071075b7 _PyObject_MakeTpCall + 359
13 org.python.python 0x00000001071dfe9c call_function + 876
14 org.python.python 0x00000001071dd2a2 _PyEval_EvalFrameDefault + 25554
15 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
16 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
17 org.python.python 0x00000001071dfe0c call_function + 732
18 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
19 org.python.python 0x0000000107107d28 function_code_fastcall + 104
20 org.python.python 0x00000001071dfe0c call_function + 732
21 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
22 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
23 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
24 org.python.python 0x00000001071dfe0c call_function + 732
25 org.python.python 0x00000001071dd34b _PyEval_EvalFrameDefault + 25723
26 org.python.python 0x0000000107107d28 function_code_fastcall + 104
27 org.python.python 0x00000001071dfe0c call_function + 732
28 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
29 org.python.python 0x0000000107107d28 function_code_fastcall + 104
30 org.python.python 0x00000001071dfe0c call_function + 732
31 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
32 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
33 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
34 org.python.python 0x0000000107109d6a method_vectorcall + 202
35 org.python.python 0x00000001071dfe0c call_function + 732
36 org.python.python 0x00000001071dd2a2 _PyEval_EvalFrameDefault + 25554
37 org.python.python 0x0000000107107d28 function_code_fastcall + 104
38 org.python.python 0x00000001071dfe0c call_function + 732
39 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
40 org.python.python 0x0000000107107d28 function_code_fastcall + 104
41 org.python.python 0x00000001071dfe0c call_function + 732
42 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
43 org.python.python 0x0000000107107d28 function_code_fastcall + 104
44 org.python.python 0x00000001071dfe0c call_function + 732
45 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
46 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
47 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
48 org.python.python 0x00000001071dfe0c call_function + 732
49 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
50 org.python.python 0x0000000107107d28 function_code_fastcall + 104
51 org.python.python 0x00000001071dfe0c call_function + 732
52 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
53 org.python.python 0x0000000107107d28 function_code_fastcall + 104
54 org.python.python 0x00000001071dfe0c call_function + 732
55 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
56 org.python.python 0x0000000107107d28 function_code_fastcall + 104
57 org.python.python 0x00000001071dfe0c call_function + 732
58 org.python.python 0x00000001071dd27e _PyEval_EvalFrameDefault + 25518
59 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
60 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
61 org.python.python 0x0000000107107982 PyVectorcall_Call + 162
62 org.python.python 0x00000001071dd989 _PyEval_EvalFrameDefault + 27321
63 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
64 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
65 org.python.python 0x0000000107109d6a method_vectorcall + 202
66 org.python.python 0x00000001071dfe0c call_function + 732
67 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
68 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
69 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
70 org.python.python 0x0000000107107982 PyVectorcall_Call + 162
71 org.python.python 0x00000001071dd989 _PyEval_EvalFrameDefault + 27321
72 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
73 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
74 org.python.python 0x0000000107109d6a method_vectorcall + 202
75 org.python.python 0x00000001071dfe0c call_function + 732
76 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
77 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
78 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
79 org.python.python 0x00000001071dfe0c call_function + 732
80 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
81 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
82 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
83 org.python.python 0x00000001071dfe0c call_function + 732
84 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
85 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
86 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
87 org.python.python 0x00000001071dd989 _PyEval_EvalFrameDefault + 27321
88 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
89 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
90 org.python.python 0x0000000107109e59 method_vectorcall + 441
91 org.python.python 0x00000001071dd989 _PyEval_EvalFrameDefault + 27321
92 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
93 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
94 org.python.python 0x00000001071dfe0c call_function + 732
95 org.python.python 0x00000001071dd34b _PyEval_EvalFrameDefault + 25723
96 org.python.python 0x0000000107107d28 function_code_fastcall + 104
97 org.python.python 0x00000001071dfe0c call_function + 732
98 org.python.python 0x00000001071dd34b _PyEval_EvalFrameDefault + 25723
99 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
100 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
101 org.python.python 0x0000000107107982 PyVectorcall_Call + 162
102 org.python.python 0x00000001071dd989 _PyEval_EvalFrameDefault + 27321
103 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
104 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
105 org.python.python 0x0000000107109d6a method_vectorcall + 202
106 org.python.python 0x00000001071dfe0c call_function + 732
107 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
