Crahs log on 1519

Case number:845829-2005192
Topic:Crash/Hang
Opened by:alcor29
Status:Open
Type:Bug
Opened on:Thursday, May 10, 2018 - 02:56
Last modified:Tuesday, May 15, 2018 - 15:22

Win10/64, main, originalUI. Clicked ligand in ligand design mode, to add atom and crashed immediately. Too may rotamers?

UNHANDLED EXCEPTION
Generated 15 rotamers for LG_50013 in 0.293s total.
1: RaiseException +98 bytes (no line)
2: alIsAuxiliaryEffectSlot +694274 bytes (no line)
3: library_main +1538359 bytes (no line)
4: library_main +45684531 bytes (no line)
5: library_main +44108717 bytes (no line)
6: library_main +44133725 bytes (no line)
7: library_main +44128722 bytes (no line)
8: library_main +44127888 bytes (no line)
9: library_main +44107736 bytes (no line)
10: library_main +39490309 bytes (no line)
11: library_main +39481952 bytes (no line)
12: library_main +35527840 bytes (no line)
13: library_main +35474407 bytes (no line)
14: library_main +4067661 bytes (no line)
15: library_main +2112612 bytes (no line)
16: library_main +2083895 bytes (no line)
17: library_main +197733 bytes (no line)
18: library_main +371112 bytes (no line)
19: library_main +3265898 bytes (no line)
20: library_main +5736869 bytes (no line)
21: library_main +5738148 bytes (no line)
22: library_main +5979758 bytes (no line)
23: library_main +3912177 bytes (no line)
24: library_main +3921376 bytes (no line)
25: library_main +6056324 bytes (no line)
26: library_main +6055700 bytes (no line)
27: library_main +371112 bytes (no line)
28: library_main +3380517 bytes (no line)
29: library_main +3381690 bytes (no line)
30: library_main +3632334 bytes (no line)
31: library_main +3426127 bytes (no line)
32: library_main +5163307 bytes (no line)
33: library_main +371112 bytes (no line)
34: library_main +3425308 bytes (no line)
35: library_main +5168227 bytes (no line)
36: library_main +5158143 bytes (no line)
37: AddClipboardFormatListener +1179 bytes (no line)
38: DispatchMessageW +2426 bytes (no line)
39: CallWindowProcW +141 bytes (no line)
40: glDebugEntry +3687 bytes (no line)
41: AddClipboardFormatListener +1179 bytes (no line)
42: DispatchMessageW +2426 bytes (no line)
43: DispatchMessageW +558 bytes (no line)
44: DispatchMessageA +16 bytes (no line)
45: library_main +5166565 bytes (no line)
46: library_main +3182521 bytes (no line)
47: library_main +13065 bytes (no line)
48: library_main +21 bytes (no line)
49: no symbol (no line)
...

(Thu, 05/10/2018 - 02:56  |  20 comments)


alcor29's picture
User offline. Last seen 6 hours 23 min ago. Offline
Joined: 11/16/2012

This happened again. Wouldn't an error note on UI be better that just crashing?

Joined: 09/22/2017
Groups: Beta Folders

Opening drug solutions I have published to scientists causes the client to open normally but then crash after 20 seconds https://pastebin.com/raw/9fdkE99J

Joined: 06/24/2008
Groups: Void Crushers

My crash report on 1519:

Process: game_dynamic [905]
Path: /Applications/Foldit.app/Contents/MacOS/game_dynamic
Identifier: edu.washington.foldit
Version: 1.0
Code Type: X86 (Native)
Parent Process: ??? [1]
Responsible: game_dynamic [905]
User ID: 501

Date/Time: 2018-05-10 13:51:31.086 -0400
OS Version: Mac OS X 10.13.4 (17E199)
Report Version: 12
Anonymous UUID: 02F110A1-8FE4-6A66-D372-CDB5BC14E36B

Time Awake Since Boot: 16000 seconds

System Integrity Protection: enabled

Crashed Thread: 12

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

Application Specific Information:
terminating with uncaught exception of type std::__1::system_error: mutex lock failed: Invalid argument
abort() called

