id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4003 OpenMM OpenCL crash on Mac in Intel graphics driver chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-19.6.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [7361] Path: /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.1.1 (1.1.1.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [7361] User ID: 501 Date/Time: 2020-12-01 16:27:11.355 -0500 OS Version: Mac OS X 10.15.7 (19H15) Report Version: 12 Anonymous UUID: 862596B2-602E-4497-51C9-D7F4F38F4EAC Time Awake Since Boot: 14000 seconds System Integrity Protection: disabled Crashed Thread: 0 CrBrowserMain Dispatch queue: opencl_runtime Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Application Specific Information: abort() called Application Specific Signatures: Graphics kernel error: 0xfffffffe Thread 0 Crashed:: CrBrowserMain Dispatch queue: opencl_runtime 0 libsystem_kernel.dylib 0x00007fff6905433a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff69110e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff68f6b93e raise + 26 3 libsystem_platform.dylib 0x00007fff691055fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 libsystem_c.dylib 0x00007fff68fdb808 abort + 120 6 libGPUSupportMercury.dylib 0x00007fff502da0a5 gpusGenerateCrashLog.cold.1 + 95 7 libGPUSupportMercury.dylib 0x00007fff502d118f gpusGenerateCrashLog + 89 8 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff251d5430 gpusKillClientExt + 9 9 libGPUSupportMercury.dylib 0x00007fff502d1b38 gpusQueueSubmitDataBuffers + 159 10 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff24e6b46a IntelCLCommandBuffer::getNew(GLDQueueRec*) + 30 11 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff24e6b379 intelSubmitCLCommands(GLDQueueRec*, unsigned int) + 69 12 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff24e6b2c4 CHAL_INTEL::ChalContext::ChalFlush() + 82 13 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x00007fff24e6b231 gldFinishQueue + 43 14 com.apple.opencl 0x00007fff38335acd 0x7fff38324000 + 72397 15 com.apple.opencl 0x00007fff3833672f 0x7fff38324000 + 75567 16 com.apple.opencl 0x00007fff3834f4e5 0x7fff38324000 + 177381 17 com.apple.opencl 0x00007fff38351067 0x7fff38324000 + 184423 18 libdispatch.dylib 0x00007fff68eb3658 _dispatch_client_callout + 8 19 libdispatch.dylib 0x00007fff68ebf6ec _dispatch_lane_barrier_sync_invoke_and_complete + 60 20 com.apple.opencl 0x00007fff38350ee9 0x7fff38324000 + 184041 21 com.apple.opencl 0x00007fff3834e75f 0x7fff38324000 + 173919 22 com.apple.opencl 0x00007fff383465f7 clEnqueueWriteBuffer + 767 23 libOpenMMOpenCL.dylib 0x0000000150113d78 OpenMM::OpenCLArray::upload(void const*, bool) + 104 24 libOpenMMOpenCL.dylib 0x00000001501ecf82 OpenMM::OpenCLCalcCustomCompoundBondForceKernel::initialize(OpenMM::System const&, OpenMM::CustomCompoundBondForce const&) + 2146 25 libOpenMM.dylib 0x000000014fcd1089 OpenMM::CustomCompoundBondForceImpl::initialize(OpenMM::ContextImpl&) + 489 26 libOpenMM.dylib 0x000000014fcbd228 OpenMM::ContextImpl::initialize() + 1160 27 libOpenMM.dylib 0x000000014fcb95b3 OpenMM::Context::Context(OpenMM::System const&, OpenMM::Integrator&, OpenMM::Platform&, std::__1::map, std::__1::allocator >, std::__1::basic_string, std::__1::allocator >, std::__1::less, std::__1::allocator > >, std::__1::allocator, std::__1::allocator > const, std::__1::basic_string, std::__1::allocator > > > > const&) + 227 28 _openmm.cpython-37m-darwin.so 0x000000014f9a771b _wrap_new_Context(_object*, _object*) + 1275 29 org.python.python 0x000000010d381c23 PyCFunction_Call + 387 30 org.python.python 0x000000010d453b3a _PyEval_EvalFrameDefault + 27370 31 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 32 org.python.python 0x000000010d381377 _PyFunction_FastCallDict + 455 33 org.python.python 0x000000010d382873 _PyObject_Call_Prepend + 131 34 org.python.python 0x000000010d3d5e3f slot_tp_init + 175 35 org.python.python 0x000000010d3d1534 type_call + 292 36 org.python.python 0x000000010d3816df _PyObject_FastCallKeywords + 575 37 org.python.python 0x000000010d456bcd call_function + 765 38 org.python.python 0x000000010d453817 _PyEval_EvalFrameDefault + 26567 39 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 40 org.python.python 0x000000010d381377 _PyFunction_FastCallDict + 455 41 org.python.python 0x000000010d382873 _PyObject_Call_Prepend + 131 42 org.python.python 0x000000010d3d5e3f slot_tp_init + 175 43 org.python.python 0x000000010d3d1534 type_call + 292 44 org.python.python 0x000000010d3816df _PyObject_FastCallKeywords + 575 45 org.python.python 0x000000010d456bcd call_function + 765 46 org.python.python 0x000000010d453817 _PyEval_EvalFrameDefault + 26567 47 org.python.python 0x000000010d381d61 function_code_fastcall + 177 48 org.python.python 0x000000010d456bd4 call_function + 772 49 org.python.python 0x000000010d4537fa _PyEval_EvalFrameDefault + 26538 50 org.python.python 0x000000010d381d61 function_code_fastcall + 177 51 org.python.python 0x000000010d456bd4 call_function + 772 52 org.python.python 0x000000010d4537fa _PyEval_EvalFrameDefault + 26538 53 org.python.python 0x000000010d381d61 function_code_fastcall + 177 54 org.python.python 0x000000010d456bd4 call_function + 772 55 org.python.python 0x000000010d4537fa _PyEval_EvalFrameDefault + 26538 56 org.python.python 0x000000010d381d61 function_code_fastcall + 177 57 org.python.python 0x000000010d456bd4 call_function + 772 58 org.python.python 0x000000010d4537fa _PyEval_EvalFrameDefault + 26538 59 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 60 org.python.python 0x000000010d381377 _PyFunction_FastCallDict + 455 61 org.python.python 0x000000010d453a3a _PyEval_EvalFrameDefault + 27114 62 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 63 org.python.python 0x000000010d381879 _PyFunction_FastCallKeywords + 217 64 org.python.python 0x000000010d456bd4 call_function + 772 65 org.python.python 0x000000010d4537fa _PyEval_EvalFrameDefault + 26538 66 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 67 org.python.python 0x000000010d381377 _PyFunction_FastCallDict + 455 68 org.python.python 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QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219 108 QtGui 0x000000011a979355 QWindowSystemInterface::flushWindowSystemEvents(QFlags) + 581 109 libqcocoa.dylib 0x0000000124ebb078 0x124e8c000 + 192632 110 libqcocoa.dylib 0x0000000124ebb248 0x124e8c000 + 193096 111 com.apple.AppKit 0x00007fff2c285d5d -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 6512 112 com.apple.AppKit 0x00007fff2c2841c9 -[NSWindow(NSEventRouting) sendEvent:] + 349 113 libqcocoa.dylib 0x0000000124ebe685 0x124e8c000 + 206469 114 com.apple.AppKit 0x00007fff2c282efe -[NSApplication(NSEvent) sendEvent:] + 2826 115 libqcocoa.dylib 0x0000000124ec570a 0x124e8c000 + 235274 116 com.apple.AppKit 0x00007fff2c0cf5bf -[NSApplication run] + 707 117 libqcocoa.dylib 0x0000000124ec1de3 0x124e8c000 + 220643 118 QtCore 0x000000011b0a993f QEventLoop::exec(QFlags) + 431 119 QtCore 0x000000011b0ae932 QCoreApplication::exec() + 130 120 QtWidgets.so 0x000000011a0717d2 meth_QApplication_exec_(_object*, _object*) + 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0x000000010d38252d _PyMethodDef_RawFastCallKeywords + 653 136 org.python.python 0x000000010d3818b9 _PyCFunction_FastCallKeywords + 41 137 org.python.python 0x000000010d456b60 call_function + 656 138 org.python.python 0x000000010d4538ae _PyEval_EvalFrameDefault + 26718 139 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 140 org.python.python 0x000000010d381879 _PyFunction_FastCallKeywords + 217 141 org.python.python 0x000000010d456bd4 call_function + 772 142 org.python.python 0x000000010d4538ae _PyEval_EvalFrameDefault + 26718 143 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 144 org.python.python 0x000000010d381377 _PyFunction_FastCallDict + 455 145 org.python.python 0x000000010d4b1af3 pymain_run_module + 147 146 org.python.python 0x000000010d4b0bdc pymain_main + 5900 147 org.python.python 0x000000010d4af4c3 