Author Topic: Ovito segmentation fault  (Read 1657 times)

andershaf

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Ovito segmentation fault
« on: March 07, 2017, 10:00:14 PM »
I have used Ovito 2.8.2 to study displacement of atoms in a crystal with a spherical cavity.

My setup has produced a crash in Ovito multiple times, but I haven't found a way to reproduce it. I have uploaded a file which contains the scene and data file (sorry it's big, ~270MB). You can find the file here: https://dl.dropboxusercontent.com/u/9786132/ovito_bug.zip, see README for location of data file.

It crashes with this call stack from the crash log (full crash log is in the .zip-file):


Thread 8 Crashed:: Thread (pooled)
0   com.apple.CoreServices.CarbonCore   0x00007fff890e9ff6 SetItemSize(OpaqueCollection*, int, int) + 62
1   com.apple.CoreServices.CarbonCore   0x00007fff890e9f1a RemoveItem(OpaqueCollection*, int) + 96
2   com.apple.CoreServices.CarbonCore   0x00007fff890e43a1 RemoveCollectionItem + 47
3   com.apple.HIToolbox              0x00007fff877c76a8 TSMRemoveDocumentProperty_Internal + 1148
4   com.apple.AppKit                 0x00007fff8601c754 -[NSTextInputContext dealloc] + 137
5   libobjc.A.dylib                  0x00007fff9cf3925a _object_remove_assocations + 406
6   libobjc.A.dylib                  0x00007fff9cf39091 objc_destructInstance + 105
7   libobjc.A.dylib                  0x00007fff9cf39017 object_dispose + 22
8   com.apple.AppKit                 0x00007fff85d4e1b9 -[NSResponder dealloc] + 139
9   com.apple.AppKit                 0x00007fff85d4cbd2 -[NSView dealloc] + 381
10  libqcocoa.dylib                  0x000000010f516608 -[QNSView dealloc] + 392
11  libobjc.A.dylib                  0x00007fff9cf39e60 (anonymous namespace)::AutoreleasePoolPage::pop(void*) + 808
12  libobjc.A.dylib                  0x00007fff9cf3d0fc (anonymous namespace)::AutoreleasePoolPage::tls_dealloc(void*) + 110
13  libsystem_pthread.dylib          0x00007fff9da3f50f _pthread_tsd_cleanup + 544
14  libsystem_pthread.dylib          0x00007fff9da3f249 _pthread_exit + 152
15  libsystem_pthread.dylib          0x00007fff9da3dab6 _pthread_body + 191
16  libsystem_pthread.dylib          0x00007fff9da3d9f7 _pthread_start + 286
17  libsystem_pthread.dylib          0x00007fff9da3d1fd thread_start + 13

If I find a way to reproduce it I'll upload the steps here.

Maybe this is enough for you to understand what has happened :)

Alexander Stukowski

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Re: Ovito segmentation fault
« Reply #1 on: March 08, 2017, 11:44:32 PM »
The stack trace you posted indicates that OVITO crashed while doing... basically nothing. That is very strange.

I checked the scene file that you posted (also on a macOS system). First, everything worked normally. But then I switched to another application, and minutes later OVITO spontaneously crashed while I was working in the other program.

I currently have no explanation for this and I haven't seen this before. So far I wasn't able to reproduce the crash again, I only observed this one occurrence. That means it happens only very infrequently (or it requires some very specific type of user interaction to trigger the crash).

I will keep an eye on this. Let me know if you are able to narrow it down, perhaps to a specific user action or element in the scene that leads to the crash.

andershaf

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Re: Ovito segmentation fault
« Reply #2 on: March 09, 2017, 08:32:41 AM »
Ok, interesting. What Qt version are you building Ovito with?

I'll keep you posted on any changes.

Alexander Stukowski

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Re: Ovito segmentation fault
« Reply #3 on: March 09, 2017, 09:17:50 AM »
The macOS version of Ovito 2.8.2 uses Qt 5.7.1.

andershaf

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Re: Ovito segmentation fault
« Reply #4 on: March 11, 2017, 05:58:19 AM »
Another random crash in a different system. This could be a Qt 5.7.1 issue...

Thread 5 Crashed:: Thread (pooled)
0   libsystem_c.dylib                0x00007fffaff1d4db __abort + 172
1   libsystem_c.dylib                0x00007fffaff1d42f abort + 144
2   libsystem_malloc.dylib           0x00007fffb001cc0a nanozone_error + 525
3   libsystem_malloc.dylib           0x00007fffb0012d26 nano_realloc + 392
4   libsystem_malloc.dylib           0x00007fffb000e179 malloc_zone_realloc + 115
5   libsystem_malloc.dylib           0x00007fffb000e068 realloc + 256
6   com.apple.CoreServices.CarbonCore   0x00007fff9b741865 CSMemSetHandleSize + 207
7   com.apple.CoreServices.CarbonCore   0x00007fff9b74178d SetHandleSize + 9
8   com.apple.CoreServices.CarbonCore   0x00007fff9b7419e9 ResizeData(OpaqueCollection*, int) + 35
9   com.apple.CoreServices.CarbonCore   0x00007fff9b74d12c SetItemSize(OpaqueCollection*, int, int) + 372
10  com.apple.CoreServices.CarbonCore   0x00007fff9b74cf1a RemoveItem(OpaqueCollection*, int) + 96
11  com.apple.CoreServices.CarbonCore   0x00007fff9b7473a1 RemoveCollectionItem + 47
12  com.apple.HIToolbox              0x00007fff99e2a6a8 TSMRemoveDocumentProperty_Internal + 1148
13  com.apple.AppKit                 0x00007fff9867f754 -[NSTextInputContext dealloc] + 137
14  libobjc.A.dylib                  0x00007fffaf59c25a _object_remove_assocations + 406
15  libobjc.A.dylib                  0x00007fffaf59c091 objc_destructInstance + 105
16  libobjc.A.dylib                  0x00007fffaf59c017 object_dispose + 22
17  com.apple.AppKit                 0x00007fff983b11b9 -[NSResponder dealloc] + 139
18  com.apple.AppKit                 0x00007fff983afbd2 -[NSView dealloc] + 381
19  libqcocoa.dylib                  0x0000000111cd5608 -[QNSView dealloc] + 392
20  libobjc.A.dylib                  0x00007fffaf59ce60 (anonymous namespace)::AutoreleasePoolPage::pop(void*) + 808
21  libobjc.A.dylib                  0x00007fffaf5a00fc (anonymous namespace)::AutoreleasePoolPage::tls_dealloc(void*) + 110
22  libsystem_pthread.dylib          0x00007fffb00a250f _pthread_tsd_cleanup + 544
23  libsystem_pthread.dylib          0x00007fffb00a2249 _pthread_exit + 152
24  libsystem_pthread.dylib          0x00007fffb00a0ab6 _pthread_body + 191
25  libsystem_pthread.dylib          0x00007fffb00a09f7 _pthread_start + 286
26  libsystem_pthread.dylib          0x00007fffb00a01fd thread_start + 13