Thread 0:: Dispatch queue: com.apple.main-thread
0 com.apple.GeForceGLDriver 0x0c71c168 0xc50d000 + 2158952
1 com.apple.GeForceGLDriver 0x0cbb070d 0xc50d000 + 6960909
2 com.apple.GeForceGLDriver 0x0c7f2cd2 0xc50d000 + 3038418
3 com.apple.GeForceGLDriver 0x0c80fa5a 0xc50d000 + 3156570
4 com.apple.GeForceGLDriver 0x0c82bba0 0xc50d000 + 3271584
5 libGPUSupportMercury.dylib 0xa2c24241 gldUpdateDrawFramebuffer + 109
6 GLEngine 0x9b67e172 gleUpdateDrawFramebufferState + 555
7 GLEngine 0x9b67f563 gleDoDrawDispatchCore + 99
8 GLEngine 0x9b642a64 glDrawArrays_IMM_Exec + 218
9 libGL.dylib 0x9a9c8488 glDrawArrays + 29
10 game_library.dylib 0x036120ef interactive::render::Triangle::render(interactive::render::Mode, interactive::render::LevelOfDetail, numeric::xyzVector const*) + 8651
11 game_library.dylib 0x03609c86 interactive::poseview::StrandResidueGeom::StrandTriangle::render(bool) const + 1146
12 game_library.dylib 0x035894fa interactive::geom::Viewport::on_render() + 1338
13 game_library.dylib 0x03597277 interactive::gui::Container::on_render() + 111
14 game_library.dylib 0x035c68da interactive::gui::TopLevel::on_render() + 392
15 game_library.dylib 0x035dc722 cocoa_wrapper_render + 296
16 game_library.dylib 0x035dbdbf -[CocoaOpenGLView drawRect:] + 76
17 com.apple.AppKit 0x91bfca6e _NSViewDrawRect + 86
18 com.apple.AppKit 0x914b235d -[NSView _drawRect:clip:] + 2005
19 com.apple.AppKit 0x914f776e -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 1921
20 com.apple.AppKit 0x914f7ac2 -[NSView _recursiveDisplayAllDirtyWithLockFocus:visRect:] + 2773
21 com.apple.AppKit 0x914b03b8 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 905
22 com.apple.AppKit 0x914b0dd5 -[NSView _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 3494
23 com.apple.AppKit 0x914afbc7 -[NSThemeFrame _recursiveDisplayRectIfNeededIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:topView:] + 304
24 com.apple.AppKit 0x91bfe56a -[NSView _oldDisplayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:] + 2927
25 com.apple.AppKit 0x914af077 -[NSView _displayRectIgnoringOpacity:isVisibleRect:rectIsVisibleRectForView:] + 119
26 com.apple.AppKit 0x914ab600 -[NSView displayIfNeeded] + 1347
27 com.apple.AppKit 0x914ab044 -[NSWindow displayIfNeeded] + 403
28 com.apple.AppKit 0x91c2dde7 ___NSWindowGetDisplayCycleObserver_block_invoke.5988 + 371
29 com.apple.AppKit 0x914aa894 __37+[NSDisplayCycle currentDisplayCycle]_block_invoke + 188
30 com.apple.QuartzCore 0x9c2ff0a5 CA::Transaction::run_commit_handlers(CATransactionPhase) + 45
31 com.apple.QuartzCore 0x9c2fdbec CA::Transaction::commit() + 184
32 com.apple.AppKit 0x91c50b66 __65+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayRefresh]_block_invoke + 465
33 com.apple.CoreFoundation 0x937977a6 _runLoopObserverWithBlockContext + 22
34 com.apple.CoreFoundation 0x937974b6 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 22
35 com.apple.CoreFoundation 0x937973d2 __CFRunLoopDoObservers + 498
36 com.apple.CoreFoundation 0x9377a81d __CFRunLoopRun + 1661
37 com.apple.CoreFoundation 0x93779e71 CFRunLoopRunSpecific + 641
38 com.apple.CoreFoundation 0x93779bda CFRunLoopRunInMode + 122
39 com.apple.HIToolbox 0x92d7737b RunCurrentEventLoopInMode + 321
40 com.apple.HIToolbox 0x92d770a2 ReceiveNextEventCommon + 777
41 com.apple.HIToolbox 0x92d76d7b _BlockUntilNextEventMatchingListInModeWithFilter + 71
42 com.apple.AppKit 0x91379b2d _DPSNextEvent + 2101
43 com.apple.AppKit 0x91aebe8c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 2859
44 com.apple.AppKit 0x91aeb359 -[NSApplication(NSEvent) nextEventMatchingMask:untilDate:inMode:dequeue:] + 134
45 com.apple.AppKit 0x9136ea7d -[NSApplication run] + 763
46 game_library.dylib 0x035df634 cocoa_glue_start + 981
47 game_library.dylib 0x035dd919 interactive::guiwrapper::cocoa::CocoaWrapper::start() + 39
48 game_library.dylib 0x033827c0 interactive::application::interactive_main(utility::vector1, std::__1::allocator >, std::__1::allocator, std::__1::allocator > > > const&, boost::function, boost::function, bool) + 3147
49 game_library.dylib 0x039da812 game::application::game_main(int, char**, char const*, game::application::ExecutableKindEnum) + 2338
50 game_library.dylib 0x0010b950 library_main + 32
51 edu.washington.foldit 0x000083a2 run_library_main(std::__1::basic_string, std::__1::allocator > const&, bool, std::__1::basic_string, std::__1::allocator > const&, int&, int, char**, std::__1::basic_string, std::__1::allocator >&) + 178
52 edu.washington.foldit 0x00008155 main + 353
53 edu.washington.foldit 0x000058a5 start + 53

