VisIt 3.x Abort Trap 6 in VTK on Mac

[lefebvrera]

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Hi,
I am attempting to update my C++ application to use VisIt 3.1.4 or 3.2.1 instead of 2.12 however I’m experiencing some problems.

• The VisIt GUI’s Plots button won’t activate when clicked… first indication something isn’t right
  • The buttons will activate when I pop out the VisIt GUI from my application
• When I attempt to Draw any of the tire.silo data (or other data sets) I receive an Abort Trap: 6 error

I receive this error on Mac HighSierra and Catalina using Qt 5.9 or Qt 5.12 and XCode 10 and 12. I am using CMake 3.20.5 with the following build_visitx_x_x invocation:

bash ../build_visit3_2_0 --system-cmake --system-qt  --vtk --hdf5 --netcdf --silo --cflag -Wno-error=implicit-function-declaration --prefix /Users/Shared/ornldev/code/visit/3.2.1/install  --cxxflag -Wno-error=implicit-function-declaration --makeflags -j8   --stdout --visit  --visit-build-hostname workbench.cmake

When using XCode 12 I have had to patch silo as specified in llnl/Silo#210 (comment) and extend compiler flags with -Wno-error=implicit-function-declaration to prevent HDF5 from failing to compile due to isnatty warning turned to compile error due to xcode12.

Here is the stacktrace from my Catalina machine:

