OpenChemistry / tomviz

Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
https://tomviz.org/
BSD 3-Clause "New" or "Revised" License
325 stars 87 forks source link

Non-reproducible crash loading data #1200

Closed ElliotPadgett closed 5 years ago

ElliotPadgett commented 7 years ago

I still encounter quite a few crashes doing ordinary things that I'm not able to reproduce. I don't know how you all want to handle this kind of issue, but I grabbed the crash report and I though I might as well post it in case you can spot the issue. I'll collect other similar crash reports here.

This happened trying to load a raw file. After clicking ok on the dialog with the data parameters tomviz crashed and gave this report:

Process: tomviz [20236] Path: /Applications/tomviz_1.0.app/Contents/MacOS/tomviz Identifier: ??? Version: ??? (1.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: tomviz [20236] User ID: 505

Date/Time: 2017-07-07 11:09:01.587 -0400 OS Version: Mac OS X 10.10.5 (14F2315) Report Version: 11 Anonymous UUID: 18BBB43E-2C59-C148-4A96-8E58580894EF

Time Awake Since Boot: 5600000 seconds

Crashed Thread: 2 QThread

Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00007fefac8b7e00

VM Regions Near 0x7fefac8b7e00: VM_ALLOCATE 000000014b35d000-000000014db17000 [ 39.7M] rw-/rw- SM=PRV
--> MALLOC_TINY 00007ff1aa400000-00007ff1aa500000 [ 1024K] rw-/rwx SM=PRV