Py_Main + 51 148 edu.ucsf.cgl.ChimeraX 0x000000010d356dc8 main + 120 149 libdyld.dylib 0x00007fff68f0ccc9 start + 1 Thread 1: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x000000010ed7fc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 2: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x000000010ed7fc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 3: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x000000010ed7fc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 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QtWebEngineCore 0x000000011faa49bc 0x11d8d3000 + 35461564 7 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 8 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 6:: DnsConfigService 0 libsystem_kernel.dylib 0x00007fff69052766 kevent + 10 1 QtWebEngineCore 0x000000011fd369a9 0x11d8d3000 + 38156713 2 QtWebEngineCore 0x000000011fd33cbd 0x11d8d3000 + 38145213 3 QtWebEngineCore 0x000000011faeacdc 0x11d8d3000 + 35749084 4 QtWebEngineCore 0x000000011fa52085 0x11d8d3000 + 35123333 5 QtWebEngineCore 0x000000011faa49bc 0x11d8d3000 + 35461564 6 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 7 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 8 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 7:: TaskSchedulerServiceThread 0 libsystem_kernel.dylib 0x00007fff69052766 kevent + 10 1 QtWebEngineCore 0x000000011fd369a9 0x11d8d3000 + 38156713 2 QtWebEngineCore 0x000000011fd33cbd 0x11d8d3000 + 38145213 3 QtWebEngineCore 0x000000011faeacc4 0x11d8d3000 + 35749060 4 QtWebEngineCore 0x000000011fa52085 0x11d8d3000 + 35123333 5 QtWebEngineCore 0x000000011fa93a74 0x11d8d3000 + 35392116 6 QtWebEngineCore 0x000000011faa49bc 0x11d8d3000 + 35461564 7 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 8 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 8:: TaskSchedulerForegroundWorker 0 libsystem_kernel.dylib 0x00007fff6904ddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff6904e170 mach_msg + 60 2 QtWebEngineCore 0x000000011fa7532d 0x11d8d3000 + 35267373 3 QtWebEngineCore 0x000000011fa75421 0x11d8d3000 + 35267617 4 QtWebEngineCore 0x000000011fa8cd28 0x11d8d3000 + 35364136 5 QtWebEngineCore 0x000000011fa8d65b 0x11d8d3000 + 35366491 6 QtWebEngineCore 0x000000011fa8d2c4 0x11d8d3000 + 35365572 7 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 8 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0x11d8d3000 + 35267373 3 QtWebEngineCore 0x000000011fa75421 0x11d8d3000 + 35267617 4 QtWebEngineCore 0x000000011fa8cd28 0x11d8d3000 + 35364136 5 QtWebEngineCore 0x000000011fa8d65b 0x11d8d3000 + 35366491 6 QtWebEngineCore 0x000000011fa8d2c4 0x11d8d3000 + 35365572 7 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 8 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 11:: TaskSchedulerBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff6904ddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff6904e170 mach_msg + 60 2 QtWebEngineCore 0x000000011fa7532d 0x11d8d3000 + 35267373 3 QtWebEngineCore 0x000000011fa75421 0x11d8d3000 + 35267617 4 QtWebEngineCore 0x000000011fa8cd28 0x11d8d3000 + 35364136 5 QtWebEngineCore 0x000000011fa8d65b 0x11d8d3000 + 35366491 6 QtWebEngineCore 0x000000011fa8d234 0x11d8d3000 + 35365428 7 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 8 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 12:: Chrome_IOThread 0 libsystem_kernel.dylib 0x00007fff69052766 kevent + 10 1 QtWebEngineCore 0x000000011fd369a9 0x11d8d3000 + 38156713 2 QtWebEngineCore 0x000000011fd33cbd 0x11d8d3000 + 38145213 3 QtWebEngineCore 0x000000011faeacc4 0x11d8d3000 + 35749060 4 QtWebEngineCore 0x000000011fa52085 0x11d8d3000 + 35123333 5 QtWebEngineCore 0x000000011f3c0fe4 0x11d8d3000 + 28237796 6 QtWebEngineCore 0x000000011faa49bc 0x11d8d3000 + 35461564 7 QtWebEngineCore 0x000000011fae4717 0x11d8d3000 + 35723031 8 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 13:: TaskSchedulerSingleThreadSharedBackgroundBlocking0 0 libsystem_kernel.dylib 0x00007fff6904ddfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff6904e170 