thread visit-dav/visit#12095, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
 * frame #0: 0x0000000000000000
   frame visit-dav/visit#12095: 0x0000000113e578a5 libvtkRenderingOpenGL2-8.1.1.dylib`vtkOpenGLRenderTimer::ReusableStart(this=0x00000001714c2980) at vtkOpenGLRenderTimer.cxx:0 [opt]
   frame visit-dav/visit#12094: 0x0000000113e43967 libvtkRenderingOpenGL2-8.1.1.dylib`vtkOpenGLPolyDataMapper::RenderPieceStart(this=0x0000000115c0e600, ren=0x0000000169ee2100, actor=0x00000001714c4520) at vtkOpenGLPolyDataMapper.cxx:2358:21 [opt]
   frame visit-dav/visit#12096: 0x0000000113e4402c libvtkRenderingOpenGL2-8.1.1.dylib`vtkOpenGLPolyDataMapper::RenderPiece(this=0x0000000115c0e600, ren=0x0000000169ee2100, actor=0x00000001714c4520) at vtkOpenGLPolyDataMapper.cxx:2567:9 [opt]
   frame visit-dav/visit#12097: 0x00000001142e2b07 libvtkRenderingCore-8.1.1.dylib`vtkPolyDataMapper::Render(this=0x0000000115c0e600, ren=<unavailable>, act=<unavailable>) at vtkPolyDataMapper.cxx:68:11 [opt]
   frame visit-dav/visit#12098: 0x0000000113de2528 libvtkRenderingOpenGL2-8.1.1.dylib`vtkOpenGLActor::Render(this=0x00000001714c4520, ren=0x0000000169ee2100, mapper=0x0000000115c0e600) at vtkOpenGLActor.cxx:100:11 [opt]
   frame visit-dav/visit#12099: 0x00000001142767da libvtkRenderingCore-8.1.1.dylib`vtkFollower::RenderOpaqueGeometry(this=0x00000001714c4000, vp=0x0000000169ee2100) at vtkFollower.cxx:199:11 [opt]
   frame visit-dav/visit#12100: 0x000000010f10e462 libavtplotter_ser.dylib`vtkVisItAxisActor::RenderOpaqueGeometry(vtkViewport*) + 98
   frame visit-dav/visit#12101: 0x000000010f1190ec libavtplotter_ser.dylib`vtkVisItCubeAxesActor::RenderOpaqueGeometry(vtkViewport*) + 380
   frame visit-dav/visit#12102: 0x00000001142f7647 libvtkRenderingCore-8.1.1.dylib`vtkRenderer::UpdateOpaquePolygonalGeometry(this=0x0000000169ee2100) at vtkRenderer.cxx:693:35 [opt]
   frame visit-dav/visit#12103: 0x0000000113e6648b libvtkRenderingOpenGL2-8.1.1.dylib`vtkOpenGLRenderer::UpdateGeometry(this=0x0000000169ee2100) at vtkOpenGLRenderer.cxx:229:11 [opt]
   frame visit-dav/visit#12104: 0x0000000113e65994 libvtkRenderingOpenGL2-8.1.1.dylib`vtkOpenGLRenderer::DeviceRender(this=0x0000000169ee2100) at vtkOpenGLRenderer.cxx:170:11 [opt]
   frame visit-dav/visit#12105: 0x00000001142f61d0 libvtkRenderingCore-8.1.1.dylib`vtkRenderer::Render(this=0x0000000169ee2100) at vtkRenderer.cxx:351:9 [opt]
   frame visit-dav/visit#12106: 0x00000001142f49df libvtkRenderingCore-8.1.1.dylib`vtkRendererCollection::Render(this=0x00000001714371d0) at vtkRendererCollection.cxx:51:14 [opt]
   frame visit-dav/visit#12107: 0x0000000114309afe libvtkRenderingCore-8.1.1.dylib`vtkRenderWindow::DoStereoRender(this=0x0000000115bff200) at vtkRenderWindow.cxx:789:22 [opt]
   frame visit-dav/visit#12108: 0x0000000114308de5 libvtkRenderingCore-8.1.1.dylib`vtkRenderWindow::Render(this=0x0000000115bff200) at vtkRenderWindow.cxx:450:11 [opt]
   frame visit-dav/visit#12109: 0x0000000113dd82cf libvtkRenderingOpenGL2-8.1.1.dylib`vtkGenericOpenGLRenderWindow::Render(this=0x0000000115bff200) at vtkGenericOpenGLRenderWindow.cxx:241:23 [opt]
   frame visit-dav/visit#12110: 0x000000010f32bb55 libavtviswindow_ser.dylib`VisWinRendering::Render() + 293
   frame visit-dav/visit#12111: 0x000000010f32b956 libavtviswindow_ser.dylib`VisWinRendering::EnableUpdates() + 54
   frame visit-dav/visit#12112: 0x000000010f36000c libavtviswindow_ser.dylib`VisWindow::EnableUpdates() + 44
   frame visit-dav/visit#12113: 0x000000010f5503d4 libviewercore_ser.dylib`ViewerPlotList::UpdateWindow(std::__1::vector<int, std::__1::allocator<int> > const&, bool) + 2052
   frame visit-dav/visit#12114: 0x000000010f54e85d libviewercore_ser.dylib`ViewerPlotList::UpdateFrameForPlots(std::__1::vector<int, std::__1::allocator<int> > const&) + 45
   frame visit-dav/visit#12115: 0x000000010f54de0f libviewercore_ser.dylib`ViewerPlotList::UpdateFrame(bool) + 415
   frame visit-dav/visit#12116: 0x000000010f52f3bc libviewercore_ser.dylib`ViewerActionManager::HandleAction(ViewerRPC const&) + 60
   frame visit-dav/visit#12117: 0x00000001102aae4b libviewer.dylib`ViewerSubject::HandleViewerRPCEx() + 491
   frame visit-dav/visit#12118: 0x00000001102aac0b libviewer.dylib`ViewerSubject::HandleViewerRPC() + 11
   frame visit-dav/visit#12119: 0x0000000111847d3c QtCore`QMetaObject::activate(QObject*, int, int, void**) + 3132
   frame visit-dav/visit#12120: 0x000000010fa9c45c libvisitcommon.dylib`Subject::Notify() + 204