Thread 0:: Dispatch queue: com.apple.main-thread 0 libsystem_platform.dylib 0x00007fff95a17cd1 _os_lock_spin_lock + 12 1 libsystem_malloc.dylib 0x00007fff9a6008d6 szone_free_definite_size + 983 2 libvtkPVCommon.1.dylib 0x00000001140deb04 vtkPVXMLElement::AddAttribute(char const, char const) + 276 3 libvtkPVServerManagerCore.1.dylib 0x0000000112b40cb5 vtkSMDomain::SaveState(vtkPVXMLElement, char const) + 85 4 libvtkPVServerManagerCore.1.dylib 0x0000000112b6ebbe vtkSMProperty::SaveDomainState(vtkPVXMLElement, char const) + 638 5 libvtkPVServerManagerCore.1.dylib 0x0000000112b6e905 vtkSMProperty::SaveState(vtkPVXMLElement, char const, char const, int) + 133 6 libvtkPVServerManagerCore.1.dylib 0x0000000112b7fda0 vtkSMProxy::SaveXMLState(vtkPVXMLElement, vtkSMPropertyIterator) + 816 7 libvtkPVServerManagerCore.1.dylib 0x0000000112b7fa4e vtkSMProxy::SaveXMLState(vtkPVXMLElement) + 46 8 0x000000010e982976 tomviz::serialize(vtkSMProxy, vtkpugi::xml_node&, QStringList const&, QDir const) + 966 9 0x000000010e964d14 tomviz::RecentFilesMenu::pushDataReader(tomviz::DataSource, vtkSMProxy) + 1204 10 0x000000010e91d75a tomviz::LoadDataReaction::loadData(QStringList const&, bool, bool) + 1130 11 0x000000010e91cb88 tomviz::LoadDataReaction::loadData() + 1480 12 0x000000010e91c581 tomviz::LoadDataReaction::onTriggered() + 17 13 org.qt-project.QtCore 0x00000001153e62e1 QMetaObject::activate(QObject*, int, int, void*) + 913 14 org.qt-project.QtWidgets 0x000000010fc5c57f QAction::activate(QAction::ActionEvent) + 303 15 org.qt-project.QtCore 0x00000001153e62e1 QMetaObject::activate(QObject, int, int, void) + 913 16 org.qt-project.QtCore 0x00000001153df38c QObject::event(QEvent) + 156 17 org.qt-project.QtWidgets 0x000000010fc6558d QApplicationPrivate::notify_helper(QObject, QEvent) + 269 18 org.qt-project.QtWidgets 0x000000010fc67ed2 QApplication::notify(QObject, QEvent) + 5906 19 org.qt-project.QtCore 0x00000001153b5544 QCoreApplication::notifyInternal2(QObject, QEvent) + 164 20 org.qt-project.QtCore 0x00000001153b61c8 QCoreApplicationPrivate::sendPostedEvents(QObject, int, QThreadData) + 600 21 libqcocoa.dylib 0x0000000119c38f5e QCocoaEventDispatcherPrivate::processPostedEvents() + 190 22 libqcocoa.dylib 0x0000000119c39821 QCocoaEventDispatcherPrivate::postedEventsSourceCallback(void) + 33 23 com.apple.CoreFoundation 0x00007fff941f0a01 CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION + 17 24 com.apple.CoreFoundation 0x00007fff941e2b8d CFRunLoopDoSources0 + 269 25 com.apple.CoreFoundation 0x00007fff941e21bf CFRunLoopRun + 927 26 com.apple.CoreFoundation 0x00007fff941e1bd8 CFRunLoopRunSpecific + 296 27 com.apple.AppKit 0x00007fff9b4503dd _NSUnhighlightCarbonMenu + 272 28 com.apple.AppKit 0x00007fff9b448986 -[NSCarbonMenuImpl performActionWithHighlightingForItemAtIndex:] + 124 29 libsystem_trace.dylib 0x00007fff974accd7 _os_activity_initiate + 75 30 com.apple.AppKit 0x00007fff9b50fb00 -[NSMenu performActionForItemAtIndex:] + 131 31 com.apple.AppKit 0x00007fff9b50fa66 -[NSMenu _internalPerformActionForItemAtIndex:] + 35 32 com.apple.AppKit 0x00007fff9b50f8b2 -[NSCarbonMenuImpl _carbonCommandProcessEvent:handlerCallRef:] + 107 33 com.apple.AppKit 0x00007fff9b430d6b NSSLMMenuEventHandler + 724 34 com.apple.HIToolbox 0x00007fff8ec74b6c DispatchEventToHandlers(EventTargetRec, OpaqueEventRef, HandlerCallRec) + 1260 35 com.apple.HIToolbox 0x00007fff8ec73fae SendEventToEventTargetInternal(OpaqueEventRef, OpaqueEventTargetRef, HandlerCallRec) + 386 36 com.apple.HIToolbox 0x00007fff8ec89cb6 SendEventToEventTarget + 40 37 com.apple.HIToolbox 0x00007fff8ecc3f45 SendHICommandEvent(unsigned int, HICommand const, unsigned int, unsigned int, unsigned char, void const, OpaqueEventTargetRef, OpaqueEventTargetRef, OpaqueEventRef) + 428 38 com.apple.HIToolbox 0x00007fff8ed01b8d SendMenuCommandWithContextAndModifiers + 59 39 com.apple.HIToolbox 0x00007fff8ed01b30 SendMenuItemSelectedEvent + 188 40 com.apple.HIToolbox 0x00007fff8ed01a09 FinishMenuSelection(SelectionData, MenuResult, MenuResult) + 96 41 com.apple.HIToolbox 0x00007fff8ed02481 MenuSelectCore(MenuData, Point, double, unsigned int, OpaqueMenuRef*, unsigned short) + 702 42 com.apple.HIToolbox 0x00007fff8ed020fe _HandleMenuSelection2 + 446 43 com.apple.AppKit 0x00007fff9b34ece0 _NSHandleCarbonMenuEvent + 277 44 com.apple.AppKit 0x00007fff9b285bfd _DPSNextEvent + 1828 45 com.apple.AppKit 0x00007fff9b284e58 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 346 46 com.apple.AppKit 0x00007fff9b27aaf3 -[NSApplication run] + 594 47 libqcocoa.dylib 0x0000000119c386bf QCocoaEventDispatcher::processEvents(QFlags) + 2143 48 org.qt-project.QtCore 0x00000001153b1781 QEventLoop::exec(QFlags) + 401 49 org.qt-project.QtCore 0x00000001153b5bb5 QCoreApplication::exec() + 341 50 0x000000010e8c6c71 main + 2017 51 libdyld.dylib 0x00007fff914205c9 start + 1

