eLBOW crashes Phenix

3 Nov 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" : 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Xavier Brazzolotto

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