   frame visit-dav/visit#12121: 0x000000010f986852 libvisitcommon.dylib`AttributeSubject::Notify() + 18
   frame visit-dav/visit#12122: 0x0000000111847d3c QtCore`QMetaObject::activate(QObject*, int, int, void**) + 3132
   frame visit-dav/visit#12123: 0x00000001105d4015 QtWidgets`QAction::activate(QAction::ActionEvent) + 309
   frame visit-dav/visit#12124: 0x00000001106c7a83 QtWidgets`___lldb_unnamed_symbol1029$$QtWidgets + 147
   frame visit-dav/visit#12125: 0x00000001106c8c0f QtWidgets`QAbstractButton::mouseReleaseEvent(QMouseEvent*) + 271
   frame visit-dav/visit#12126: 0x00000001107c01df QtWidgets`QToolButton::mouseReleaseEvent(QMouseEvent*) + 15
   frame visit-dav/visit#12127: 0x000000011061918d QtWidgets`QWidget::event(QEvent*) + 445
   frame visit-dav/visit#12128: 0x00000001107c076f QtWidgets`QToolButton::event(QEvent*) + 319
   frame visit-dav/visit#12129: 0x00000001105dd65d QtWidgets`QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
   frame visit-dav/visit#12130: 0x00000001105e039c QtWidgets`QApplication::notify(QObject*, QEvent*) + 7052
   frame visit-dav/visit#12131: 0x0000000100443048 libGui_GraphicsLib.04.dylib`Scale::Graphics::FulcrumApplication::notify(this=0x00007ffeefbff518, receiver=0x0000000169c18180, event=0x00007ffeefbfd5b0) at FulcrumApplication.cpp:31:30
   frame visit-dav/visit#12132: 0x00000001118169d4 QtCore`QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
   frame visit-dav/visit#12133: 0x00000001105ddf80 QtWidgets`QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool, bool) + 896
   frame visit-dav/visit#12134: 0x00000001106386de QtWidgets`___lldb_unnamed_symbol481$$QtWidgets + 1710
   frame visit-dav/visit#12135: 0x0000000110637399 QtWidgets`___lldb_unnamed_symbol476$$QtWidgets + 233
   frame visit-dav/visit#12136: 0x00000001105dd65d QtWidgets`QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
   frame visit-dav/visit#12137: 0x00000001105dea01 QtWidgets`QApplication::notify(QObject*, QEvent*) + 497
   frame visit-dav/visit#12138: 0x0000000100443048 libGui_GraphicsLib.04.dylib`Scale::Graphics::FulcrumApplication::notify(this=0x00007ffeefbff518, receiver=0x00000001698c5040, event=0x00007ffeefbfda50) at FulcrumApplication.cpp:31:30
   frame visit-dav/visit#12139: 0x00000001118169d4 QtCore`QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
   frame visit-dav/visit#12140: 0x0000000110ba3ff9 QtGui`QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 3961
   frame visit-dav/visit#12141: 0x0000000110b8ab1b QtGui`QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 219
   frame visit-dav/visit#12142: 0x000000011cb82b20 libqcocoa.dylib`___lldb_unnamed_symbol686$$libqcocoa.dylib + 320
   frame visit-dav/visit#12143: 0x000000011cb83288 libqcocoa.dylib`___lldb_unnamed_symbol698$$libqcocoa.dylib + 40
   frame visit-dav/visit#12144: 0x00007fff2f23f7e2 CoreFoundation`__CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
   frame visit-dav/visit#12145: 0x00007fff2f23f781 CoreFoundation`__CFRunLoopDoSource0 + 103
   frame visit-dav/visit#12146: 0x00007fff2f23f59b CoreFoundation`__CFRunLoopDoSources0 + 209
   frame visit-dav/visit#12147: 0x00007fff2f23e2ca CoreFoundation`__CFRunLoopRun + 927
   frame visit-dav/visit#12148: 0x00007fff2f23d8ce CoreFoundation`CFRunLoopRunSpecific + 462
   frame visit-dav/visit#12149: 0x00007fff2de69abd HIToolbox`RunCurrentEventLoopInMode + 292
   frame visit-dav/visit#12150: 0x00007fff2de696f4 HIToolbox`ReceiveNextEventCommon + 359
   frame visit-dav/visit#12151: 0x00007fff2de69579 HIToolbox`_BlockUntilNextEventMatchingListInModeWithFilter + 64
   frame visit-dav/visit#12152: 0x00007fff2c4b0039 AppKit`_DPSNextEvent + 883
   frame visit-dav/visit#12153: 0x00007fff2c4ae880 AppKit`-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
   frame visit-dav/visit#12154: 0x00007fff2c4a058e AppKit`-[NSApplication run] + 658
   frame visit-dav/visit#12155: 0x000000011cb82003 libqcocoa.dylib`___lldb_unnamed_symbol679$$libqcocoa.dylib + 2579
   frame visit-dav/visit#12156: 0x0000000111811fbf QtCore`QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 431
   frame visit-dav/visit#12157: 0x0000000111816fe2 QtCore`QCoreApplication::exec() + 130
   frame visit-dav/visit#12158: 0x0000000100028976 Workbench`main(argc=1, argv=0x00007ffeefbff6b0) at Fulcrum.cpp:191:18
   frame visit-dav/visit#12159: 0x00007fff692fccc9 libdyld.dylib`start + 1