Thread 1:: Dispatch queue: com.apple.libdispatch-manager 0 libsystem_kernel.dylib 0x00007fff95723232 kevent64 + 10 1 libdispatch.dylib 0x00007fff949af26e _dispatch_mgr_thread + 52

Thread 2 Crashed:: QThread 0 0x000000010e8efc13 tomviz::PopulateHistogram(vtkImageData, vtkTable) + 6963 1 0x000000010e8f02be tomviz::HistogramMaker::makeHistogram(vtkSmartPointer, vtkSmartPointer) + 62 2 0x000000010e8f219a tomviz::HistogramMaker::qt_static_metacall(QObject*, QMetaObject::Call, int, void*) + 346 3 org.qt-project.QtCore 0x00000001153df38c QObject::event(QEvent) + 156 4 org.qt-project.QtWidgets 0x000000010fc6558d QApplicationPrivate::notify_helper(QObject, QEvent) + 269 5 org.qt-project.QtWidgets 0x000000010fc67ed2 QApplication::notify(QObject, QEvent) + 5906 6 org.qt-project.QtCore 0x00000001153b5544 QCoreApplication::notifyInternal2(QObject, QEvent) + 164 7 org.qt-project.QtCore 0x00000001153b61c8 QCoreApplicationPrivate::sendPostedEvents(QObject, int, QThreadData) + 600 8 org.qt-project.QtCore 0x0000000115408c49 QEventDispatcherUNIX::processEvents(QFlags) + 73 9 org.qt-project.QtCore 0x00000001153b1781 QEventLoop::exec(QFlags) + 401 10 org.qt-project.QtCore 0x00000001151efeee QThread::exec() + 110 11 org.qt-project.QtCore 0x00000001151f385a 0x1151c9000 + 174170 12 libsystem_pthread.dylib 0x00007fff8ec3405a _pthread_body + 131 13 libsystem_pthread.dylib 0x00007fff8ec33fd7 _pthread_start + 176 14 libsystem_pthread.dylib 0x00007fff8ec313ed thread_start + 13

Thread 3: 0 libsystem_kernel.dylib 0x00007fff9571d4de mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff9571c64f mach_msg + 55 2 com.apple.CoreFoundation 0x00007fff941e2eb4 CFRunLoopServiceMachPort + 212 3 com.apple.CoreFoundation 0x00007fff941e237b CFRunLoopRun + 1371 4 com.apple.CoreFoundation 0x00007fff941e1bd8 CFRunLoopRunSpecific + 296 5 com.apple.AppKit 0x00007fff9b34d56b _NSEventThread + 137 6 libsystem_pthread.dylib 0x00007fff8ec3405a _pthread_body + 131 7 libsystem_pthread.dylib 0x00007fff8ec33fd7 _pthread_start + 176 8 libsystem_pthread.dylib 0x00007fff8ec313ed thread_start + 13

Thread 4: 0 libsystem_kernel.dylib 0x00007fff9572294a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8ec313dd start_wqthread + 13

Thread 5: 0 libsystem_kernel.dylib 0x00007fff9572294a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8ec313dd start_wqthread + 13

Thread 2 crashed with X86 Thread State (64-bit): rax: 0x000000000025d905 rbx: 0x0000000000000000 rcx: 0x000000014917c02c rdx: 0x00000000000000ff rdi: 0x00007ff1b3787240 rsi: 0xffffffff80000000 rbp: 0x000000011e795650 rsp: 0x000000011e795560 r8: 0x00007ff1ac8ec000 r9: 0x00000000f8000000 r10: 0x00007ff1b38e90b0 r11: 0x000000000fda0815 r12: 0x0000000114789d00 r13: 0xb0002937753c9e53 r14: 0x00007ff1b5413390 r15: 0x00007ff1ac8b7e00 rip: 0x000000010e8efc13 rfl: 0x0000000000010a12 cr2: 0x00007fefac8b7e00