Thread 1:: com.apple.audio.IOThread.client
0 libsystem_kernel.dylib 0xa7547422 mach_msg_trap + 10
1 libsystem_kernel.dylib 0xa7546a5f mach_msg + 47
2 com.apple.audio.CoreAudio 0x93356d34 HALB_MachPort::SendMessageWithReply(unsigned int, unsigned int, unsigned long, unsigned long, mach_msg_header_t*, bool, unsigned int) + 124
3 com.apple.audio.CoreAudio 0x933303a3 HALB_MachPort::SendSimpleMessageWithSimpleReply(unsigned int, unsigned int, int, int&, bool, unsigned int) + 49
4 com.apple.audio.CoreAudio 0x9332d2ec HALC_ProxyIOContext::IOWorkLoop() + 1600
5 com.apple.audio.CoreAudio 0x9332ca52 HALC_ProxyIOContext::IOThreadEntry(void*) + 236
6 com.apple.audio.CoreAudio 0x933600e1 invocation function for block in HALC_ProxyIOContext::HALC_ProxyIOContext(unsigned long, unsigned int) + 20
7 com.apple.audio.CoreAudio 0x9332c91b HALB_IOThread::Entry(void*) + 71
8 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
9 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
10 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 2:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0xa7547422 mach_msg_trap + 10
1 libsystem_kernel.dylib 0xa7546a5f mach_msg + 47
2 com.apple.CoreFoundation 0x9377ba88 __CFRunLoopServiceMachPort + 296
3 com.apple.CoreFoundation 0x9377aa76 __CFRunLoopRun + 2262
4 com.apple.CoreFoundation 0x93779e71 CFRunLoopRunSpecific + 641
5 com.apple.CoreFoundation 0x93779bda CFRunLoopRunInMode + 122
6 com.apple.AppKit 0x914a957c _NSEventThread + 165
7 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
8 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
9 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 3:
0 libsystem_kernel.dylib 0xa7551152 __semwait_signal + 10
1 libsystem_c.dylib 0xa74bcdb7 nanosleep$UNIX2003 + 189
2 libsystem_c.dylib 0xa74bcca4 usleep$UNIX2003 + 54
3 game_library.dylib 0x03649bd5 interactive::util::Thread::sleep(double) + 47
4 game_library.dylib 0x0349b8f3 interactive::application::appposeview::VoidGeom::VoidThread::operator()() + 143
5 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
6 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
7 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
8 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
9 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 4:
0 libsystem_kernel.dylib 0xa7551152 __semwait_signal + 10
1 libsystem_c.dylib 0xa74bcdb7 nanosleep$UNIX2003 + 189
2 libsystem_c.dylib 0xa74bcca4 usleep$UNIX2003 + 54
3 game_library.dylib 0x03649bd5 interactive::util::Thread::sleep(double) + 47
4 game_library.dylib 0x03490b41 interactive::application::appposeview::HydrophobicComposite::HydroThread::operator()() + 171
5 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
6 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
7 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
8 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
9 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 5:
0 libsystem_kernel.dylib 0xa7551152 __semwait_signal + 10
1 libsystem_c.dylib 0xa74bcdb7 nanosleep$UNIX2003 + 189
2 libsystem_c.dylib 0xa74bcca4 usleep$UNIX2003 + 54
3 game_library.dylib 0x03649bd5 interactive::util::Thread::sleep(double) + 47
4 game_library.dylib 0x0349880d interactive::application::appposeview::ResidueBurialComposite::ResidueBurialThread::operator()() + 185
5 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
6 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
7 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
8 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
9 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 6:
0 libsystem_kernel.dylib 0xa7551152 __semwait_signal + 10
1 libsystem_c.dylib 0xa74bcdb7 nanosleep$UNIX2003 + 189
2 libsystem_c.dylib 0xa74bcca4 usleep$UNIX2003 + 54
3 game_library.dylib 0x03649bd5 interactive::util::Thread::sleep(double) + 47
4 game_library.dylib 0x0372517d standalone::application::StandaloneApplication::autosave_thread_body() + 33
5 game_library.dylib 0x037871f0 boost::detail::function::void_function_obj_invoker0, boost::_bi::list1 > >, void>::invoke(boost::detail::function::function_buffer&) + 32
6 game_library.dylib 0x035bdc03 boost::function0::operator()() const + 35
7 game_library.dylib 0x03649c07 interactive::util::Thread::operator()() + 45
8 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
9 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
10 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
11 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
12 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 7:
0 libsystem_kernel.dylib 0xa7551152 __semwait_signal + 10
1 libsystem_c.dylib 0xa74bcdb7 nanosleep$UNIX2003 + 189
2 libsystem_c.dylib 0xa74bcca4 usleep$UNIX2003 + 54
3 game_library.dylib 0x03649bd5 interactive::util::Thread::sleep(double) + 47
4 game_library.dylib 0x0392dd3e game::application::BoincThread::periodically_send_and_check_boinc() + 418
5 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
6 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
7 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
8 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
9 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 8:
0 libsystem_kernel.dylib 0xa75510aa __select + 10
1 game_library.dylib 0x03a43aa7 game::util::IRC::run(boost::function) + 431
2 game_library.dylib 0x0397e261 game::application::IRCThread::operator()() + 1015
3 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
4 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
5 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
6 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
7 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 9:
0 libsystem_kernel.dylib 0xa755171a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0xa7704e64 _pthread_wqthread + 1035
2 libsystem_pthread.dylib 0xa7704a32 start_wqthread + 34

Thread 10:
0 libsystem_kernel.dylib 0xa755171a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0xa7705059 _pthread_wqthread + 1536
2 libsystem_pthread.dylib 0xa7704a32 start_wqthread + 34

Thread 11:
0 libsystem_pthread.dylib 0xa7704a10 start_wqthread + 0
1 game_library.dylib 0x001e0021 af_face_globals_compute_style_coverage + 977

Thread 12 Crashed:
0 libsystem_kernel.dylib 0xa7550eda __pthread_kill + 10
1 libsystem_pthread.dylib 0xa7708427 pthread_kill + 363
2 libsystem_c.dylib 0xa749f956 abort + 133
3 libc++abi.dylib 0xa5861ea7 abort_message + 134
4 libc++abi.dylib 0xa586206a default_terminate_handler() + 250
5 libc++abi.dylib 0xa587b657 std::__terminate(void (*)()) + 14
6 libc++abi.dylib 0xa587b0c1 __cxa_throw + 116
7 libc++.1.dylib 0xa58512d7 std::__1::__throw_system_error(int, char const*) + 103
8 libc++.1.dylib 0xa58436c2 std::__1::mutex::lock() + 52
9 game_library.dylib 0x03693c59 interactive::util::ligand::ThreadedRDKitRotamerLibrarySpecification::generate_library(core::chemical::ResidueType const&) + 83
10 game_library.dylib 0x036943bc boost::detail::function::void_function_obj_invoker0, boost::_bi::list2, boost::_bi::value > >, void>::invoke(boost::detail::function::function_buffer&) + 38
11 game_library.dylib 0x035bdc03 boost::function0::operator()() const + 35
12 game_library.dylib 0x03649c07 interactive::util::Thread::operator()() + 45
13 game_library.dylib 0x03649dd5 interactive::util::Thread::thread_entry_func() + 31
14 game_library.dylib 0x03649a17 interactive::util::Thread::pthread_startup_helper(void*) + 17
15 libsystem_pthread.dylib 0xa77054d5 _pthread_body + 347
16 libsystem_pthread.dylib 0xa770537a _pthread_start + 357
17 libsystem_pthread.dylib 0xa7704a56 thread_start + 34

Thread 12 crashed with X86 Thread State (32-bit):
eax: 0x00000000 ebx: 0xb32c4000 ecx: 0xb32c38bc edx: 0x00000000
edi: 0xa77082ca esi: 0x0000002d ebp: 0xb32c38e8 esp: 0xb32c38bc
ss: 0x00000023 efl: 0x00000206 eip: 0xa7550eda cs: 0x0000000b
ds: 0x00000023 es: 0x00000023 fs: 0x00000023 gs: 0x0000000f
cr2: 0xa99bd340

