[phenixbb] eLBOW crashes Phenix
Xavier Brazzolotto
xbrazzolotto at gmail.com
Wed Nov 3 10:26:42 PDT 2021
Hi,
I am using the latest stable Phenix release (1.19.2-4158) on macOS (v12.0.1) and I do have an odd bug with Phenix eLBOW.
The program by it self runs and generates the expected cif files.
If I open REEL to check the models, I do see them but as soon as I exit REEL, it crashes the whole Phenix process.
Is it a know bug ?
I paste the crash report below if this helps.
-------------------------------------
Translated Report (Full Report Below)
-------------------------------------
Process: python [57745]
Path: /Applications/phenix-1.19.2-4158/*/python.app/Contents/MacOS/python
Identifier: com.continuum.python
Version: ???
Code Type: X86-64 (Native)
Parent Process: launchd [1]
User ID: 501
Date/Time: 2021-11-03 18:05:27.1449 +0100
OS Version: macOS 12.0.1 (21A559)
Report Version: 12
Bridge OS Version: 6.0 (19P548)
Anonymous UUID: 461A1FA5-1FFE-CC49-2057-0C0BB25A7143
Sleep/Wake UUID: 335CBE5C-1D37-4713-B3EA-80B0E830794F
Time Awake Since Boot: 300000 seconds
Time Since Wake: 13706 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 0x0000000000000020
Exception Codes: 0x0000000000000001, 0x0000000000000020
Exception Note: EXC_CORPSE_NOTIFY
Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11
Terminating Process: exc handler [57745]
VM Region Info: 0x20 is not in any region. Bytes before following region: 4480602080
REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 10b109000-10b10a000 [ 4K] r-x/rwx SM=COW .../MacOS/python
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libobjc.A.dylib 0x7ff81e00bc4f objc_release + 31
1 Foundation 0x7ff81f1ecde8 empty + 58
2 Foundation 0x7ff81f094dd9 dealloc + 38
3 Foundation 0x7ff81f094d64 -[NSConcreteMapTable dealloc] + 54
4 libobjc.A.dylib 0x7ff81e0290fe objc_object::sidetable_release(bool, bool) + 232
5 AppKit 0x7ff8212d8c4c ___NSTouchBarFinderSetNeedsUpdateOnMain_block_invoke_2 + 2233
6 AppKit 0x7ff820d3130c NSDisplayCycleObserverInvoke + 155
7 AppKit 0x7ff820d30e97 NSDisplayCycleFlush + 952
8 QuartzCore 0x7ff8252a5434 CA::Transaction::run_commit_handlers(CATransactionPhase) + 98
9 QuartzCore 0x7ff8252a41b2 CA::Transaction::commit() + 376
10 AppKit 0x7ff820dd24e2 __62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 285
11 AppKit 0x7ff821518724 ___NSRunLoopObserverCreateWithHandler_block_invoke + 41
12 CoreFoundation 0x7ff81e23bc07 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23
13 CoreFoundation 0x7ff81e23baa4 __CFRunLoopDoObservers + 543
14 CoreFoundation 0x7ff81e23af37 __CFRunLoopRun + 841
15 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563
16 HIToolbox 0x7ff826e583e1 RunCurrentEventLoopInMode + 292
17 HIToolbox 0x7ff826e58008 ReceiveNextEventCommon + 284
18 HIToolbox 0x7ff826e57ed5 _BlockUntilNextEventMatchingListInModeWithFilter + 70
19 AppKit 0x7ff820c658f0 _DPSNextEvent + 886
20 AppKit 0x7ff820c63f5c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1411
21 AppKit 0x7ff820c56359 -[NSApplication run] + 586
22 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d2b0a23 wxGUIEventLoop::OSXDoRun() + 115
23 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d192ce4 wxCFEventLoop::DoRun() + 52
24 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d0c2885 wxEventLoopBase::Run() + 165
25 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d087521 wxAppConsoleBase::MainLoop() + 209
26 _core_.so 0x10bd94114 wxPyApp::MainLoop() + 84
27 _core_.so 0x10bdf7902 _wrap_PyApp_MainLoop(_object*, _object*) + 82
28 libpython2.7.dylib 0x10b4967ee PyEval_EvalFrameEx + 30382
29 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147
30 libpython2.7.dylib 0x10b409a84 function_call + 388
31 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97
32 libpython2.7.dylib 0x10b3ee5d4 instancemethod_call + 180
33 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97