Logical CPU: 2 Error Code: 0x00000006 Trap Number: 14

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0x7fff9a587ffb com.apple.LDAPFramework (2.4.28 - 194.5) /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP 0x7fff9a5cf000 - 0x7fff9a5d7ffb libcopyfile.dylib (118.1.2) <0C68D3A6-ACDD-3EF3-991A-CC82C32AB836> /usr/lib/system/libcopyfile.dylib 0x7fff9a5fc000 - 0x7fff9a618ff7 libsystem_malloc.dylib (53.30.1) /usr/lib/system/libsystem_malloc.dylib 0x7fff9a687000 - 0x7fff9a692ff7 com.apple.CrashReporterSupport (10.10 - 631) /System/Library/PrivateFrameworks/CrashReporterSupport.framework/Versions/A/CrashReporterSupport 0x7fff9a693000 - 0x7fff9a69bff7 com.apple.icloud.FindMyDevice (1.0 - 1) <9CE67F85-2BA8-3093-97BA-07BF5C04A5D6> /System/Library/PrivateFrameworks/FindMyDevice.framework/Versions/A/FindMyDevice 0x7fff9a69c000 - 0x7fff9a720ff7 com.apple.ViewBridge (105.1 - 105.1) <98E9733F-D863-30CE-BF25-E6768C73AF21> /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge 0x7fff9a729000 - 0x7fff9a72eff7 com.apple.MediaAccessibility (1.0 - 61) <00A3E0B6-79AC-387E-B282-AADFBD5722F6> /System/Library/Frameworks/MediaAccessibility.framework/Versions/A/MediaAccessibility 0x7fff9a72f000 - 0x7fff9a813fff libcrypto.0.9.8.dylib (52.40.1) /usr/lib/libcrypto.0.9.8.dylib 0x7fff9a814000 - 0x7fff9a844ff3 com.apple.GSS (4.0 - 2.0) <97F2A028-44CF-3188-B863-F4EEB39CBDBD> /System/Library/Frameworks/GSS.framework/Versions/A/GSS 0x7fff9a845000 - 0x7fff9a876ff7 com.apple.ProtectedCloudStorage (1.0 - 1) <9D76F2E0-C28A-3DBC-A91F-E87888D46BF0> /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage 0x7fff9a88a000 - 0x7fff9a88bff7 libsystem_blocks.dylib (65) <9615D10A-FCA7-3BE4-AA1A-1B195DACE1A1> /usr/lib/system/libsystem_blocks.dylib 0x7fff9a88c000 - 0x7fff9a97dfff libJP2.dylib (1248) <1E5E95F9-8B0B-3708-A7C3-4A04CAAF061D> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib 0x7fff9a97e000 - 0x7fff9a98cff7 com.apple.opengl (11.1.6 - 11.1.6) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff9a98d000 - 0x7fff9a98dfff com.apple.audio.units.AudioUnit (1.12 - 1.12) /System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit 0x7fff9a98e000 - 0x7fff9ac5dff3 com.apple.CoreImage (10.3.5) <0224F5A6-636A-374B-B46C-13E066596725> /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Versions/A/CoreImage 0x7fff9ac5e000 - 0x7fff9ac63fff libsystem_stats.dylib (163.30.2) <5563862F-FEB4-3F0C-AE54-20C1CC49252A> /usr/lib/system/libsystem_stats.dylib 0x7fff9ac64000 - 0x7fff9aedafff com.apple.security (7.0 - 57031.40.8) /System/Library/Frameworks/Security.framework/Versions/A/Security 0x7fff9af04000 - 0x7fff9af5efff com.apple.Suggestions (4.0 - 165) <34A8FB72-F663-3085-B4D0-6982B0BDCF21> /System/Library/PrivateFrameworks/Suggestions.framework/Versions/A/Suggestions 0x7fff9af73000 - 0x7fff9b1ddff7 com.apple.imageKit (2.6.1 - 850) <612201FE-768E-386B-82E3-764038B40120> /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/ImageKit 0x7fff9b1de000 - 0x7fff9b1f3ff7 com.apple.AppContainer (4.0 - 238.20.2) <2AA2EF49-9F38-31F6-8B08-8CC7C26F57F3> /System/Library/PrivateFrameworks/AppContainer.framework/Versions/A/AppContainer 0x7fff9b1f4000 - 0x7fff9bd75ff7 com.apple.AppKit (6.9 - 1348.17) /System/Library/Frameworks/AppKit.framework/Versions/C/AppKit