Logical CPU: 0
Error Code: 0x00080148
Trap Number: 132

Binary Images:
0x5000 - 0x9ff7 +edu.washington.foldit (1.0) <55866821-E6C1-3C1D-A37C-0B7CD951B203> /Applications/Foldit.app/Contents/MacOS/game_dynamic
0x80000 - 0xc605f dyld (551.3) /usr/lib/dyld
0x10a000 - 0x4d18fff +game_library.dylib (1) <3C6A8580-CBDA-3EF5-83C2-76EC2A851099> /Applications/Foldit.app/Contents/Resources/cmp-binary-dda876e993e6a4bc8a3dcf9641acd3bf/game_library.dylib
0xbdcb000 - 0xc31fff7 com.apple.driver.AppleIntelHD5000GraphicsGLDriver (10.32.48 - 10.3.2) <97C4EB81-3C7E-3084-AEC6-9DDCB4F1916B> /System/Library/Extensions/AppleIntelHD5000GraphicsGLDriver.bundle/Contents/MacOS/AppleIntelHD5000GraphicsGLDriver
0xc50d000 - 0xce63fff com.apple.GeForceGLDriver (10.30.25 - 10.3.0) <42A2C64B-E6F9-30FB-B640-8E4C464743A4> /System/Library/Extensions/GeForceGLDriver.bundle/Contents/MacOS/GeForceGLDriver
0xd432000 - 0xdafbff7 libclh.dylib (10.30.25) <9B2CFDC2-C78F-3F33-8DAB-20312ADC2545> /System/Library/Extensions/GeForceGLDriver.bundle/Contents/MacOS/libclh.dylib
0xdb52000 - 0xdb56fff com.apple.audio.AppleHDAHALPlugIn (281.51 - 281.51) /System/Library/Extensions/AppleHDA.kext/Contents/PlugIns/AppleHDAHALPlugIn.bundle/Contents/MacOS/AppleHDAHALPlugIn
0xdbf8000 - 0xddb6ff3 com.apple.audio.units.Components (1.14 - 1.14) /System/Library/Components/CoreAudio.component/Contents/MacOS/CoreAudio
0x1040f000 - 0x10779fff com.apple.RawCamera.bundle (8.03.0 - 1017.3.4) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x90015000 - 0x9001cfff com.apple.agl (3.3.1 - AGL-3.3.1) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x9029e000 - 0x9029efff com.apple.Accelerate (1.11 - Accelerate 1.11) <4FE55EFA-2AAB-3639-8340-CB00CC245170> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x9029f000 - 0x902b5ff7 libCGInterfaces.dylib (417.2) <6E14C5E9-EEE4-31D1-9712-2A021BA38B7D> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x902b6000 - 0x909f7fdf com.apple.vImage (8.1 - ???) <7BA2CB00-F6B3-3798-9CED-D0C3BB3E5231> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x909f8000 - 0x90b32ff7 libBLAS.dylib (1211.50.2) <056DFB80-2D9C-39BA-8953-EB264FDFDEAA> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x90b33000 - 0x90b60ffb libBNNS.dylib (38.1) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib
0x90b61000 - 0x90ed4fff libLAPACK.dylib (1211.50.2) <88232E9D-AD52-3E4F-8ACE-C2468400B626> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x90ed5000 - 0x90eebffb libLinearAlgebra.dylib (1211.50.2) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
0x90eec000 - 0x90f05ff7 libSparseBLAS.dylib (1211.50.2) <43DB3D39-727E-3C75-9286-11045DEFC21D> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
0x90f06000 - 0x91065fc7 libvDSP.dylib (622.50.5) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
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0xa40f3000 - 0xa411dfff com.apple.MultitouchSupport.framework (1404.4 - 1404.4) <591C5CFA-F49A-3AA3-9ACB-5076483D6BB0> /System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
0xa423c000 - 0xa4246fff com.apple.NetAuth (6.2 - 6.2) /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth
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0xa44a2000 - 0xa44c4fff com.apple.RemoteViewServices (2.0 - 125) <54C07CCF-E480-3033-979D-A7E6BCC6281F> /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
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0xa45b8000 - 0xa45b9fff com.apple.performance.SignpostNotification (1.2.4 - 2.4) /System/Library/PrivateFrameworks/SignpostNotification.framework/Versions/A/SignpostNotification
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0xa55e9000 - 0xa55e9fff libOpenScriptingUtil.dylib (174) /usr/lib/libOpenScriptingUtil.dylib
0xa563d000 - 0xa5641fff libScreenReader.dylib (562.18.4) <24F173B6-9EB9-3730-A6CE-D43827265020> /usr/lib/libScreenReader.dylib
0xa5642000 - 0xa5643fff libSystem.B.dylib (1252.50.4) /usr/lib/libSystem.B.dylib
0xa5652000 - 0xa5667ff7 libapple_nghttp2.dylib (1.24) <480C0C04-2533-3D44-8232-006B6CBA7758> /usr/lib/libapple_nghttp2.dylib
0xa5668000 - 0xa5693fff libarchive.2.dylib (54) /usr/lib/libarchive.2.dylib
0xa5694000 - 0xa57e3ffb libate.dylib (1.13.1) /usr/lib/libate.dylib
0xa57e7000 - 0xa57e7ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0xa57e8000 - 0xa57f8fff libbsm.0.dylib (39) <6A4D8D43-8AD8-3B0C-A19C-22A77D30DD8E> /usr/lib/libbsm.0.dylib
0xa57f9000 - 0xa5805ff7 libbz2.1.0.dylib (38) <77C24A36-BE84-3702-A786-935C597A0A86> /usr/lib/libbz2.1.0.dylib
0xa5806000 - 0xa585fffb libc++.1.dylib (400.9) /usr/lib/libc++.1.dylib
0xa5860000 - 0xa5881fff libc++abi.dylib (400.8.2) <60422228-2A4A-3A12-AB94-3110E9082D62> /usr/lib/libc++abi.dylib
0xa5883000 - 0xa5894ff7 libcmph.dylib (6) /usr/lib/libcmph.dylib
0xa5895000 - 0xa58a8ff7 libcompression.dylib (47.50.1) <6C767502-0001-3CF8-8DA4-450D177D6170> /usr/lib/libcompression.dylib
0xa58a9000 - 0xa58c0ffb libcoretls.dylib (155.50.1) /usr/lib/libcoretls.dylib
0xa58c1000 - 0xa58c2fff libcoretls_cfhelpers.dylib (155.50.1) /usr/lib/libcoretls_cfhelpers.dylib
0xa5a43000 - 0xa5beaff3 libcrypto.35.dylib (22.50.2) /usr/lib/libcrypto.35.dylib
0xa5daa000 - 0xa5e01fff libcups.2.dylib (462.2) <2DD22F09-B4DA-3D2C-9470-B3113EC7EA03> /usr/lib/libcups.2.dylib
0xa5f18000 - 0xa5f18fff libenergytrace.dylib (16) <34FC43C7-D9B6-3C01-8B65-E49059D31279> /usr/lib/libenergytrace.dylib
0xa5f4c000 - 0xa5f50fff libheimdal-asn1.dylib (520.50.6) /usr/lib/libheimdal-asn1.dylib
0xa5f7c000 - 0xa606cff3 libiconv.2.dylib (51.50.1) /usr/lib/libiconv.2.dylib
0xa606d000 - 0xa628fff7 libicucore.A.dylib (59173.0.1) <12FFE9D1-76F7-39FF-B93D-33E17C203292> /usr/lib/libicucore.A.dylib