Additionally, I see the following Qt painter warnings that could play a role in the :

Qt: Warning: QPainter::begin: Paint device returned engine == 0, type: 2
Qt: Warning: QPainter::scale: Painter not active
Qt: Warning: QPainter::setPen: Painter not active
Qt: Warning: Window position QRect(1600,1460 640x480) outside any known screen, using primary screen

Any ideas for resolving or working around this issue will be appreciated.

Thank you in advance,
Rob Lefebvre

[lefebvrera]

I should also add, I attempted to use the included Qt5 but this results in Qt failing to compile. I have opted for an LTS version (5.9 or 5.12) as these are what is available on my CI infrastructure.

[biagas]

I am not a Mac user/developer so my ability to assist with your problem may be limited. Can you attach your build_visit log file (zipped) here? Was your system Qt compiled using the same compiler and version as used by build_visit?

[lefebvrera]

Oddly, there is no build_visit3_2_0_log file (perhaps because of --stdout?).

I receive the following on stdout

Processing bsd license.
using system cmake
version: 3.20.5

CMake suite maintained and supported by Kitware (kitware.com/cmake). build: /opt/local bin: /opt/local/bin root: /opt/local/share/cmake-3.20
using system qt
[build_visit invocation arguments] --system-cmake --system-qt --vtk --hdf5 --netcdf --silo --cflag -Wno-error=implicit-function-declaration --prefix /Users/Shared/ornldev/code/visit/3.2.1/install --cxxflag -Wno-error=implicit-function-declaration --makeflags -j8 --stdout --visit --visit-build-hostname workbench.cmake
[build_visit build mode ] Release
apple clang version 12.0.0
Fortran support for thirdparty libraries disabled.
enabling any dependent libraries
initializing module variables
initialize module variables for cmake
initialize module variables for python
initialize module variables for qt
initalizing qt vars
initialize module variables for qwt
initialize module variables for vtk
initalizing vtk vars
initialize module variables for zlib
initialize module variables for hdf5
initialize module variables for netcdf
Checking for files . . .
Checking for openssl-1.0.2j
Checking for python-3.7.7
Checking for qwt-6.1.2
Checking for vtk-8.1.0
Checking for zlib-1.2.11
Found existing GIT visit directory, using that . . .
Checking optional 3rd party libs
Checking for hdf5-1.8.14
Checking for netcdf-4.1.1
Checking for silo-4.10.2
building required libraries
cmake already installed, skipping
openssl already installed, skipping
checking if python is installed
<module 'PIL' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/Pillow-7.1.2-py3.7-macosx-10.15-x86_64.egg/PIL/__init__.py'>
<module 'numpy' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/numpy-1.16.6-py3.7-macosx-10.15-x86_64.egg/numpy/__init__.py'>
<module 'requests' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/requests-2.22.0-py3.7.egg/requests/__init__.py'>
<module 'pyparsing' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/pyparsing-2.4.6-py3.7.egg/pyparsing.py'>
<module 'seedme' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/seedme-1.2.4-py3.7.egg/seedme.py'>
<module 'sphinx' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/Sphinx-2.2.1-py3.7.egg/sphinx/__init__.py'>
<module 'sphinx_rtd_theme' from '/Users/Shared/ornldev/code/visit/3.2.0/doit/third_party/python/3.7.7/i386-apple-darwin19_clang/lib/python3.7/site-packages/sphinx_rtd_theme-0.4.3-py3.7.egg/sphinx_rtd_theme/__init__.py'>
python already installed, skipping
qt already installed, skipping
qwt already installed, skipping
vtk already installed, skipping
zlib already installed, skipping
building optional libraries
hdf5 already installed, skipping
netcdf already installed, skipping
silo already installed, skipping
Creating host.conf
External Hostname variable found: Using workbench.cmake
Creating workbench.cmake

Done creating workbench.cmake
Building VisIt (~50 minutes)
Building VisIt in visit/build . . .
Configuring VisIt . . .
/opt/local/bin/cmake -DVISIT_CONFIG_SITE:FILEPATH=/Users/Shared/ornldev/code/visit/3.2.0/doit/workbench.cmake -DVISIT_QT_DIR:PATH=/Users/Shared/ornldev/code/Qt5.12.11//5.12.11/clang_64 -DVISIT_INSTALL_THIRD_PARTY:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=Release -DVISIT_C_COMPILER:FILEPATH=clang -DVISIT_CXX_COMPILER:FILEPATH=clang++ -DVISIT_C_FLAGS:STRING="-fno-common -fexceptions -O2 -Wno-error=implicit-function-declaration" -DVISIT_CXX_FLAGS:STRING="-fno-common -fexceptions -O2 -Wno-error=implicit-function-declaration" -DCMAKE_INSTALL_PREFIX:PATH=/Users/Shared/ornldev/code/visit/3.2.1/install -DCPACK_INSTALL_PREFIX:PATH=/Users/Shared/ornldev/code/visit/3.2.1/install -DCPACK_PACKAGING_INSTALL_PREFIX:PATH=/Users/Shared/ornldev/code/visit/3.2.1/install ../src
CMake Error: Unknown argument -O2
CMake Error: Run 'cmake --help' for all supported options.
VisIt configure failed.  Giving up
Unable to build or install VisIt. Bailing out.

The CMake error didn't make sense to me so I invoked the exact same cmake command inside the visit/build directory and managed to have it install the libraries needed by my application.

[markcmiller86]

User was using system CMake (which is probably newer version than VisIt requires) and CMake complained with CMake Error: Unknown argument -O2 which suggets lack of quotes around args to -DVISIT_C_FLAGS:STRING= and/or -DVISIT_CXX_FLAGS:STRING=. The log output in the above comment doesn't shows quotes for those args but remember that we independently echo our commands to the log file instead of capturing the actual commands executed with set -x and set +x and so I highly suspect the actual CMake commands are failing to quote something here. In any event, the user was able to get past this manually.