External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 60 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: 489949860 thread_create: 0 thread_set_state: 0

VM Region Summary: ReadOnly portion of Libraries: Total=362.9M resident=217.0M(60%) swapped_out_or_unallocated=145.9M(40%) Writable regions: Total=765.6M written=256.7M(34%) resident=441.6M(58%) swapped_out=88K(0%) unallocated=323.9M(42%)

REGION TYPE VIRTUAL =========== ======= Activity Tracing 2048K CG backing stores 91.5M CG image 384K CG shared images 592K CoreAnimation 29.6M CoreGraphics 16K CoreImage 16K CoreUI image data 668K Dispatch continuations 16.0M Foundation 4K IOKit 183.3M Image IO 24K Kernel Alloc Once 8K MALLOC 284.3M MALLOC (admin) 32K Memory Tag 242 12K Memory Tag 251 20K OpenCL 52K OpenGL GLSL 256K STACK GUARD 56.0M Stack 10.1M VM_ALLOCATE 139.2M DATA 34.9M GLSLBUILTINS 2588K IMAGE 528K LINKEDIT 100.6M TEXT 262.3M UNICODE 552K mapped file 203.3M shared memory 4K =========== ======= TOTAL 1.4G

Model: iMac15,1, BootROM IM151.0207.B05, 4 processors, Intel Core i7, 4 GHz, 32 GB, SMC 2.23f11 Graphics: AMD Radeon R9 M295X, AMD Radeon R9 M295X, PCIe, 4096 MB Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x802C, 0x31364B544631473634485A2D314736453220 Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x802C, 0x31364B544631473634485A2D314736453220 Memory Module: BANK 0/DIMM1, 8 GB, DDR3, 1600 MHz, 0x802C, 0x31364B544631473634485A2D314736453220 Memory Module: BANK 1/DIMM1, 8 GB, DDR3, 1600 MHz, 0x802C, 0x31364B544631473634485A2D314736453220 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x142), Broadcom BCM43xx 1.0 (7.15.166.24.3) Bluetooth: Version 4.3.6f4 17916, 3 services, 27 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en1 Serial ATA Device: APPLE SSD SM0128G, 121.33 GB Serial ATA Device: APPLE HDD ST3000DM001, 3 TB USB Device: G-DRIVE mobile USB USB Device: P'9220 Mobile Drive USB Device: G-DRIVE mobile USB USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller USB Device: FaceTime HD Camera (Built-in) USB Device: USB2.0 Hub USB Device: USB2.0 Hub USB Device: MT1806 USB Device: Keyboard Hub USB Device: Apple Keyboard Thunderbolt Bus: iMac, Apple Inc., 26.1

mathturtle commented 7 years ago

Loading a RAW file I have a guess what happened. Can you double check the dimensions and data type you specified to the RAW reader? There aren't any guards on these parameters so it will just use what you gave it. And if you mess up it is very easy to tell it the file is bigger than it is rather than smaller. If you do that it will read invalid memory and crash. I seem to recall an issue to improve and sanity check the RAW reader's dialog, but I can't find it right now.

ercius commented 7 years ago

Ill quickly note that its very easy to type in the wrong values for loading raw data. This is because the extent values start with 0. So, if you know your file 1024 pixels along X then you need to type in 0 -- 1023 into the first extent boxes. Just a thought.

mathturtle commented 7 years ago

One of the things on my to-do list is fixing the UI for the RAW reader to perform sanity checks and make it easier to use (just let you put in the dimensions rather than VTK extents). I guess I'll use this issue to track that since I don't see any others related to the RAW reader.

mathturtle commented 7 years ago

@cryos The RAW reader dialog is merged now, can we close this?

ElliotPadgett commented 5 years ago

Tested this and issues look solved. No crashes even if the size is wrong. The helper for matching data size is nice. I will close the issue.