0xa62d7000 - 0xa62d8fff liblangid.dylib (128) <120FE992-47E4-3A73-A039-1B401F5696DC> /usr/lib/liblangid.dylib
0xa62d9000 - 0xa62f1ff7 liblzma.5.dylib (10) <8A5C9679-430A-3A19-AF68-9D21BAC442C7> /usr/lib/liblzma.5.dylib
0xa62f2000 - 0xa6307fff libmarisa.dylib (9) <805453EE-B829-3DA5-8DF3-5132D03D5B74> /usr/lib/libmarisa.dylib
0xa63bc000 - 0xa65d9fff libmecabra.dylib (779.7.6) /usr/lib/libmecabra.dylib
0xa67a0000 - 0xa6917ffb libnetwork.dylib (1229.51.2) /usr/lib/libnetwork.dylib
0xa6918000 - 0xa6cf80fb libobjc.A.dylib (723) <069E8DD2-ECBD-3296-9688-199A93DB8F1F> /usr/lib/libobjc.A.dylib
0xa6cfc000 - 0xa6cfffff libpam.2.dylib (22) <7106F43C-84DD-3F26-905A-B52780AFEB3E> /usr/lib/libpam.2.dylib
0xa6d02000 - 0xa6d33fff libpcap.A.dylib (79.20.1) <154889CF-5F83-3012-953E-0FC8FEE50FF8> /usr/lib/libpcap.A.dylib
0xa6d71000 - 0xa6d8cffb libresolv.9.dylib (65) <65A43F5B-CF88-3948-AE5C-D7CA02D814A1> /usr/lib/libresolv.9.dylib
0xa6dd7000 - 0xa6f61ffb libsqlite3.dylib (274.8.1) <2865CDEE-96C4-3ECC-9F4B-876D0CD27C41> /usr/lib/libsqlite3.dylib
0xa7105000 - 0xa7164fff libusrtcp.dylib (1229.51.2) /usr/lib/libusrtcp.dylib
0xa7165000 - 0xa7168ff7 libutil.dylib (51.20.1) <86BD9675-16A2-345D-9B8D-E8A3397F2365> /usr/lib/libutil.dylib
0xa7169000 - 0xa7177ff7 libxar.1.dylib (400) <4B664A7E-EC05-34AD-ACC6-C879B69DBA7C> /usr/lib/libxar.1.dylib
0xa7178000 - 0xa7256ff7 libxml2.2.dylib (31.10) /usr/lib/libxml2.2.dylib
0xa7257000 - 0xa727fff3 libxslt.1.dylib (15.12) <2A385CB5-9458-3408-A4F2-1F51553823F4> /usr/lib/libxslt.1.dylib
0xa7280000 - 0xa728fff7 libz.1.dylib (70) <588F445F-0065-3D77-8002-BA9411DA1D70> /usr/lib/libz.1.dylib
0xa72ca000 - 0xa72cefff libcache.dylib (80) /usr/lib/system/libcache.dylib
0xa72cf000 - 0xa72d9fff libcommonCrypto.dylib (60118.50.1) <95434E97-2B85-3607-9E02-2A8CFD178D23> /usr/lib/system/libcommonCrypto.dylib
0xa72da000 - 0xa72dffff libcompiler_rt.dylib (62) /usr/lib/system/libcompiler_rt.dylib
0xa72e0000 - 0xa72eaff3 libcopyfile.dylib (146.50.5) <6A3EF295-2778-3405-BE11-8947695F4A31> /usr/lib/system/libcopyfile.dylib
0xa72eb000 - 0xa7353ff7 libcorecrypto.dylib (562.50.17) /usr/lib/system/libcorecrypto.dylib
0xa73be000 - 0xa73f3fff libdispatch.dylib (913.50.12) /usr/lib/system/libdispatch.dylib
0xa73f4000 - 0xa7411fff libdyld.dylib (551.3) <42AC1F77-75EC-3464-B24D-8E95F72FFE21> /usr/lib/system/libdyld.dylib
0xa7412000 - 0xa7412fff libkeymgr.dylib (28) <35604C10-4B09-3AA0-9694-87D40C15E706> /usr/lib/system/libkeymgr.dylib
0xa7413000 - 0xa741fff7 libkxld.dylib (4570.51.1) <127EA762-C4AC-34D7-9ABF-CEF26FDF18E0> /usr/lib/system/libkxld.dylib
0xa7420000 - 0xa7420fff liblaunch.dylib (1205.50.76) <7EBFA8BE-2176-3A74-9218-3ED02CC6945D> /usr/lib/system/liblaunch.dylib
0xa7421000 - 0xa7426fff libmacho.dylib (906) <14070ABC-E6F7-3CD5-9527-56E38D65BC74> /usr/lib/system/libmacho.dylib
0xa7427000 - 0xa7429fff libquarantine.dylib (86) <2660EB51-FA02-36ED-9416-83A4A6849026> /usr/lib/system/libquarantine.dylib
0xa742a000 - 0xa742bfff libremovefile.dylib (45) /usr/lib/system/libremovefile.dylib
0xa742c000 - 0xa7443ff7 libsystem_asl.dylib (356.50.1) <8C2103F0-0293-3450-A4D5-CDA224D6B1DD> /usr/lib/system/libsystem_asl.dylib
0xa7444000 - 0xa7444fff libsystem_blocks.dylib (67) /usr/lib/system/libsystem_blocks.dylib
0xa7445000 - 0xa74d1ff3 libsystem_c.dylib (1244.50.9) <3A7B32B2-F70C-3148-A2B0-38412EF1489F> /usr/lib/system/libsystem_c.dylib
0xa74d2000 - 0xa74d5fff libsystem_configuration.dylib (963.50.8) /usr/lib/system/libsystem_configuration.dylib
0xa74d6000 - 0xa74d9fff libsystem_coreservices.dylib (51) /usr/lib/system/libsystem_coreservices.dylib
0xa74da000 - 0xa74dbfff libsystem_darwin.dylib (1244.50.9) <326B9F59-5784-3C79-8A44-7C40D662C695> /usr/lib/system/libsystem_darwin.dylib
0xa74dc000 - 0xa74e2ff3 libsystem_dnssd.dylib (878.50.17) <7B2BF425-F98C-34F8-A574-CB1FD08F169C> /usr/lib/system/libsystem_dnssd.dylib
0xa74e3000 - 0xa7532ffb libsystem_info.dylib (517.30.1) /usr/lib/system/libsystem_info.dylib
0xa7533000 - 0xa7557ff3 libsystem_kernel.dylib (4570.51.1) /usr/lib/system/libsystem_kernel.dylib
0xa7558000 - 0xa75a7fdb libsystem_m.dylib (3147.50.1) <14D10C6D-5426-33AA-B0EB-A55B5CD6FF9A> /usr/lib/system/libsystem_m.dylib
0xa75a8000 - 0xa75c2fff libsystem_malloc.dylib (140.50.6) <970603BE-8A36-3776-81A6-BC1B1D04AC35> /usr/lib/system/libsystem_malloc.dylib
0xa75c3000 - 0xa76e6ff3 libsystem_network.dylib (1229.51.2) <179546B6-7D74-3C3D-83B4-6FAD3FCAF914> /usr/lib/system/libsystem_network.dylib
0xa76e7000 - 0xa76f1fff libsystem_networkextension.dylib (767.50.25) <42DC977C-3E83-34BA-9AEA-45270B973BF2> /usr/lib/system/libsystem_networkextension.dylib
0xa76f2000 - 0xa76faff3 libsystem_notify.dylib (172) <27A79E60-9B05-3B28-B389-5759A72F7321> /usr/lib/system/libsystem_notify.dylib
0xa76fb000 - 0xa7701ffb libsystem_platform.dylib (161.50.1) <04C8CF15-A241-3BD8-87B5-DD5DA2DCD564> /usr/lib/system/libsystem_platform.dylib
0xa7702000 - 0xa770cff3 libsystem_pthread.dylib (301.50.1) <95F98870-7DB1-3273-9E61-DEC04059BF18> /usr/lib/system/libsystem_pthread.dylib
0xa770d000 - 0xa7710ff3 libsystem_sandbox.dylib (765.50.51) /usr/lib/system/libsystem_sandbox.dylib
0xa7711000 - 0xa7713fff libsystem_secinit.dylib (30) /usr/lib/system/libsystem_secinit.dylib
0xa7714000 - 0xa771cff7 libsystem_symptoms.dylib (820.50.37) /usr/lib/system/libsystem_symptoms.dylib
0xa771d000 - 0xa772fffb libsystem_trace.dylib (829.50.17) <3786EA81-F02C-3115-A8B6-3AC9088EA04C> /usr/lib/system/libsystem_trace.dylib
0xa7731000 - 0xa7737fff libunwind.dylib (35.3) /usr/lib/system/libunwind.dylib
0xa7738000 - 0xa7761ff7 libxpc.dylib (1205.50.76) <1C1C908A-B0A5-3BAF-8B3F-F0B2F19B4698> /usr/lib/system/libxpc.dylib

