id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2895 Crash during close goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-02-27) Description Last time you used ChimeraX it crashed. Had 4 structures open 4u25, 4u25 assembly 1, 4hus, 4hur, soft lighting, had selected a few ligands ACO, virginamycin. Then I typed commmand ""close"" and it crashed. Process: ChimeraX [13834] Path: /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 0.91.0 (0.91.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [13834] User ID: 501 Date/Time: 2020-02-27 17:24:52.285 -0800 OS Version: Mac OS X 10.15.3 (19D76) Report Version: 12 Anonymous UUID: 766E337C-4F5E-2774-C27E-AD8F8656F11F Sleep/Wake UUID: FB607EE3-58D3-41D2-8132-6933651D739B Time Awake Since Boot: 120000 seconds Time Since Wake: 26000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00000001319a5c00 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0x1319a5c00: VM_ALLOCATE 00000001315e0000-0000000131620000 [ 256K] rw-/rwx SM=PRV --> VM_ALLOCATE 00000001319df000-0000000131a1f000 [ 256K] rw-/rwx SM=PRV Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff65f0a7fa __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff65fc7bc1 pthread_kill + 432 2 libsystem_c.dylib 0x00007fff65e213a2 raise + 26 3 libsystem_platform.dylib 0x00007fff65fbc42d _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 org.python.python 0x0000000107d55f48 subtype_dealloc + 408 6 org.python.python 0x0000000107d365c9 free_keys_object + 137 7 org.python.python 0x0000000107d38cd8 dict_dealloc + 200 8 org.python.python 0x0000000107d22b46 func_dealloc + 198 9 org.python.python 0x0000000107d38c94 dict_dealloc + 132 10 org.python.python 0x0000000107d56264 subtype_dealloc + 1204 11 org.python.python 0x0000000107d4d2d0 set_clear_internal + 528 12 org.python.python 0x0000000107d504c9 set_clear + 9 13 org.python.python 0x0000000107d0c0fe _PyMethodDef_RawFastCallKeywords + 798 14 org.python.python 0x0000000107d11b82 _PyMethodDescr_FastCallKeywords + 82 15 org.python.python 0x0000000107dd505b call_function + 763 16 org.python.python 0x0000000107dcd660 _PyEval_EvalFrameDefault + 5536 17 org.python.python 0x0000000107d0b893 function_code_fastcall + 195 18 org.python.python 0x0000000107dd5031 call_function + 721 19 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libsystem_pthread.dylib 0x00007fff65fc383b thread_start + 15 Thread 14:: CompositorTileWorker1/73987 0 libsystem_kernel.dylib 0x00007fff65f06ce6 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff65fc8185 _pthread_cond_wait + 701 2 QtWebEngineCore 0x000000011a181058 0x117f68000 + 35754072 3 QtWebEngineCore 0x000000011b109658 0x117f68000 + 52041304 4 QtWebEngineCore 0x000000011a141754 0x117f68000 + 35493716 5 QtWebEngineCore 0x000000011a1827c7 0x117f68000 + 35760071 6 libsystem_pthread.dylib 0x00007fff65fc7e65 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff65fc383b thread_start + 15 Thread 15:: AudioThread 0 libsystem_kernel.dylib 0x00007fff65f0425a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff65f045d0 mach_msg + 60 2 QtWebEngineCore 0x000000011a1133ed 0x117f68000 + 35304429 3 QtWebEngineCore 0x000000011a1132ef 0x117f68000 + 35304175 4 QtWebEngineCore 0x000000011a0c711d 0x117f68000 + 34992413 5 QtWebEngineCore 0x000000011a0f0145 0x117f68000 + 35160389 6 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0x000000011a12ade8 0x117f68000 + 35401192 5 QtWebEngineCore 0x000000011a12b47f 0x117f68000 + 35402879 6 QtWebEngineCore 0x000000011a12b384 0x117f68000 + 35402628 7 QtWebEngineCore 0x000000011a1827c7 0x117f68000 + 35760071 8 libsystem_pthread.dylib 0x00007fff65fc7e65 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff65fc383b thread_start + 15 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000114e24dc0 rcx: 0x00007f86b8037a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007f86b8037a80 rsp: 0x00007f86b8037a58 r8: 0x00007f86b8037f48 r9: 0xf0332d3f42a1e8e5 r10: 0x0000000114e24dc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x00000001319a5c10 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff65f0a7fa rfl: 0x0000000000000246 cr2: 0xffffffa400e90000 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Binary Images: 0x107ce1000 - 0x107ce1fff +edu.ucsf.cgl.ChimeraX (0.91.0 - 0.91.0.0) 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0x7fff61fb3ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk 0x7fff622f4000 - 0x7fff622f6ff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport 0x7fff622f7000 - 0x7fff6230affd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login 0x7fff6233c000 - 0x7fff62348ffd com.apple.perfdata (1.0 - 51.40.3) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata 0x7fff6260d000 - 0x7fff62619ff3 libAudioStatistics.dylib (1104.33) /usr/lib/libAudioStatistics.dylib 0x7fff6261a000 - 0x7fff62650ffa libAudioToolboxUtility.dylib (1104.33) /usr/lib/libAudioToolboxUtility.dylib 0x7fff62657000 - 0x7fff6268cff7 libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib 0x7fff6268f000 - 0x7fff62699ff3 libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib 0x7fff6269a000 - 0x7fff62723fff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib 0x7fff62726000 - 0x7fff62728ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff6276d000 - 0x7fff62924ff3 libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib 0x7fff6294b000 - 0x7fff62951ff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib 0x7fff62a31000 - 0x7fff62a38fff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib 0x7fff62a68000 - 0x7fff62a87fff libMobileGestalt.dylib (826.80.1) /usr/lib/libMobileGestalt.dylib 0x7fff62afc000 - 0x7fff62bd9ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib 0x7fff62bee000 - 0x7fff62befff3 libSystem.B.dylib (1281) /usr/lib/libSystem.B.dylib 0x7fff62bf0000 - 0x7fff62c7dff7 libTelephonyUtilDynamic.dylib (3852) /usr/lib/libTelephonyUtilDynamic.dylib 0x7fff62c7e000 - 0x7fff62c7ffff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib 0x7fff62c97000 - 0x7fff62cadfff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib 0x7fff62ce2000 - 0x7fff62d54ff7 libarchive.2.dylib (72.40.2) /usr/lib/libarchive.2.dylib 0x7fff62d55000 - 0x7fff62debfc5 libate.dylib (2.0.9) /usr/lib/libate.dylib 0x7fff62def000 - 0x7fff62defff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff62df0000 - 0x7fff62eb5ffe libboringssl.dylib (283.60.3) /usr/lib/libboringssl.dylib 0x7fff62eb6000 - 0x7fff62ec6ff3 libbsm.0.dylib (60) /usr/lib/libbsm.0.dylib 0x7fff62ec7000 - 0x7fff62ed3fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib 0x7fff62ed4000 - 0x7fff62f27ff7 libc++.1.dylib (800.7) /usr/lib/libc++.1.dylib 0x7fff62f28000 - 0x7fff62f3cfff libc++abi.dylib (800.7) /usr/lib/libc++abi.dylib 0x7fff62f3d000 - 0x7fff62f3dffb libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib 0x7fff62f3e000 - 0x7fff62f4fffb libcmph.dylib (8) /usr/lib/libcmph.dylib 0x7fff62f50000 - 0x7fff62f67fe7 libcompression.dylib (87) /usr/lib/libcompression.dylib 0x7fff63237000 - 0x7fff6324dff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib 0x7fff6324e000 - 0x7fff6324ffff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff633f2000 - 0x7fff634ecfff libcrypto.35.dylib (47.11.1) /usr/lib/libcrypto.35.dylib 0x7fff636f3000 - 0x7fff637f7fe7 libcrypto.44.dylib (47.11.1) /usr/lib/libcrypto.44.dylib 0x7fff637fa000 - 0x7fff63805ff7 libcsfde.dylib (551) /usr/lib/libcsfde.dylib 0x7fff6380d000 - 