Opened 3 years ago

Last modified 6 months ago

#46007 new defect

pymol crashes on Yosemite after a while

Reported by: barak.raveh@… Owned by: howarth.at.macports@…
Priority: Normal Milestone:
Component: ports Version: 2.3.3
Keywords: Cc:
Port: pymol

Description (last modified by ryandesign (Ryan Schmidt))

Pymol seems to work normally on yosemite but then crushes after a short while with message:

*** Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'NSScreen reconfig must only happen on the main thread.'
abort() called terminating with uncaught exception of type NSException

Log below:

Process:               Python [1079]
Path:                  /opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            org.python.python
Version:               2.7.8 (2.7.8)
Code Type:             X86-64 (Native)
Parent Process:        bash [688]
Responsible:           Terminal [685]
User ID:               501

Date/Time:             2014-11-24 16:10:56.440 -0800
OS Version:            Mac OS X 10.10.1 (14B25)
Report Version:        11
Anonymous UUID:        C6F9D0BE-F02B-FF6C-5BBB-AAC0CD6EB628


Time Awake Since Boot: 1100 seconds

Crashed Thread:        4  Dispatch queue: com.apple.Xplugin.CGEventPort

Exception Type:        EXC_CRASH (SIGABRT)
Exception Codes:       0x0000000000000000, 0x0000000000000000

Application Specific Information:
*** Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'NSScreen reconfig must only happen on the main thread.'
abort() called
terminating with uncaught exception of type NSException

Application Specific Backtrace 1:
0   CoreFoundation                      0x00007fff8ff8064c __exceptionPreprocess + 172
1   libobjc.A.dylib                     0x00007fff8bc256de objc_exception_throw + 43
2   CoreFoundation                      0x00007fff8ff8042a +[NSException raise:format:arguments:] + 106
3   Foundation                          0x00007fff8d8fd5b9 -[NSAssertionHandler handleFailureInMethod:object:file:lineNumber:description:] + 195
4   AppKit                              0x00007fff8b5c6f13 +[NSScreen _invalidateIfNeededForReason:] + 139
5   AppKit                              0x00007fff8b347ffd -[NSApplication _reactToDockChanged] + 29
6   AppKit                              0x00007fff8b27f16c _NSCoreDockMessageReceive + 802
7   HIToolbox                           0x00007fff8ef5fe48 _ZL12DockCallbackjjPvS_ + 1845
8   HIServices                          0x00007fff8bbd8c16 dockClientNotificationProc + 171
9   CoreGraphics                        0x00007fff92e3fb33 _ZNK21CGSConnectionNotifier16invoke_callbacksEjPvm + 601
10  CoreGraphics                        0x00007fff92e3f872 _ZN12_GLOBAL__N_123notify_datagram_handlerEj15CGSDatagramTypePvmS1_ + 103
11  CoreGraphics                        0x00007fff92df7fe7 _ZN21CGSDatagramReadStream22dispatch_next_datagramEv + 779
12  CoreGraphics                        0x00007fff92df7ccc _ZN21CGSDatagramReadStream18dispatch_datagramsEv + 50
13  CoreGraphics                        0x00007fff92df7ae1 CGSDatagramReadStreamDispatchDatagramsWithData + 109
14  CoreGraphics                        0x00007fff92df7897 CGSSnarfAndDispatchDatagrams + 427
15  CoreGraphics                        0x00007fff92df75e8 CGSGetNextEventRecordInternal + 92
16  CoreGraphics                        0x00007fff92df7533 CGEventCreateNextEvent + 48
17  libXplugin.1.dylib                  0x000000010559495c ___xp_init_service_cg_event_port_block_invoke + 106
18  libdispatch.dylib                   0x00007fff94922c13 _dispatch_client_callout + 8
19  libdispatch.dylib                   0x00007fff9492d87e _dispatch_source_latch_and_call + 721
20  libdispatch.dylib                   0x00007fff9492662b _dispatch_source_invoke + 412
21  libdispatch.dylib                   0x00007fff94926154 _dispatch_queue_drain + 571
22  libdispatch.dylib                   0x00007fff94927ecc _dispatch_queue_invoke + 202
23  libdispatch.dylib                   0x00007fff949256b7 _dispatch_root_queue_drain + 463
24  libdispatch.dylib                   0x00007fff94933fe4 _dispatch_worker_thread3 + 91
25  libsystem_pthread.dylib             0x00007fff896786cb _pthread_wqthread + 729
26  libsystem_pthread.dylib             0x00007fff896764a1 start_wqthread + 13