External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 8
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: 8411
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=399.2M resident=0K(0%) swapped_out_or_unallocated=399.2M(100%)
Writable regions: Total=768.0M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=768.0M(100%)

VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 2
Activity Tracing 256K 2
CG backing stores 5652K 4
CG image 52K 5
CoreAnimation 104K 13
CoreGraphics 8K 2
CoreImage 16K 3
CoreUI image data 740K 10
CoreUI image file 180K 4
Foundation 4K 2
Kernel Alloc Once 8K 2
MALLOC 716.8M 127
MALLOC guard page 48K 13
Memory Tag 242 12K 2
Memory Tag 249 156K 2
OpenGL GLSL 128K 3
Stack 19.5M 41
Stack (reserved) 24.0M 2 reserved VM address space (unallocated)
Stack Guard 32.0M 14
VM_ALLOCATE 220K 25
VM_ALLOCATE (reserved) 36K 2 reserved VM address space (unallocated)
__DATA 17.3M 236
__FONT_DATA 4K 2
__GLSLBUILTINS 2588K 2
__LINKEDIT 150.0M 11
__OBJC 3212K 87
__TEXT 249.1M 237
__UNICODE 560K 2
mapped file 311.2M 211
shared memory 744K 12
=========== ======= =======
TOTAL 1.5G 1050
TOTAL, minus reserved VM space 1.5G 1050