mach_msg + 60 2 QtWebEngineCore 0x000000011fa7532d 0x11d8d3000 + 35267373 3 QtWebEngineCore 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9 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 23: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000150d55c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 24: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000150d55c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 25: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000150d55c3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 26: 0 libsystem_pthread.dylib 0x00007fff6910cb68 start_wqthread + 0 Thread 27: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 org.python.python 0x000000010d49b0af PyThread_acquire_lock_timed + 351 3 org.python.python 0x000000010d4e69df acquire_timed + 111 4 org.python.python 0x000000010d4e675c lock_PyThread_acquire_lock + 44 5 org.python.python 0x000000010d38256a _PyMethodDef_RawFastCallKeywords + 714 6 org.python.python 0x000000010d388571 _PyMethodDescr_FastCallKeywords + 81 7 org.python.python 0x000000010d456bfe call_function + 814 8 org.python.python 0x000000010d4537fa _PyEval_EvalFrameDefault + 26538 9 org.python.python 0x000000010d457a2c _PyEval_EvalCodeWithName + 3276 10 org.python.python 0x000000010d381879 _PyFunction_FastCallKeywords + 217 11 org.python.python 0x000000010d456bd4 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0x000000010d4e7287 t_bootstrap + 71 27 org.python.python 0x000000010d49ad19 pythread_wrapper + 25 28 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 29 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 28: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 29: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 30: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 31: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 32: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 33: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 34: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 35: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000014fd1dd21 OpenMM::threadBody(void*) + 65 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 36: 0 libsystem_kernel.dylib 0x00007fff69050882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff69111425 _pthread_cond_wait + 698 2 libOpenMMOpenCL.dylib 0x00000001501333cd threadBody(void*) + 109 3 libsystem_pthread.dylib 0x00007fff69111109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff6910cb8b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010da6cdc0 rcx: 0x00007ff933d77a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007ff933d77a80 rsp: 0x00007ff933d77a58 r8: 0x00007ff933d77f48 r9: 0xcab3ddf6a4a186a6 r10: 0x000000010da6cdc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x00007ff9346de800 r14: 0x0000000000000006 r15: 0x0000000000000016 rip: 0x00007fff6905433a rfl: 0x0000000000000246 cr2: 0x000000010d5bcf7c Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x10d356000 - 0x10d356ff3 +edu.ucsf.cgl.ChimeraX (1.1.1 - 1.1.1.0) 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0x7fff68cee000 - 0x7fff68cf3ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff68cf4000 - 0x7fff68cfffff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff68d00000 - 0x7fff68d07fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff68d08000 - 0x7fff68d11ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff68d12000 - 0x7fff68da4fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib 0x7fff68eb1000 - 0x7fff68ef1ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff68ef2000 - 0x7fff68f28fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib 0x7fff68f29000 - 0x7fff68f29ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff68f2a000 - 0x7fff68f36ff3 libkxld.dylib (6153.141.2.2) /usr/lib/system/libkxld.dylib 0x7fff68f37000 - 0x7fff68f37ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib 0x7fff68f38000 - 0x7fff68f3dff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff68f3e000 - 0x7fff68f40ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff68f41000 - 0x7fff68f42ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff68f43000 - 0x7fff68f5aff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff68f5b000 - 0x7fff68f5bff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff68f5c000 - 0x7fff68fe3fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff68fe4000 - 0x7fff68fe7ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib 0x7fff68fe8000 - 0x7fff68febfff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff68fec000 - 0x7fff68ff4fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff68ff5000 - 0x7fff68ffcfff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff68ffd000 - 0x7fff68ffeffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff68fff000 - 0x7fff6904cff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff6904d000 - 0x7fff69079ff7 libsystem_kernel.dylib (6153.141.2.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff6907a000 - 0x7fff690c1fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff690c2000 - 0x7fff690e9fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff690ea000 - 0x7fff690f7ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff690f8000 - 0x7fff69101ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff69102000 - 0x7fff6910afef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff6910b000 - 0x7fff69115fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff69116000 - 0x7fff6911aff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib 0x7fff6911b000 - 0x7fff6911dfff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff6911e000 - 0x7fff69125ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff69126000 - 0x7fff6913cff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff6913e000 - 0x7fff69143ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff69144000 - 0x7fff69179ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 3 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: 9514 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%) Writable regions: Total=5.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.3G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 992K 2 CG image 152K 13 CoreAnimation 256K 22 CoreGraphics 8K 1 CoreImage 24K 2 CoreUI image data 3424K 30 Foundation 32K 2 Kernel Alloc Once 8K 1 MALLOC 3.6G 595 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 1984K 11 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) OpenCL 818.8M 30 OpenCL (reserved) 3576K 10 reserved VM address space (unallocated) OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 144K 36 Stack 165.8M 37 Stack Guard 56.0M 1 VM_ALLOCATE 323.2M 932 VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated) __DATA 62.1M 639 __DATA_CONST 40K 4 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 438.2M 216 __OBJC_RO 32.3M 1 __OBJC_RW 1904K 1 __TEXT 631.7M 588 __UNICODE 564K 1 mapped file 85.9M 38 shared memory 644K 17 =========== ======= ======= TOTAL 6.6G 3254 TOTAL, minus reserved VM space 6.2G 3254 Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA CorporationHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro11,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 162.0.0.0.0 SMC Version (system): 2.19f12 Software: System Software Overview: System Version: macOS 10.15.7 (19H15) Kernel Version: Darwin 19.6.0 Time since boot: 4:04 Graphics/Displays: Intel Iris Pro: Chipset Model: Intel Iris Pro Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x0d26 Revision ID: 0x0008 Automatic Graphics Switching: Supported gMux Version: 4.0.8 [3.2.8] Metal: Supported, feature set macOS GPUFamily1 v4 NVIDIA GeForce GT 750M: Chipset Model: NVIDIA GeForce GT 750M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 2 GB Vendor: NVIDIA (0x10de) Device ID: 0x0fe9 Revision ID: 0x00a2 ROM Revision: 3776 Automatic Graphics Switching: Supported gMux Version: 4.0.8 [3.2.8] Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Third Party can't reproduce Tom Goddard all ChimeraX