0x7fff6386cfff libcups.2.dylib (483.2) /usr/lib/libcups.2.dylib 0x7fff6386e000 - 0x7fff638d5fff libcurl.4.dylib (118) /usr/lib/libcurl.4.dylib 0x7fff63978000 - 0x7fff63978fff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib 0x7fff63979000 - 0x7fff63992ff7 libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib 0x7fff639a0000 - 0x7fff639a2fff libfakelink.dylib (149) /usr/lib/libfakelink.dylib 0x7fff639b1000 - 0x7fff639b6fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib 0x7fff639b7000 - 0x7fff639c0ff7 libheimdal-asn1.dylib (564.60.2) /usr/lib/libheimdal-asn1.dylib 0x7fff639c1000 - 0x7fff63ab1ff7 libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib 0x7fff63ab2000 - 0x7fff63d0aff7 libicucore.A.dylib (64252.0.1) /usr/lib/libicucore.A.dylib 0x7fff63d24000 - 0x7fff63d25fff liblangid.dylib (133) /usr/lib/liblangid.dylib 0x7fff63d26000 - 0x7fff63d3eff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib 0x7fff63d56000 - 0x7fff63dfdfff libmecab.dylib (883.1.1) /usr/lib/libmecab.dylib 0x7fff63dfe000 - 0x7fff64060fe1 libmecabra.dylib (883.1.1) /usr/lib/libmecabra.dylib 0x7fff643d0000 - 0x7fff643ffff7 libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib 0x7fff6452e000 - 0x7fff649a4ff7 libnetwork.dylib (1880.60.5) /usr/lib/libnetwork.dylib 0x7fff649a5000 - 0x7fff649bbfff libnetworkextension.dylib (1095.60.2) /usr/lib/libnetworkextension.dylib 0x7fff64a43000 - 0x7fff64a74fc6 libobjc.A.dylib (781.2) /usr/lib/libobjc.A.dylib 0x7fff64a75000 - 0x7fff64a76ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib 0x7fff64a87000 - 0x7fff64a8bfff libpam.2.dylib (25) /usr/lib/libpam.2.dylib 0x7fff64a8e000 - 0x7fff64ac4ff7 libpcap.A.dylib (89.60.2) /usr/lib/libpcap.A.dylib 0x7fff64b02000 - 0x7fff64b10ff9 libperfcheck.dylib (37) /usr/lib/libperfcheck.dylib 0x7fff64b46000 - 0x7fff64b5eff7 libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff64b60000 - 0x7fff64ba4fff libsandbox.1.dylib (1217.80.1) /usr/lib/libsandbox.1.dylib 0x7fff64ba5000 - 0x7fff64bb7fff libsasl2.2.dylib (213) /usr/lib/libsasl2.2.dylib 0x7fff64bb8000 - 0x7fff64bb9ff7 libspindump.dylib (281.2) /usr/lib/libspindump.dylib 0x7fff64bba000 - 0x7fff64da7ff7 libsqlite3.dylib (308.4) /usr/lib/libsqlite3.dylib 0x7fff64e9b000 - 0x7fff64ec8ffb libssl.46.dylib (47.11.1) /usr/lib/libssl.46.dylib 0x7fff64f9d000 - 0x7fff64ff8ff8 libusrtcp.dylib (1880.60.5) /usr/lib/libusrtcp.dylib 0x7fff64ff9000 - 0x7fff64ffcffb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff64ffd000 - 0x7fff6500afff libxar.1.dylib (420) /usr/lib/libxar.1.dylib 0x7fff65010000 - 0x7fff650f2ff7 libxml2.2.dylib (32.14) /usr/lib/libxml2.2.dylib 0x7fff650f6000 - 0x7fff6511efff libxslt.1.dylib (16.7) /usr/lib/libxslt.1.dylib 0x7fff6511f000 - 0x7fff65131ffb libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff65b95000 - 0x7fff65b9aff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff65b9b000 - 0x7fff65ba6fff libcommonCrypto.dylib (60165) /usr/lib/system/libcommonCrypto.dylib 0x7fff65ba7000 - 0x7fff65baefff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff65baf000 - 0x7fff65bb8fff libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff65bb9000 - 0x7fff65c50fdb libcorecrypto.dylib (866.80.2) /usr/lib/system/libcorecrypto.dylib 0x7fff65d67000 - 0x7fff65da8ff0 libdispatch.dylib (1173.60.1) /usr/lib/system/libdispatch.dylib 0x7fff65da9000 - 0x7fff65ddeff7 libdyld.dylib (733.8) /usr/lib/system/libdyld.dylib 0x7fff65ddf000 - 0x7fff65ddfffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff65de0000 - 0x7fff65decff7 libkxld.dylib (6153.81.5) /usr/lib/system/libkxld.dylib 0x7fff65ded000 - 0x7fff65dedff7 liblaunch.dylib (1738.80.8) /usr/lib/system/liblaunch.dylib 0x7fff65dee000 - 0x7fff65df3ff7 libmacho.dylib (949.0.1) /usr/lib/system/libmacho.dylib 0x7fff65df4000 - 0x7fff65df6ff7 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff65df7000 - 0x7fff65df8ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff65df9000 - 0x7fff65e10fff libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff65e11000 - 0x7fff65e11fff libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff65e12000 - 0x7fff65e99ff7 libsystem_c.dylib (1353.60.8) /usr/lib/system/libsystem_c.dylib 0x7fff65e9a000 - 0x7fff65e9dffb libsystem_configuration.dylib (1061.80.3) /usr/lib/system/libsystem_configuration.dylib 0x7fff65e9e000 - 0x7fff65ea1ff7 libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff65ea2000 - 0x7fff65eaafff libsystem_darwin.dylib (1353.60.8) /usr/lib/system/libsystem_darwin.dylib 0x7fff65eab000 - 0x7fff65eb2ffb libsystem_dnssd.dylib (1096.60.2) /usr/lib/system/libsystem_dnssd.dylib 0x7fff65eb3000 - 0x7fff65eb4ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff65eb5000 - 0x7fff65f02fff libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff65f03000 - 0x7fff65f2fff7 libsystem_kernel.dylib (6153.81.5) /usr/lib/system/libsystem_kernel.dylib 0x7fff65f30000 - 0x7fff65f77fcf libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff65f78000 - 0x7fff65f9ffff libsystem_malloc.dylib (283.60.1) /usr/lib/system/libsystem_malloc.dylib 0x7fff65fa0000 - 0x7fff65fadffb libsystem_networkextension.dylib (1095.60.2) /usr/lib/system/libsystem_networkextension.dylib 0x7fff65fae000 - 0x7fff65fb7ff3 libsystem_notify.dylib (241) /usr/lib/system/libsystem_notify.dylib 0x7fff65fb8000 - 0x7fff65fc1fef libsystem_platform.dylib (220) /usr/lib/system/libsystem_platform.dylib 0x7fff65fc2000 - 0x7fff65fccfff libsystem_pthread.dylib (416.60.2) /usr/lib/system/libsystem_pthread.dylib 0x7fff65fcd000 - 0x7fff65fd1fff libsystem_sandbox.dylib (1217.80.1) /usr/lib/system/libsystem_sandbox.dylib 0x7fff65fd2000 - 0x7fff65fd4fff libsystem_secinit.dylib (62.80.1) /usr/lib/system/libsystem_secinit.dylib 0x7fff65fd5000 - 0x7fff65fdcffb libsystem_symptoms.dylib (1238.60.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff65fdd000 - 0x7fff65ff3ff2 libsystem_trace.dylib (1147.80.3) /usr/lib/system/libsystem_trace.dylib 0x7fff65ff5000 - 0x7fff65ffaffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff65ffb000 - 0x7fff66030ffe libxpc.dylib (1738.80.8) /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: 54149 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=892.2M resident=0K(0%) swapped_out_or_unallocated=892.2M(100%) Writable regions: Total=7.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=7.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 384K 3 Activity Tracing 256K 1 CG backing stores 1760K 2 CG image 264K 20 CoreAnimation 112K 13 CoreGraphics 8K 1 CoreImage 24K 2 CoreServices 4K 1 CoreUI image data 3124K 25 Foundation 24K 2 Kernel Alloc Once 8K 1 MALLOC 5.9G 163 MALLOC guard page 48K 9 MALLOC_MEDIUM (reserved) 704.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated) Memory Tag 242 12K 1 OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 96K 24 Stack 155.2M 25 Stack Guard 56.0M 1 VM_ALLOCATE 152.6M 335 VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated) __DATA 64.7M 539 __DATA_CONST 188K 16 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 374.0M 133 __OBJC_RO 32.0M 1 __OBJC_RW 1780K 2 __TEXT 518.2M 506 __UNICODE 564K 1 mapped file 79.9M 37 shared memory 652K 18 =========== ======= ======= TOTAL 8.2G 1901 TOTAL, minus reserved VM space 7.3G 1901 Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.92 (2020-02-27) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-3.5.5 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Core fixed Tom Goddard all ChimeraX