Model: MacBookPro11,3, BootROM MBP112.0145.B00, 4 processors, Intel Core i7, 2.6 GHz, 16 GB, SMC 2.19f12
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In
Graphics: NVIDIA GeForce GT 750M, NVIDIA GeForce GT 750M, PCIe
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533641465238412D50422020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x134), Broadcom BCM43xx 1.0 (7.77.37.29.1a7)
Bluetooth: Version 6.0.5f3, 3 services, 27 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en0
Serial ATA Device: APPLE SSD SM1024G, 1 TB
USB Device: USB 3.0 Bus
USB Device: Apple Internal Keyboard / Trackpad
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 17.1

Joined: 12/27/2012
Groups: Beta Folders

I crashed after loading a shared solution. Log file attached.

The shared solution was there when I restarted the client. I'm able to run recipes on it, no crashes so far.

I noticed that these rotamer messages appear both before and after the crash in the attached log:

Generated 20 rotamers for LG_50098 in 19.301s total.

 (unhandled exception messages....)

Generated 20 rotamers for LG_50013 in 19.332s total

I'm seeing the same message that appeared in the log JellyJump pasted:

core.chemical.GlobalResidueTypeSet: [ WARNING ] PDB component dictionary file not found at (./)[chemical/pdb_components/components.Nov01_2017.A_to_C.cif, chemical/pdb_components/components.Nov01_2017.D_to_Z.cif]

Mike Cassidy's dump shows thread 12 died doing something in:

ThreadedRDKitRotamerLibrarySpecification::generate_library

So it seems possible that these crashes have something to do with generating rotamers for the ligand. Not clear to me why it crashes one time and then is fine the next.

Susume's picture
User offline. Last seen 5 hours 59 min ago. Offline
Joined: 10/02/2011

robgee attempted to share 1519 with group. His client crashed. I looked and saw his share. I downloaded it (did not try to load) and my client crashed on download. It was a new client so log.txt is short.

Susume's picture
User offline. Last seen 5 hours 59 min ago. Offline
Joined: 10/02/2011

After I restarted the client, the share was in my local list (i.e. download was successful despite the crash) and I was able to open it and run scripts (blue fuse v1.1, ligandacious v1.0). log.txt attached.

A series of warnings beginning with "core.chemical.GlobalResidueTypeSet: [ WARNING ] PDB component dictionary file not found at (./)" appears in both logs (client that crashed and client that didn't).

Line that precedes crash is: "Generated 20 rotamers for LG_50033 in 3.467s total." It is the only line of this form in the crashed client's log. In non-crashing client, there are numerous lines of the form "Generated 15 rotamers for LG_5001 in 0.026s total." (one for each autosave loaded).

Susume's picture
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Loading the share a 3rd time in a new client, new track, did not crash. It looks like maybe only the first time you load that share it will crash - after that you can load and re-load and play it (good news!).

Starting a client from a different install of foldit (different foldit directory), the first load of the share crashed (log copy 52), and a subsequent load did not crash (log copy 53). I deleted the share from my local list and attempted to re-download it, and it crashed (log copy 54).

In all of the logs where it crashed, the "Generated 20 rotamers..." line before the crash refers to the share as LG_50033 (I am guessing it was the 33rd ligand conformation from robgee's client). In the logs where it did not crash, the exact same share is referred to as LG_5002 (2nd ligand conformation in my client?). Wild speculation: could the numbering of the ligand conformation have to do with the crash?

Joined: 09/24/2012
Groups: Go Science

When sharing to group, it crashes but it's shared.
When loading the first time, it crashes but it's loaded on local.
When loading from client, it's ok.

Then, after some manual hand fold (adding atoms), and Undos several times, it crashes again and you have to start the all process again (loading first time etc).

Joined: 12/27/2012
Groups: Beta Folders

Here's another one, crashed after loading my own share on a different client.

alcor29's picture
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Another crash (setup as above): Just shared with scientists and returned to folding UI and either crashed immediately or when I accidentaly moved the pointer.

UNHANDLED EXCEPTION
1: alIsAuxiliaryEffectSlot +598376 bytes (no line)
2: alIsAuxiliaryEffectSlot +598984 bytes (no line)
3: library_main +5297766 bytes (no line)
4: library_main +5297955 bytes (no line)
5: library_main +371112 bytes (no line)
6: library_main +3400005 bytes (no line)
7: library_main +3400443 bytes (no line)
8: BaseThreadInitThunk +36 bytes (no line)
9: RtlValidSecurityDescriptor +448 bytes (no line)
10: RtlValidSecurityDescriptor +400 bytes (no line)

alcor29's picture
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Re above: happened again. So crash occurs as soon as close the manage solutions box. Same log as above.

No object matching key 0.
hotkey pressed 1 times Ctrl+O
Sending SOPs:

Sending SOPs:

Sending SOPs:

Generated 15 rotamers for LG_50023 in 1.023s total.

UNHANDLED EXCEPTION
1: alIsAuxiliaryEffectSlot +598376 bytes (no line)
2: alIsAuxiliaryEffectSlot +598984 bytes (no line)
3: library_main +5297766 bytes (no line)
4: library_main +5297955 bytes (no line)
5: library_main +371112 bytes (no line)
6: library_main +3400005 bytes (no line)
7: library_main +3400443 bytes (no line)
8: BaseThreadInitThunk +36 bytes (no line)
9: RtlValidSecurityDescriptor +448 bytes (no line)
10: RtlValidSecurityDescriptor +400 bytes (no line)

Joined: 06/24/2008
Groups: Void Crushers

What Madde and I noticed: in devprev it 'usually' crashed when you share and and usually crashes the first time you open a share.