Thread 0:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	0x00007fff8db4f3f6 __select + 10
1   _cmd.so                       	0x0000000104cd8eab MainBusyIdle + 1051
2   libglut.3.dylib               	0x0000000105524cd8 glutMainLoop + 153
3   _cmd.so                       	0x0000000104cd7ad6 main_common + 1238
4   _cmd.so                       	0x0000000104cd7c2c main_shared + 108
5   _cmd.so                       	0x0000000104ccca2a CmdRunPyMOL + 90
6   org.python.python             	0x0000000104680021 PyEval_EvalFrameEx + 19649
7   org.python.python             	0x000000010467b052 PyEval_EvalCodeEx + 1538
8   org.python.python             	0x0000000104682ad5 fast_function + 117
9   org.python.python             	0x000000010467ec1d PyEval_EvalFrameEx + 14525
10  org.python.python             	0x000000010467b052 PyEval_EvalCodeEx + 1538
11  org.python.python             	0x000000010467aa46 PyEval_EvalCode + 54
12  org.python.python             	0x00000001046a4884 PyRun_FileExFlags + 164
13  org.python.python             	0x00000001046a4401 PyRun_SimpleFileExFlags + 769
14  org.python.python             	0x00000001046b9e98 Py_Main + 3096
15  libdyld.dylib                 	0x00007fff88e0a5c9 start + 1

Thread 1:: Dispatch queue: com.apple.libdispatch-manager
0   libsystem_kernel.dylib        	0x00007fff8db5022e kevent64 + 10
1   libdispatch.dylib             	0x00007fff94925a6a _dispatch_mgr_thread + 52

Thread 2:
0   libsystem_kernel.dylib        	0x00007fff8db4f3f6 __select + 10
1   libsystem_pthread.dylib       	0x00007fff896782fc _pthread_body + 131
2   libsystem_pthread.dylib       	0x00007fff89678279 _pthread_start + 176
3   libsystem_pthread.dylib       	0x00007fff896764b1 thread_start + 13

Thread 3:
0   libsystem_kernel.dylib        	0x00007fff8db4f3f6 __select + 10
1   org.python.python             	0x0000000104680021 PyEval_EvalFrameEx + 19649
2   org.python.python             	0x000000010467b052 PyEval_EvalCodeEx + 1538
3   org.python.python             	0x0000000104682ad5 fast_function + 117
4   org.python.python             	0x000000010467ec1d PyEval_EvalFrameEx + 14525
5   org.python.python             	0x000000010467b052 PyEval_EvalCodeEx + 1538
6   org.python.python             	0x0000000104606b6c function_call + 364
7   org.python.python             	0x00000001045e1033 PyObject_Call + 99
8   org.python.python             	0x000000010467e980 PyEval_EvalFrameEx + 13856
9   org.python.python             	0x0000000104682b72 fast_function + 274
10  org.python.python             	0x000000010467ec1d PyEval_EvalFrameEx + 14525
11  org.python.python             	0x0000000104682b72 fast_function + 274
12  org.python.python             	0x000000010467ec1d PyEval_EvalFrameEx + 14525
13  org.python.python             	0x000000010467b052 PyEval_EvalCodeEx + 1538
14  org.python.python             	0x0000000104606b6c function_call + 364
15  org.python.python             	0x00000001045e1033 PyObject_Call + 99
16  org.python.python             	0x00000001045ee226 instancemethod_call + 182
17  org.python.python             	0x00000001045e1033 PyObject_Call + 99
18  org.python.python             	0x00000001046822cd PyEval_CallObjectWithKeywords + 93
19  org.python.python             	0x00000001046bc0c6 t_bootstrap + 70
20  libsystem_pthread.dylib       	0x00007fff896782fc _pthread_body + 131
21  libsystem_pthread.dylib       	0x00007fff89678279 _pthread_start + 176
22  libsystem_pthread.dylib       	0x00007fff896764b1 thread_start + 13

Thread 4 Crashed:: Dispatch queue: com.apple.Xplugin.CGEventPort
0   libsystem_kernel.dylib        	0x00007fff8db4f282 __pthread_kill + 10
1   libsystem_c.dylib             	0x00007fff90b6fb73 abort + 129
2   libc++abi.dylib               	0x00007fff92d1ba21 abort_message + 257
3   libc++abi.dylib               	0x00007fff92d439d1 default_terminate_handler() + 267
4   libobjc.A.dylib               	0x00007fff8bc296c6 _objc_terminate() + 103
5   libc++abi.dylib               	0x00007fff92d410a1 std::__terminate(void (*)()) + 8
6   libc++abi.dylib               	0x00007fff92d41113 std::terminate() + 51
7   libobjc.A.dylib               	0x00007fff8bc294ef objc_terminate + 9
8   libdispatch.dylib             	0x00007fff94922c27 _dispatch_client_callout + 28
9   libdispatch.dylib             	0x00007fff9492d87e _dispatch_source_latch_and_call + 721
10  libdispatch.dylib             	0x00007fff9492662b _dispatch_source_invoke + 412
11  libdispatch.dylib             	0x00007fff94926154 _dispatch_queue_drain + 571
12  libdispatch.dylib             	0x00007fff94927ecc _dispatch_queue_invoke + 202
13  libdispatch.dylib             	0x00007fff949256b7 _dispatch_root_queue_drain + 463
14  libdispatch.dylib             	0x00007fff94933fe4 _dispatch_worker_thread3 + 91
15  libsystem_pthread.dylib       	0x00007fff896786cb _pthread_wqthread + 729
16  libsystem_pthread.dylib       	0x00007fff896764a1 start_wqthread + 13