108 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
109 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
110 org.python.python 0x0000000107107982 PyVectorcall_Call + 162
111 org.python.python 0x00000001071dd989 _PyEval_EvalFrameDefault + 27321
112 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
113 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
114 org.python.python 0x0000000107109d6a method_vectorcall + 202
115 org.python.python 0x00000001071dfe0c call_function + 732
116 org.python.python 0x00000001071dd3e8 _PyEval_EvalFrameDefault + 25880
117 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
118 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
119 org.python.python 0x00000001071dfe0c call_function + 732
120 org.python.python 0x00000001071dd2a2 _PyEval_EvalFrameDefault + 25554
121 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
122 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
123 org.python.python 0x00000001071dfe0c call_function + 732
124 org.python.python 0x00000001071dd34b _PyEval_EvalFrameDefault + 25723
125 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
126 org.python.python 0x00000001071d6dab PyEval_EvalCode + 139
127 org.python.python 0x00000001071d3c12 builtin_exec + 626
128 org.python.python 0x0000000107146023 cfunction_vectorcall_FASTCALL + 195
129 org.python.python 0x00000001071dfe0c call_function + 732
130 org.python.python 0x00000001071dd34b _PyEval_EvalFrameDefault + 25723
131 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
132 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
133 org.python.python 0x00000001071dfe0c call_function + 732
134 org.python.python 0x00000001071dd34b _PyEval_EvalFrameDefault + 25723
135 org.python.python 0x00000001071e0b03 _PyEval_EvalCode + 2611
136 org.python.python 0x0000000107107cb1 _PyFunction_Vectorcall + 289
137 org.python.python 0x0000000107246870 pymain_run_module + 208
138 org.python.python 0x0000000107245f87 Py_RunMain + 1431
139 org.python.python 0x000000010724658f pymain_main + 223
140 org.python.python 0x000000010724649b Py_Main + 43
141 edu.ucsf.cgl.ChimeraX 0x00000001070b9d79 main + 121
142 libdyld.dylib 0x00007fff735edcc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff73731872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff737f2425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000107eba49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff737f2109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff737edb8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff73731872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff737f2425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000107eba49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff737f2109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff737edb8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff73731872 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff737f2425 _pthread_cond_wait + 698
2 libopenblas64_.0.dylib 0x0000000107eba49f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff737f2109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff737edb8b thread_start + 15
Thread 4:
0 libsystem_pthread.dylib 0x00007fff737edb68 start_wqthread + 0
Thread 5:
0 libsystem_pthread.dylib 0x00007fff737edb68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010fd27dc0 rcx: 0x00007fb3c1055a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fb3c1055a80 rsp: 0x00007fb3c1055a58
r8: 0x00007fb3c1055f48 r9: 0x28fff7be91a8b5fd r10: 0x000000010fd27dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007fb3c45d7ca0 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff7373532a rfl: 0x0000000000000246 cr2: 0x00007fb3c1055f48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
0x1070b6000 - 0x1070b9ff3 +edu.ucsf.cgl.ChimeraX (1.4.0 - 1.4.0.0) /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX
0x1070c8000 - 0x107330fff +org.python.python (3.9.11, [c] 2001-2021 Python Software Foundation. - 3.9.11) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python
0x1074cd000 - 0x1074cffff +_heapq.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_heapq.cpython-39-darwin.so
0x1074d9000 - 0x1074ddff7 +binascii.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/binascii.cpython-39-darwin.so
0x1074e7000 - 0x1074ecfff +zlib.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/zlib.cpython-39-darwin.so
0x1074f6000 - 0x1074f8fff +_bz2.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bz2.cpython-39-darwin.so
0x107502000 - 0x107533fff +_lzma.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_lzma.cpython-39-darwin.so
0x107545000 - 0x107546fff +grp.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/grp.cpython-39-darwin.so
0x107550000 - 0x107555ff7 +_struct.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_struct.cpython-39-darwin.so
0x107564000 - 0x10756cfff +math.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/math.cpython-39-darwin.so
0x10757a000 - 0x10757bff7 +_bisect.cpython-39-darwin.so (0) /Users/USER/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bisect.cpython-39-darwin.so
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0x7fff6d50d000 - 0x7fff6d50fff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff6fff3000 - 0x7fff70026ffa libAudioToolboxUtility.dylib (1104.104) /usr/lib/libAudioToolboxUtility.dylib
0x7fff7002d000 - 0x7fff70061fff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff70064000 - 0x7fff7006efff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff700fa000 - 0x7fff700fcff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff70142000 - 0x7fff702f9ffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff70320000 - 0x7fff70326ff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff7043e000 - 0x7fff7045eff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff705d0000 - 0x7fff705d1fff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff7065e000 - 0x7fff7065ffff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff70677000 - 0x7fff7068dfff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff706c2000 - 0x7fff70734ff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib
0x7fff70735000 - 0x7fff707cefe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff707d2000 - 0x7fff707d2ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff70898000 - 0x7fff708a8ffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff708a9000 - 0x7fff708b5fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff708b6000 - 0x7fff70908fff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff70909000 - 0x7fff7091effb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff7091f000 - 0x7fff7091ffff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff70920000 - 0x7fff70931fff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff70932000 - 0x7fff70949fd7 libcompression.dylib (87.1) /usr/lib/libcompression.dylib
0x7fff70c23000 - 0x7fff70c39ff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff70c3a000 - 0x7fff70c3bfff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff711f8000 - 0x7fff71257ff7 libcups.2.dylib (483.9) /usr/lib/libcups.2.dylib
0x7fff71361000 - 0x7fff71361fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff71362000 - 0x7fff7137cff7 libexpat.1.dylib (19.60.3) /usr/lib/libexpat.1.dylib
0x7fff7138a000 - 0x7fff7138cfff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff7138d000 - 0x7fff71392f57 libffi.dylib (26) /usr/lib/libffi.dylib
0x7fff7139b000 - 0x7fff713a0fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff713a1000 - 0x7fff713aaff7 libheimdal-asn1.dylib (564.140.8) /usr/lib/libheimdal-asn1.dylib
0x7fff713ab000 - 0x7fff7149bfff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff7149c000 - 0x7fff716f3fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff7170d000 - 0x7fff7170efff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff7170f000 - 0x7fff71727ff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff7173f000 - 0x7fff717e6ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff717e7000 - 0x7fff71a49ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff71db6000 - 0x7fff71de5fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff71f15000 - 0x7fff72391ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff72432000 - 0x7fff72465fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff72478000 - 0x7fff7247cfff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff7247f000 - 0x7fff724b5fff libpcap.A.dylib (89.120.2) /usr/lib/libpcap.A.dylib
0x7fff72539000 - 0x7fff72551fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff725ad000 - 0x7fff72797ff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff729e8000 - 0x7fff729ebffb libutil.dylib (57.140.1) /usr/lib/libutil.dylib
0x7fff729ec000 - 0x7fff729f9fff libxar.1.dylib (425.7) /usr/lib/libxar.1.dylib
0x7fff729ff000 - 0x7fff72ae1fff libxml2.2.dylib (33.9) /usr/lib/libxml2.2.dylib
0x7fff72ae5000 - 0x7fff72b0dfff libxslt.1.dylib (16.12) /usr/lib/libxslt.1.dylib
0x7fff72b0e000 - 0x7fff72b20ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff733cf000 - 0x7fff733d4ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff733d5000 - 0x7fff733e0fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff733e1000 - 0x7fff733e8fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff733e9000 - 0x7fff733f2ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff733f3000 - 0x7fff73485fdb libcorecrypto.dylib (866.140.2) /usr/lib/system/libcorecrypto.dylib
0x7fff73592000 - 0x7fff735d2ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff735d3000 - 0x7fff73609fff libdyld.dylib (750.7) /usr/lib/system/libdyld.dylib
0x7fff7360a000 - 0x7fff7360affb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff7360b000 - 0x7fff73617ff3 libkxld.dylib (6153.141.59) /usr/lib/system/libkxld.dylib
0x7fff73618000 - 0x7fff73618ff7 liblaunch.dylib (1738.140.3) /usr/lib/system/liblaunch.dylib
0x7fff73619000 - 0x7fff7361eff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff7361f000 - 0x7fff73621ff3 libquarantine.dylib (110.40.6) /usr/lib/system/libquarantine.dylib
0x7fff73622000 - 0x7fff73623ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff73624000 - 0x7fff7363bff3 libsystem_asl.dylib (377.60.4) /usr/lib/system/libsystem_asl.dylib
0x7fff7363c000 - 0x7fff7363cff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff7363d000 - 0x7fff736c4fff libsystem_c.dylib (1353.100.4) /usr/lib/system/libsystem_c.dylib
0x7fff736c5000 - 0x7fff736c8ffb libsystem_configuration.dylib (1061.141.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff736c9000 - 0x7fff736ccfff libsystem_coreservices.dylib (114.1) /usr/lib/system/libsystem_coreservices.dylib
0x7fff736cd000 - 0x7fff736d5fff libsystem_darwin.dylib (1353.100.4) /usr/lib/system/libsystem_darwin.dylib
0x7fff736d6000 - 0x7fff736ddfff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff736de000 - 0x7fff736dfffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff736e0000 - 0x7fff7372dff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff7372e000 - 0x7fff7375aff7 libsystem_kernel.dylib (6153.141.59) /usr/lib/system/libsystem_kernel.dylib
0x7fff7375b000 - 0x7fff737a2fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff737a3000 - 0x7fff737cafff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff737cb000 - 0x7fff737d8ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff737d9000 - 0x7fff737e2ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff737e3000 - 0x7fff737ebfef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff737ec000 - 0x7fff737f6fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff737f7000 - 0x7fff737fbff3 libsystem_sandbox.dylib (1217.141.8) /usr/lib/system/libsystem_sandbox.dylib