Joined: 09/22/2017
Groups: Beta Folders

Tried reinstalling fold it client - did not fix issue

jeff101's picture
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Groups: Go Science

I just updated a client and started 1519 in it.
I tried downloading group-shared solutions from
the server with it. I'd download 1-2 solutions
and then the client would quit. This happened
multiple times.

alcor29's picture
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Joined: 11/16/2012

Clicked to change atom. Crash.

signed Residue: [H]Oc1c(-c2c([H])c(C(N([H])C3([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C3([H])[H])=[N+]([H])[H])c([H])c([H])c2[H])n([N+](=O)C([H])([H])[H])c([N+](=O)C([H])([H])[H])c1C(C([H])([H])[H])(C([H])([H])[H])[N+]([H])([H])[H]
FinalE finalize:
core.chemical.ResidueTypeSet: [ WARNING ] ResidueType LG_50024 of mode fa_standard is being added to a ResidueTypeSet of mode centroid
replacing residue
Tool on_action_complete called
Tool on_action_complete called
Tool on_action_complete called
Designed Residue: [H]Oc1c(-c2c([H])c(C(N([H])C3([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C3([H])[H])=[N+]([H])[H])c([H])c([H])c2[H])n([N+](=O)[O-])c([N+](=O)C([H])([H])[H])c1C(C([H])([H])[H])(C([H])([H])[H])[N+]([H])([H])[H]
FinalE finalize:
core.chemical.ResidueTypeSet: [ WARNING ] ResidueType LG_50025 of mode fa_standard is being added to a ResidueTypeSet of mode centroid
replacing residue
Tool on_action_complete called
Tool on_action_complete called
Generated 20 rotamers for LG_50024 in 8.507s total.

UNHANDLED EXCEPTION
1: alIsAuxiliaryEffectSlot +598376 bytes (no line)
2: alIsAuxiliaryEffectSlot +598984 bytes (no line)
3: library_main +5297766 bytes (no line)
4: library_main +5297955 bytes (no line)
5: library_main +371112 bytes (no line)
6: library_main +3400005 bytes (no line)
7: library_main +3400443 bytes (no line)
8: BaseThreadInitThunk +36 bytes (no line)
9: RtlValidSecurityDescriptor +448 bytes (no line)
10: RtlValidSecurityDescriptor +400 bytes (no line)

rmoretti's picture
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An update on these crashes: I think I've tracked down the issue.

For those interested in the technicalities, the code doing the "Generated NN rotamers ..." output is in a sub-thread, and when loading a new solution there's a chance this thread can stick around past the point where it's needed. It then tries to access data from the previous puzzle state - which is now missing - resulting in the crash.

I've updated the developer's internal version to make sure this doesn't happen. This may take a bit of time to work its way to devprev and main, though. Until then, you can work around the crashes by waiting a sufficient amount of time after changing the chemical structure of the ligand before loading a new solution. (Unfortunately "sufficient" depends on the chemical type. Normally 30s or so should be more than enough, but sometimes it will take more time.)

I apologize for the issues, and thanks for your efforts in troubleshooting it. Your detailed description of the issue helped me narrow down the problem.

Joined: 12/27/2012
Groups: Beta Folders

Not sure if it's the same issue, but I also get a crash when editing the description of a saved solution.

And a crash when attempting to upload a solution, but the upload fails due to too many
solutions already uploaded.

And a crash when downloading (not opening) a shared solution.

bertro's picture
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Groups: Beta Folders

seeing references to this in log.txt (seems like missing dictionary file):

Finished show_puzzle_screen...
has key .opdb
Loading restype `LG_5008` (LIG,Z) from SMILES string `[H]OC([H])(C([H])([H])[H])C([H])([H])[H]`
core.chemical.GlobalResidueTypeSet: [ WARNING ] PDB component dictionary file not found at (./)[chemical/pdb_components/components.Nov01_2017.A_to_C.cif, chemical/pdb_components/components.Nov01_2017.D_to_Z.cif]
core.chemical.GlobalResidueTypeSet: [ WARNING ] or in the Rosetta database
core.chemical.GlobalResidueTypeSet: [ WARNING ] For more information on how to obtain the file and set it for use with Rosetta, visit:

https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary

core.chemical.GlobalResidueTypeSet: [ WARNING ] If you want a quick fix, you can try to directly ftp in the file:
core.chemical.GlobalResidueTypeSet: [ WARNING ] ftp -o cmp-database-b22abac3dbaea02a314dc8f75ee1bf09\database\chemical/components.cif.gz ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
core.chemical.GlobalResidueTypeSet: [ WARNING ] and then add to your Rosetta command-line: -PDB_components_file chemical/components.cif.gz Could not find: 'LIG' in pdb components files [chemical/pdb_components/components.Nov01_2017.A_to_C.cif, chemical/pdb_components/components.Nov01_2017.D_to_Z.cif]! Skipping residue...
core.chemical.GlobalResidueTypeSet: [ WARNING ] Could not find: 'LIG' in pdb components files [chemical/pdb_components/components.Nov01_2017.A_to_C.cif, chemical/pdb_components/components.Nov01_2017.D_to_Z.cif]! Skipping residue...
has key .opuzzle_setup
has key .ofilters
has key .osmiles_queue
starting score : -432.038
puzzle loaded

rmoretti's picture
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Sorry about these warning messages -- the dictionary it's complaining about shouldn't be present in Foldit (it's big and unused), but a setting to skip looking at it was missed. It shouldn't affect the puzzle though.

The next update should include an update to the settings such that these messages will no longer get printed.

bertro's picture
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Groups: Beta Folders

Thanks

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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