34 libpython2.7.dylib 0x10b4957b6 PyEval_EvalFrameEx + 26230
35 libpython2.7.dylib 0x10b49c631 fast_function + 337
36 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441
37 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147
38 libpython2.7.dylib 0x10b49c54a fast_function + 106
39 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441
40 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147
41 libpython2.7.dylib 0x10b48e642 PyEval_EvalCode + 34
42 libpython2.7.dylib 0x10b4c0901 PyRun_FileExFlags + 161
43 libpython2.7.dylib 0x10b4c035f PyRun_SimpleFileExFlags + 847
44 libpython2.7.dylib 0x10b4d8dfb Py_Main + 3483
45 dyld 0x11609f4fe start + 462
Thread 1:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x7ff81e138aba mach_msg_trap + 10
1 libsystem_kernel.dylib 0x7ff81e138e2b mach_msg + 59
2 CoreFoundation 0x7ff81e23ca42 __CFRunLoopServiceMachPort + 319
3 CoreFoundation 0x7ff81e23b11b __CFRunLoopRun + 1325
4 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563
5 AppKit 0x7ff820dd3cec _NSEventThread + 132
6 libsystem_pthread.dylib 0x7ff81e175514 _pthread_start + 125
7 libsystem_pthread.dylib 0x7ff81e17102f thread_start + 15
Thread 2:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 3:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 4:: Dispatch queue: com.apple.NSXPCConnection.user.endpoint.NSRemoteView.IMKTextInputFunctionRowItemServiceViewController
0 CoreFoundation 0x7ff81e1c5746 CFHash + 134
1 CoreFoundation 0x7ff81e1e49fb CFBasicHashAddValue + 223
2 CoreFoundation 0x7ff81e22e09c CFSetCreate + 66
3 CoreFoundation 0x7ff81e223179 CFRunLoopPerformBlock + 288
4 ViewBridge 0x7ff82572020d deferBlockOntoMainThread + 280
5 ViewBridge 0x7ff82572d4d5 deferNSXPCInvocationOntoMainThread + 130
6 Foundation 0x7ff81f0acc12 -[NSXPCConnection _decodeAndInvokeMessageWithEvent:flags:] + 1576
7 Foundation 0x7ff81f063f1a message_handler + 206
8 libxpc.dylib 0x7ff81deba530 _xpc_connection_call_event_handler + 56
9 libxpc.dylib 0x7ff81deb928c _xpc_connection_mach_event + 1387
10 libdispatch.dylib 0x7ff81dfbed63 _dispatch_client_callout4 + 9
11 libdispatch.dylib 0x7ff81dfd78b7 _dispatch_mach_msg_invoke + 452
12 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335
13 libdispatch.dylib 0x7ff81dfd83fb _dispatch_mach_invoke + 484
14 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335
15 libdispatch.dylib 0x7ff81dfc57c8 _dispatch_lane_invoke + 366
16 libdispatch.dylib 0x7ff81dfcf7e1 _dispatch_workloop_worker_thread + 758
17 libsystem_pthread.dylib 0x7ff81e17208f _pthread_wqthread + 326
18 libsystem_pthread.dylib 0x7ff81e17101b start_wqthread + 15
Thread 5:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 6:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 7:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 8:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 9:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 10:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 11:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 12:
0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x6000000000000000 rbx: 0x0000000000000018 rcx: 0x0000000000000000 rdx: 0x00007f8ec5973a00
rdi: 0x00007f8ea57830d0 rsi: 0x0000000000000000 rbp: 0x00007ff7b4df3260 rsp: 0x00007ff7b4df3238
r8: 0x0000000000000200 r9: 0x00007f8ec5972d20 r10: 0x00007ff85f8105d0 r11: 0x00007ff81f094d2e
r12: 0x00007f8f01f8e7c0 r13: 0x00007ff85f966a01 r14: 0x00007f8f01f8e7c8 r15: 0x000000000000000d
rip: 0x00007ff81e00bc4f rfl: 0x0000000000010246 cr2: 0x0000000000000020
Logical CPU: 0
Error Code: 0x00000004 (no mapping for user data read)
Trap Number: 14
Thread 0 instruction stream:
34 48 89 c2 48 01 ca 72-12 f0 48 0f b1 17 74 25 4H..H..r..H...t%
a8 01 75 e4 31 f6 e9 7c-d7 01 00 31 f6 e9 eb 86 ..u.1..|...1....
00 00 48 b9 f8 ff ff ff-ff 7f 00 00 48 21 c8 f6 ..H.........H!..
40 1c 01 74 df 48 89 f8-c3 90 90 90 90 90 90 90 @..t.H..........
