id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3520 Some kind of graphics crash running ISOLDE ville.paavilainen@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Darwin-19.5.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-04-03) Description I was running ISOLDE with a small molecule bound protein structure on a MacBook Pro. Process: ChimeraX [90814] Path: /private/var/folders/*/ChimeraX-0.93.app/Contents/MacOS/ChimeraX Identifier: ChimeraX Version: ??? Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [90814] User ID: 1979659624 Date/Time: 2020-07-15 22:09:29.303 +0300 OS Version: Mac OS X 10.15.5 (19F101) Report Version: 12 Bridge OS Version: 4.5 (17P5300) Anonymous UUID: EDA71157-7254-FBD7-9940-05741977D717 Sleep/Wake UUID: A28DD2FB-8F9B-4EFE-ADD3-5DA1D8DE71E7 Time Awake Since Boot: 1100000 seconds Time Since Wake: 4400 seconds System Integrity Protection: enabled Notes: Translocated Process Crashed Thread: 45 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: 0xfffffffa Thread 0:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 org.python.python 0x0000000103610ab8 listiter_next + 40 1 org.python.python 0x00000001035dfb10 PyIter_Next + 16 2 org.python.python 0x0000000103622d2f dict_merge + 415 3 org.python.python 0x00000001036518b6 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libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 21: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 22: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 23: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 24: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 25: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 26: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 27: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 28: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 29: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 30: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 31: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 32: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 33: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 34: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 35: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libOpenMMOpenCL.dylib 0x000000013b6ea41d threadBody(void*) + 109 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 36: 0 libsystem_kernel.dylib 0x00007fff73052f02 swtch_pri + 10 1 libsystem_pthread.dylib 0x00007fff73113698 sched_yield + 11 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc05 blas_thread_server + 565 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 37: 0 libsystem_kernel.dylib 0x00007fff73052f02 swtch_pri + 10 1 libsystem_pthread.dylib 0x00007fff73113698 sched_yield + 11 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc05 blas_thread_server + 565 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 38: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 39: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 40: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 41: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 42: 0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698 2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 43: 0 libsystem_pthread.dylib 0x00007fff73111b68 start_wqthread + 0 Thread 44: 0 libsystem_pthread.dylib 0x00007fff73111b68 start_wqthread + 0 Thread 45 Crashed:: Dispatch queue: opencl_runtime 0 libsystem_kernel.dylib 0x00007fff7305933a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff73115e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff72f7093e raise + 26 3 libsystem_platform.dylib 0x00007fff7310a5fd _sigtramp + 29 4 ??? 0x0000000000000001 0 + 1 5 libsystem_c.dylib 0x00007fff72fe0808 abort + 120 6 libGPUSupportMercury.dylib 0x00007fff5a3310a5 gpusGenerateCrashLog.cold.1 + 95 7 libGPUSupportMercury.dylib 0x00007fff5a32818f gpusGenerateCrashLog + 89 8 com.apple.AMDRadeonX6000GLDriver 0x00000001252aad5d gpusKillClientExt + 9 9 libGPUSupportMercury.dylib 0x00007fff5a328b38 gpusQueueSubmitDataBuffers + 159 10 com.apple.AMDRadeonX6000GLDriver 0x000000012527b5b2 glrAMDCompSubmitPackets + 228 11 com.apple.AMDRadeonX6000GLDriver 0x000000012527b49a glrAMDFlush + 30 12 com.apple.AMDRadeonX6000GLDriver 0x000000012527b840 gldFlushQueue + 37 13 com.apple.AMDRadeonX6000GLDriver 0x000000012527b85f gldFinishQueue + 19 14 com.apple.opencl 0x00007fff4256aacd 0x7fff42559000 + 72397 15 com.apple.opencl 0x00007fff4256af0c 0x7fff42559000 + 73484 16 com.apple.opencl 0x00007fff425843ff 0x7fff42559000 + 177151 17 com.apple.opencl 0x00007fff4258605d 0x7fff42559000 + 184413 18 libdispatch.dylib 0x00007fff72eb8658 _dispatch_client_callout + 8 19 libdispatch.dylib 0x00007fff72ec46ec _dispatch_lane_barrier_sync_invoke_and_complete + 60 20 com.apple.opencl 0x00007fff42585ee9 0x7fff42559000 + 184041 21 com.apple.opencl 0x00007fff42583531 0x7fff42559000 + 173361 22 com.apple.opencl 0x00007fff4257abd6 clEnqueueReadBuffer + 751 23 libOpenMMOpenCL.dylib 0x000000013b6cb2d8 OpenMM::OpenCLArray::download(void*, bool) const + 104 24 libOpenMMOpenCL.dylib 0x000000013b713304 OpenMM::OpenCLIntegrationUtilities::getLastStepSize() + 84 25 libOpenMMOpenCL.dylib 0x000000013b7cc273 OpenMM::OpenCLIntegrateVariableLangevinStepKernel::execute(OpenMM::ContextImpl&, OpenMM::VariableLangevinIntegrator const&, double) + 2035 26 libOpenMM.dylib 0x000000013b442b30 OpenMM::VariableLangevinIntegrator::step(int) + 144 27 libopenmm.dylib 0x000000012e649c19 isolde::OpenMM_Thread_Handler::_step_threaded(unsigned long, bool) + 345 28 libopenmm.dylib 0x000000012e64dfbd void* std::__1::__thread_proxy >, void (isolde::OpenMM_Thread_Handler::*)(unsigned long, bool), isolde::OpenMM_Thread_Handler*, unsigned long, bool> >(void*) + 77 29 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148 30 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15 Thread 45 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000070000e286000 rcx: 0x000070000e284f48 rdx: 0x0000000000000000 rdi: 0x000000000001a9ab rsi: 0x0000000000000006 rbp: 0x000070000e284f70 rsp: 0x000070000e284f48 r8: 0x000070000e285430 r9: 0x0a897b68e7e1dc03 r10: 0x000070000e286000 r11: 0x0000000000000246 r12: 0x000000000001a9ab r13: 0x00007fa1ca6041b0 r14: 0x0000000000000006 r15: 0x0000000000000016 rip: 0x00007fff7305933a rfl: 0x0000000000000246 cr2: 0x00007f97872fc09b Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x1035c7000 - 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0x7fff72f60ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff72f61000 - 0x7fff72fe8fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff72fe9000 - 0x7fff72fecffb libsystem_configuration.dylib (1061.120.2) /usr/lib/system/libsystem_configuration.dylib 0x7fff72fed000 - 0x7fff72ff0fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff72ff1000 - 0x7fff72ff9fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff72ffa000 - 0x7fff73001fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff73002000 - 0x7fff73003ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff73004000 - 0x7fff73051ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff73052000 - 0x7fff7307eff7 libsystem_kernel.dylib (6153.121.2) /usr/lib/system/libsystem_kernel.dylib 0x7fff7307f000 - 0x7fff730c6fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff730c7000 - 0x7fff730eefff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff730ef000 - 0x7fff730fcffb libsystem_networkextension.dylib (1095.120.6) /usr/lib/system/libsystem_networkextension.dylib 0x7fff730fd000 - 0x7fff73106ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff73107000 - 0x7fff7310ffef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff73110000 - 0x7fff7311afff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff7311b000 - 0x7fff7311fff3 libsystem_sandbox.dylib (1217.120.7) /usr/lib/system/libsystem_sandbox.dylib 0x7fff73120000 - 0x7fff73122fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff73123000 - 0x7fff7312affb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff7312b000 - 0x7fff73141ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff73143000 - 0x7fff73148ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff73149000 - 0x7fff7317effe libxpc.dylib (1738.120.8) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 17 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: 1765139 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=4.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 1232K 2 CG image 548K 33 CoreAnimation 4160K 72 CoreGraphics 8K 1 CoreImage 28K 3 CoreUI image data 3836K 34 Foundation 24K 2 Kernel Alloc Once 8K 1 MALLOC 2.5G 1512 MALLOC guard page 32K 6 MALLOC_LARGE (reserved) 640K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Memory Tag 242 12K 1 Memory Tag 251 12K 1 OpenCL 122.5M 67 OpenCL (reserved) 24K 4 reserved VM address space (unallocated) OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 56.2M 46 Stack 158.4M 46 VM_ALLOCATE 703.7M 856 VM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated) __DATA 67.1M 640 __DATA_CONST 132K 6 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 425.9M 218 __OBJC_RO 32.2M 1 __OBJC_RW 1888K 1 __TEXT 606.3M 593 __UNICODE 564K 1 mapped file 118.9M 54 shared memory 668K 21 =========== ======= ======= TOTAL 5.3G 4239 TOTAL, minus reserved VM space 4.8G 4239 Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-3.9.15 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Third Party 0.93 fixed Tom Goddard all ChimeraX