Thread 4 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000000000006  rcx: 0x000000010d778748  rdx: 0x0000000000000000
  rdi: 0x000000000000291b  rsi: 0x0000000000000006  rbp: 0x000000010d778770  rsp: 0x000000010d778748
   r8: 0x0000000000000000   r9: 0x00007fff90b99d90  r10: 0x000000000c000000  r11: 0x0000000000000206
  r12: 0x000000010d7788d0  r13: 0x0000000000000000  r14: 0x000000010d779000  r15: 0x000000010d7787b0
  rip: 0x00007fff8db4f282  rfl: 0x0000000000000206  cr2: 0x00007fff7779cfd8
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


Binary Images:
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    0x7fff94324000 -     0x7fff943a1fff  com.apple.CoreServices.OSServices (640.3 - 640.3) <28445162-08E9-3E24-84E4-617CE5FE1367> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
    0x7fff943a2000 -     0x7fff943dafff  com.apple.RemoteViewServices (2.0 - 99) <C9A62691-B0D9-34B7-B71C-A48B5F4DC553> /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
    0x7fff947cc000 -     0x7fff948affff  libcrypto.0.9.8.dylib (52) <7208EEE2-C090-383E-AADD-7E1BD1321BEC> /usr/lib/libcrypto.0.9.8.dylib
    0x7fff948b0000 -     0x7fff94904fff  libc++.1.dylib (120) <1B9530FD-989B-3174-BB1C-BDC159501710> /usr/lib/libc++.1.dylib
    0x7fff94905000 -     0x7fff9491bff7  libsystem_asl.dylib (267) <F153AC5B-0542-356E-88C8-20A62CA704E2> /usr/lib/system/libsystem_asl.dylib
    0x7fff94921000 -     0x7fff9494bff7  libdispatch.dylib (442.1.4) <502CF32B-669B-3709-8862-08188225E4F0> /usr/lib/system/libdispatch.dylib
    0x7fff9494c000 -     0x7fff9494cfff  com.apple.Accelerate.vecLib (3.10 - vecLib 3.10) <A48738CA-5B6F-3D14-97E9-2BFDFC3DCC06> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
    0x7fff9494d000 -     0x7fff94972ff7  libPng.dylib (1231) <2D5AC0EE-4056-3F76-97E7-BBD415F072B5> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
    0x7fff94973000 -     0x7fff94a14ff7  com.apple.Bluetooth (4.3.1 - 4.3.1f2) <EDC78AEE-28E7-324C-9947-41A0814A8154> /System/Library/Frameworks/IOBluetooth.framework/Versions/A/IOBluetooth
    0x7fff94a8a000 -     0x7fff94a8cff7  libsystem_coreservices.dylib (9) <41B7C578-5A53-31C8-A96F-C73E030B0938> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff94b97000 -     0x7fff94bb3ff7  libsystem_malloc.dylib (53.1.1) <19BCC257-5717-3502-A71F-95D65AFA861B> /usr/lib/system/libsystem_malloc.dylib
    0x7fff94bb4000 -     0x7fff94bc7ff7  com.apple.CoreBluetooth (1.0 - 1) <FA9B43B3-E183-3040-AE25-66EF9870CF35> /System/Library/Frameworks/CoreBluetooth.framework/Versions/A/CoreBluetooth
    0x7fff94bd5000 -     0x7fff94c23fff  libcurl.4.dylib (83.1.2) <337A1FF8-E8B1-3173-9F29-C0D4C851D8E1> /usr/lib/libcurl.4.dylib
    0x7fff94c24000 -     0x7fff95077fc7  com.apple.vImage (8.0 - 8.0) <33BE7B31-72DB-3364-B37E-C322A32748C5> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
    0x7fff95078000 -     0x7fff9507aff7  libsystem_sandbox.dylib (358.1.1) <DB9962EF-8898-31CC-9B87-E01F8CE74C9D> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff956ae000 -     0x7fff956d8fff  GLRendererFloat (11.0.7) <3B3B74F4-E63C-3241-8807-E2407C4020B2> /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
    0x7fff956e5000 -     0x7fff9577aff7  com.apple.ColorSync (4.9.0 - 4.9.0) <F06733BD-A10C-3DB3-B050-825351130392> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync
    0x7fff95790000 -     0x7fff95804fff  com.apple.ApplicationServices.ATS (360 - 375) <62828B40-231D-3F81-8067-1903143DCB6B> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 1
    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: 531
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=203.8M resident=106.3M(52%) swapped_out_or_unallocated=97.5M(48%)
Writable regions: Total=179.9M written=31.8M(18%) resident=64.3M(36%) swapped_out=0K(0%) unallocated=115.6M(64%)
 