90 48 85 ff 74 76 89 f8-83 e0 01 48 85 c0 75 6c .H..tv.....H..ul
48 8b 07 48 b9 f8 ff ff-ff ff 7f 00 00 48 21 c1 H..H.........H!.
[48]8b 51 20 f6 c2 04 74-54 a8 01 74 6f 48 b9 00 H.Q ...tT..toH.. <==
00 00 00 00 00 80 00 48-ba 00 00 00 00 00 00 00 .......H........
01 48 39 c8 72 36 48 89-c6 48 29 d6 72 17 f0 48 .H9.r6H..H).r..H
0f b1 37 74 22 a8 01 75-e8 31 f6 ba 01 00 00 00 ..7t"..u.1......
e9 82 d3 01 00 48 85 c8-75 3a 48 8b 35 18 f5 99 .....H..u:H.5...
41 ff 25 f2 d2 e6 3f 48-39 ce 72 ee c3 f6 c2 02 A.%...?H9.r.....
Binary Images:
0x7ff81e003000 - 0x7ff81e03cfff libobjc.A.dylib (*) <7cfcdc89-2bee-3784-b7af-c676f60fe211> /usr/lib/libobjc.A.dylib
0x7ff81f042000 - 0x7ff81f3fcfff com.apple.Foundation (6.9) <d7fd0214-4bbb-3d84-88f7-820b25a6e16c> /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
0x7ff820c27000 - 0x7ff821ab3fff com.apple.AppKit (6.9) <dd0028a3-78e3-3a8a-a51b-ddd68123adef> /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
0x7ff8252a2000 - 0x7ff825589fff com.apple.QuartzCore (1.11) <7e85dee1-5bb8-3ac2-ad98-2552838e01ca> /System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
0x7ff81e1bc000 - 0x7ff81e6befff com.apple.CoreFoundation (6.9) <3002b545-6841-3fc8-91a2-bcfbe5872465> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7ff826e29000 - 0x7ff827120fff com.apple.HIToolbox (2.1.1) <4163a93f-bf71-3219-80ed-6f65e9266b81> /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
0x10d07d000 - 0x10dd33fff libwx_osx_cocoau-3.0.0.2.0.dylib (*) <72694e85-a8dd-368c-b1ab-3157eceee77a> /Applications/phenix-1.19.2-4158/*/libwx_osx_cocoau-3.0.0.2.0.dylib
0x10bd93000 - 0x10bec9fff _core_.so (*) <58a38f93-fa30-3ff4-9c13-36bb95f0c81e> /Applications/phenix-1.19.2-4158/*/_core_.so
0x10b3cd000 - 0x10b51dfff libpython2.7.dylib (*) <92f45f91-3cd1-3a32-9811-5b8e3c7e2fc3> /Applications/phenix-1.19.2-4158/*/libpython2.7.dylib
0x11609a000 - 0x116105fff dyld (*) <1a6ae033-9438-33c0-8077-988fd885250a> /usr/lib/dyld
0x7ff81e138000 - 0x7ff81e16efff libsystem_kernel.dylib (*) <12bd6f13-c452-35ee-9069-51befef29f1a> /usr/lib/system/libsystem_kernel.dylib
0x7ff81e16f000 - 0x7ff81e17afff libsystem_pthread.dylib (*) <29a2750e-f31b-3630-8761-242a6bc3e99e> /usr/lib/system/libsystem_pthread.dylib
0x7ff82571a000 - 0x7ff82580dfff com.apple.ViewBridge (637.9) <ff66b120-2752-3809-87d8-9c95c0bb2988> /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7ff81dead000 - 0x7ff81dee3fff libxpc.dylib (*) <900e1f8b-6333-3e4d-b64c-751264bb7223> /usr/lib/system/libxpc.dylib
0x7ff81dfbc000 - 0x7ff81e002fff libdispatch.dylib (*) <be53a13c-8ce1-3e40-b9bc-98473d3eed3e> /usr/lib/system/libdispatch.dylib
0x0 - 0xffffffffffffffff ??? (*) <00000000-0000-0000-0000-000000000000> ???