0x7fff737fc000 - 0x7fff737fefff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff737ff000 - 0x7fff73806ffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff73807000 - 0x7fff7381dff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff7381f000 - 0x7fff73824ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff73825000 - 0x7fff7385affe libxpc.dylib (1738.140.3) /usr/lib/system/libxpc.dylib
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: 15915
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=659.3M resident=0K(0%) swapped_out_or_unallocated=659.3M(100%)
Writable regions: Total=408.9M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=408.9M(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Activity Tracing 256K 1
Dispatch continuations 8192K 1
Kernel Alloc Once 8K 1
MALLOC 260.8M 175
MALLOC guard page 16K 4
MALLOC_LARGE (reserved) 256K 2 reserved VM address space (unallocated)
STACK GUARD 20K 5
Stack 10.5M 6
Stack Guard 56.0M 1
VM_ALLOCATE 96.0M 3
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 25.3M 332
__DATA_CONST 372K 21
__FONT_DATA 4K 1
__LINKEDIT 403.4M 131
__OBJC_RO 32.3M 1
__OBJC_RW 1860K 2
__TEXT 256.3M 323
__UNICODE 564K 1
mapped file 27.3M 2
shared memory 48K 6
=========== ======= =======
TOTAL 1.2G 1020
TOTAL, minus reserved VM space 1.2G 1020
Log:
UCSF ChimeraX version: 1.4.dev202205120056 (2022-05-12)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-14.7.23
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
Boot ROM Version: 428.60.3.0.0
SMC Version (system): 2.32f21
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1824)
Kernel Version: Darwin 19.6.0
Time since boot: 7:35
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.38.2
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202205120056
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-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
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: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
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-NIHPresets: 1.0.5
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 1.1
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
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: 2.6
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: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.19.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
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-XMAS: 1.1
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
et-xmlfile: 1.1.0
filelock: 3.4.2
fonttools: 4.31.2
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.2
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.4
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openpyxl: 3.0.9
openvr: 1.16.802
packaging: 21.0
pandas: 1.4.2
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
PyQt6: 6.2.3
PyQt6-Qt6: 6.2.4
PyQt6-sip: 13.2.0
PyQt6-WebEngine: 6.2.1
PyQt6-WebEngine-Qt6: 6.2.4
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.0.1
QtRangeSlider: 0.1.5
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
seaborn: 0.11.2
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
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tables: 3.7.0
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File attachment: cmds.cxc
Attachments (1)
Change History (4)
by , 3 years ago
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Nogui save crash with labels / ensure exported graphics is up to date |
As per the description, the "save" command is doing a session.update_loop.update_graphics_now() to ensure that exported graphics (e.g. GLTF) are up to date. That call causes a crash when there are labels present in nogui mode, no matter what kind of file is being saved. The question is, what is the correct solution? I can see at least two myself and maybe you can think of better ones:
1) Have the exporter functions themselves ensure the graphics are up to date, rather than the "save" command
2) Have the "save" command only make the update call when the file type is "Generic 3D objects" -- which covers GLTF and its ilk
As at least a stopgap solution, I have implemented #2 -- which seems decent from a practical perspective. Will still be problematic if there are labels as the GLTF is being saved.
comment:2 by , 3 years ago
First the crash seems to be a Qt bug. It segfaults in QFontMetrics.boundingRect() when computing the image of the label
fm = QFontMetrics(f)
r = fm.boundingRect(text if text else ' ')
At stderr Qt issues the error
QGuiApplication::font(): no QGuiApplication instance and no application font set.
The Qt 6.4 QFontMetrics documentation does not say you need a QGuiApplication(). It would be more usable if the method gave an empty bounding rectangle instead of seg faulting. But given that it segfaults we should probably protect it with a check in our Python code and handle it gracefully by say making a blank label and warning that labels are not supported in nogui mode due to this Qt limitation.
I wonder how many other ChimeraX crashes are caused by Qt just deciding to wipe out. It is startling that it does not even call abort().
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
I made the text_image_rgba() return a blank image when in nogui mode to avoid the Qt crash.
Then I got a different error because the OpenGL code tried to use OpenGL enumeration values even though the label texture was never used. So I fixed that so it only uses the enumeration values when rendering.
Now the attached script works correctly without errors.
In general it should be safe to use labels in nogui mode, although they won't be embedded with correct label textures in GLTF because the fonts aren't available from Qt in no gui mode. I don't recall whether our GLTF export will even try to include textures. In any case I think labels in GLTF is currently rarely desired. In the future we can probably figure out how to render labels in no gui mode if needed.
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