REGION TYPE                      VIRTUAL
===========                      =======
ATS (font support)                 32.3M
ATS (font support) (reserved)         4K        reserved VM address space (unallocated)
CG backing stores                   644K
CG image                              4K
CG shared images                    208K
CoreServices                       1028K
CoreUI image data                     4K
Dispatch continuations             8192K
IOKit                              6796K
Kernel Alloc Once                     8K
MALLOC                            104.8M
MALLOC (admin)                       32K
MALLOC_LARGE (reserved)            1484K        reserved VM address space (unallocated)
Memory Tag 251                        8K
OpenGL GLSL                         256K
STACK GUARD                        56.0M
Stack                              13.1M
VM_ALLOCATE                        11.0M
__DATA                             20.8M
__GLSLBUILTINS                     2588K
__IMAGE                             528K
__LINKEDIT                         74.5M
__TEXT                            129.3M
__UNICODE                           544K
mapped file                        65.4M
shared memory                        68K
===========                      =======
TOTAL                             529.0M
TOTAL, minus reserved VM space    527.6M
 

Model: MacBookAir4,2, BootROM MBA41.0077.B11, 2 processors, Intel Core i5, 1.7 GHz, 4 GB, SMC 1.73f66
Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 384 MB
Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1333 MHz, 0x80CE, 0x4D34373142353737334448302D4348392020
Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1333 MHz, 0x80CE, 0x4D34373142353737334448302D4348392020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xE9), Broadcom BCM43xx 1.0 (5.106.98.100.24)
Bluetooth: Version 4.3.1f2 15015, 3 services, 19 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM256C, 251 GB
USB Device: Hub
USB Device: Internal Memory Card Reader
USB Device: Hub
USB Device: Apple Internal Keyboard / Trackpad
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: FaceTime Camera (Built-in)
Thunderbolt Bus: MacBook Air, Apple Inc., 8.1

Change History (4)

comment:1 Changed 3 years ago by ryandesign (Ryan Schmidt)

  • Description modified (diff)
  • Keywords pymol NSScreen removed
  • Owner changed from macports-tickets@… to howarth.at.macports@…

Please remember to use WikiFormatting.

pymol will be updated to a newer version soon; see #45721. Maybe that will help.

comment:2 Changed 3 years ago by larryv (Lawrence Velázquez)

  • Summary changed from pymol crushes on Yosemite after a while to pymol crashes on Yosemite after a while

comment:3 Changed 3 years ago by howarth.at.macports@…

Are you using the appropriate variants for of tcl and tk for pymol as designated in Portfile for pymol as...

require_active_variants tcl "" corefoundation
require_active_variants tk "" quartz

which is tcl -corefoundation and tk -quartz? The X11 version of pymol uses blt which. due to its use of fork() on exec()...

http://www.linuxprogrammingblog.com/threads-and-fork-think-twice-before-using-them

...requires the CoreFoundation support to be avoided since it internally uses threads. Likewise, the tk needs to be the non-quartz variant for the X11 version. Perhaps we need to add some sort of post-installation check to sanity check that the correct variants installed since port is incapable of honoring variant dependencies.

ps If you are still having problems, you might try using the tcl -threads -corefoundation variant. In theory, you shouldn't be able to use the threads variant but in practice I have never seen it crash.

comment:4 Changed 6 months ago by gvdb (Glen van den Bergen)

I found a solution for this and I thought I'd post it here since this is the top result in Google for the error message: "Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'NSScreen reconfig must only happen on the main thread.'"

I had literally spent days trying to fix this issue, implementing all the suggested fixes here and elsewhere, to no avail. It still kept crashing after 2 minutes.

Eventually I figured out it was related to some user data, but I didn't know what exactly. I created a test account on my Mac, ran pymol and the crash didn't happen.

The user data that was causing problems on my regular Mac account was a plugin I'd written and installed to pymol. The particular line which was causing problems in the plugin was importing the colour map library from matplotlib. Once I removed that import (which I wasn't even using in my plugin), pymol stopped crashing.

To any other poor soul that has wasted days trying to fix this crash, I hope this helps you. Good luck.

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