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=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)
Writable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 896K 7
Activity Tracing 256K 1
CG backing stores 2528K 4
CG image 1596K 41
CG raster data 184K 21
ColorSync 228K 26
CoreAnimation 139.5M 206
CoreGraphics 12K 2
CoreImage 608K 35
CoreUI image data 2480K 21
Foundation 80K 2
Kernel Alloc Once 8K 1
MALLOC 511.7M 149
MALLOC guard page 48K 9
MALLOC_MEDIUM (reserved) 880.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
STACK GUARD 56.0M 13
Stack 14.1M 13
VM_ALLOCATE 1128K 27
VM_ALLOCATE (reserved) 768.0M 1 reserved VM address space (unallocated)
__DATA 41.4M 510
__DATA_CONST 23.2M 234
__DATA_DIRTY 969K 139
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 682.2M 110
__OBJC_RO 81.5M 1
__OBJC_RW 3120K 2
__TEXT 529.9M 498
__UNICODE 588K 1
dyld private memory 3072K 3
mapped file 158.3M 26
shared memory 1296K 19
=========== ======= =======
TOTAL 4.2G 2133
TOTAL, minus reserved VM space 2.2G 2133
-----------
Full Report
-----------
{"app_name":"python","timestamp":"2021-11-03 18:05:27.00 +0100","app_version":"","slice_uuid":"41b01d14-4c6e-3a14-a84e-812c0ee8d9cd","build_version":"","platform":1,"bundleID":"com.continuum.python","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.0.1 (21A559)","incident_id":"3B71C390-9A85-4125-A53A-7058CF9E1361","name":"python"}
{
"uptime" : 300000,
"procLaunch" : "2021-11-03 18:04:29.4653 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"procStartAbsTime" : 303473294854732,
"coalitionID" : 1512,
"osVersion" : {
"train" : "macOS 12.0.1",
"build" : "21A559",
"releaseType" : "User"
},
"captureTime" : "2021-11-03 18:05:27.1449 +0100",
"incident" : "3B71C390-9A85-4125-A53A-7058CF9E1361",
"bug_type" : "309",
"pid" : 57745,
"procExitAbsTime" : 303530973462636,
"cpuType" : "X86-64",
"procName" : "python",
"procPath" : "\/Applications\/phenix-1.19.2-4158\/*\/python.app\/Contents\/MacOS\/python",
"bundleInfo" : {"CFBundleIdentifier":"com.continuum.python"},
"storeInfo" : {"deviceIdentifierForVendor":"4FD8A66E-22D2-5A3D-904B-4E69B0B05DAE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "org.pythonmac.unspecified.phenix-1.19.2-4158",
"crashReporterKey" : "461A1FA5-1FFE-CC49-2057-0C0BB25A7143",
"responsiblePid" : 57744,
"wakeTime" : 13706,
"bridgeVersion" : {"build":"19P548","train":"6.0"},
"sleepWakeUUID" : "335CBE5C-1D37-4713-B3EA-80B0E830794F",
"sip" : "enabled",
"vmRegionInfo" : "0x20 is not in any region. Bytes before following region: 4480602080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b109000-10b10a000 [ 4K] r-x\/rwx SM=COW ...\/MacOS\/python",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000020","rawCodes":[1,32],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000020"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":57745},
"vmregioninfo" : "0x20 is not in any region. Bytes before following region: 4480602080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b109000-10b10a000 [ 4K] r-x\/rwx SM=COW ...\/MacOS\/python",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":3110783,"instructionState":{"instructionStream":{"bytes":[52,72,137,194,72,1,202,114,18,240,72,15,177,23,116,37,168,1,117,228,49,246,233,124,215,1,0,49,246,233,235,134,0,0,72,185,248,255,255,255,255,127,0,0,72,33,200,246,64,28,1,116,223,72,137,248,195,144,144,144,144,144,144,144,144,72,133,255,116,118,137,248,131,224,1,72,133,192,117,108,72,139,7,72,185,248,255,255,255,255,127,0,0,72,33,193,72,139,81,32,246,194,4,116,84,168,1,116,111,72,185,0,0,0,0,0,0,128,0,72,186,0,0,0,0,0,0,0,1,72,57,200,114,54,72,137,198,72,41,214,114,23,240,72,15,177,55,116,34,168,1,117,232,49,246,186,1,0,0,0,233,130,211,1,0,72,133,200,117,58,72,139,53,24,245,153,65,255,37,242,210,230,63,72,57,206,114,238,195,246,194,2],"offset":96}},"threadState":{"r13":{"value":140704732310017,"symbolLocation":33,"symbol":"loadImageFuncs"},"rax":{"value":6917529027641081856},"rflags":{"value":66118},"cpu":{"value":0},"r14":{"value":140252190140360},"rsi":{"value":0},"r8":{"value":512},"cr2":{"value":32},"rdx":{"value":140251177105920},"r10":{"value":140704730908112,"symbolLocation":0,"symbol":"OBJC_CLASS_$_NSConcreteMapTable"},"r9":{"value":140251177102624},"r15":{"value":13},"rbx":{"value":24},"trap":{"value":14,"description":"(no 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