[Paraview] segfault playing a simulation

Sun Jul 12 21:51:20 EDT 2015

Sergi,

Your VTI file extents should only describe the region of the whole image
they occupy, so you are on the right track. In situations like these where
it isn't obvious what is wrong, I tend to start from the beginning with a
very small example and build up from there. For example, you could start
with a small image - say 2 x 4 pixels (2D) split into two pieces. Start
with one data array for this example and make sure it works - use ASCII
encoding so that you know for sure what is in the XML file and then switch
to raw binary, then zipped binary. Then add a second data array. When you
are confident that works, change the example to four pieces, then make the
image 3D and so on.

It can take a while to do this, but you'll come out really understanding
the file format and will probably figure out what you had wrong in the
first place.

Thanks,
Cory

On Sat, Jul 11, 2015 at 5:32 AM, Sergi Mateo Bellido <
sergi.mateo.bellido at gmail.com> wrote:

>  Hi Cory,
>
> Thanks for your time. I have been playing a bit with the files too and I
> realized that replacing the whole_extent of each *.vti  by the whole
> dataset everything works.
>
> I would like to generate something like this:
> http://vtk.1045678.n5.nabble.com/Example-vti-file-td3381382.html . In
> this example, each imagedata has whole_extent=whole size but its pieces
> only contain a portion of the whole dataset. Does this configuration make
> sense?
>
> I have been trying to generate something like that but I failed. My code
> looks like this one: http://www.vtk.org/Wiki/VTK/Examples/Cxx/IO/WriteVTI
> but using VtkFloatArray as buffers and attaching them to the VtkImageData.
> I tried defining the set of the VtkImageData as the whole dataset and
> defining the VtkFloatArrays of the size of each portion but it didn't work
> :(
>
> Any clue?
>
> Thanks!
> Sergi
>
>
> On 07/09/2015 05:00 PM, Cory Quamen wrote:
>
> Hi Sergi,
>
>  I played with your data set a little but haven't found what is wrong. I
> am suspicious of two things in the data file, the extent and the offset in
> the second data array (it looks too small).
>
>  What are the dimensions of your grid? Note that the whole extent upper
> values need to be the dimension - 1, e.g., for a 300x300x300 grid, the
> whole extent should be 0 299 0 299 0 299.
>
>  Thanks,
> Cory
>
> On Wed, Jul 1, 2015 at 12:27 PM, Sergi Mateo Bellido <
> sergi.mateo.bellido at gmail.com> wrote:
>
>>  Hi Cory,
>>
>> Thanks for your time. These data files have been produced by a software
>> that I'm developing with some colleagues.
>>
>> Best regards,
>>
>> Sergi
>>
>>
>> On 07/01/2015 03:59 PM, Cory Quammen wrote:
>>
>> Sergi,
>>
>>  I can confirm the crash you are seeing in the same location in the
>> code. I'm looking for the cause.
>>
>>  What software produced these data files?
>>
>>  Thanks,
>> Cory
>>
>> On Wed, Jul 1, 2015 at 1:59 AM, Sergi Mateo Bellido <
>> sergi.mateo.bellido at gmail.com> wrote:
>>
>>>  Hi Cory,
>>>
>>> Thanks for your answer. I reproduced the segfault in two different ways,
>>> but it's always after loading a data set:
>>> - After loading a data set, I tried to play the simulation ->segfault
>>> - After loading a data set, I tried to filter some fields from the model
>>> (Pointer array status). As soon as I clicked the 'apply' button, paraview
>>> crashed with a segfault.
>>>
>>> Thanks,
>>> Sergi
>>>
>>>
>>>
>>> On 06/30/2015 06:21 AM, Cory Quammen wrote:
>>>
>>> Hi Sergi,
>>>
>>>  Could you clarify when you are seeing this crash? Is it right when
>>> starting ParaView or when first loading a data set?
>>>
>>>  Thanks,
>>> Cory
>>>
>>> On Tue, Jun 23, 2015 at 8:55 AM, Sergi Mateo Bellido <
>>> sergi.mateo.bellido at gmail.com> wrote:
>>>
>>>>  Hi,
>>>>
>>>> I'm trying to reproduce a simulation with ParaView 4.3.1 and it always
>>>> crashes when I start it. You can find the backtrace below:
>>>>
>>>> =========================================================
>>>> Process id 6681 Caught SIGSEGV at 0x925b124 address not mapped to object
>>>> Program Stack:
>>>> WARNING: The stack trace will not use advanced capabilities because
>>>> this is a release build.
>>>> 0x7f54ce081d40 : ??? [(???) ???:-1]
>>>> 0x7f54ce19caf6 : ??? [(???) ???:-1]
>>>> 0x7f54cb123736 : vtkXMLPStructuredDataReader::CopySubExtent(int*, int*,
>>>> long long*, int*, int*, long long*, int*, int*, vtkDataArray*,
>>>> vtkDataArray*) [(libvtkIOXML-pv4.3.so.1) ???:-1]
>>>> 0x7f54cb12389f :
>>>> vtkXMLPStructuredDataReader::CopyArrayForPoints(vtkDataArray*,
>>>> vtkDataArray*) [(libvtkIOXML-pv4.3.so.1) ???:-1]
>>>> 0x7f54cb11cc1f : vtkXMLPDataReader::ReadPieceData()
>>>> [(libvtkIOXML-pv4.3.so.1) ???:-1]
>>>> 0x7f54cb11ca14 : vtkXMLPDataReader::ReadPieceData(int)
>>>> [(libvtkIOXML-pv4.3.so.1) ???:-1]
>>>> 0x7f54cb124d7a : vtkXMLPStructuredDataReader::ReadXMLData()
>>>> [(libvtkIOXML-pv4.3.so.1) ???:-1]
>>>> 0x7f54cb1280eb : vtkXMLReader::RequestData(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*) [(libvtkIOXML-pv4.3.so.1)
>>>> ???:-1]
>>>> 0x7f54cb1273b6 : vtkXMLReader::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*) [(libvtkIOXML-pv4.3.so.1)
>>>> ???:-1]
>>>> 0x7f54cd6200f9 : vtkFileSeriesReader::RequestData(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkPVVTKExtensionsDefault-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd61f07f : vtkFileSeriesReader::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkPVVTKExtensionsDefault-pv4.3.so.1) ???:-1]
>>>> 0x7f54d2706204 : vtkExecutive::CallAlgorithm(vtkInformation*, int,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d27016cc : vtkDemandDrivenPipeline::ExecuteData(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d2700201 : vtkCompositeDataPipeline::ExecuteData(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d2704067 :
>>>> vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d271d959 :
>>>> vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d26fe387 :
>>>> vtkCompositeDataPipeline::ForwardUpstream(vtkInformation*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d2704010 :
>>>> vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d271d959 :
>>>> vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d26fe387 :
>>>> vtkCompositeDataPipeline::ForwardUpstream(vtkInformation*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d2704010 :
>>>> vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d271d959 :
>>>> vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*,
>>>> vtkInformationVector**, vtkInformationVector*)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d27035ae : vtkDemandDrivenPipeline::UpdateData(int)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54d271e87f : vtkStreamingDemandDrivenPipeline::Update(int)
>>>> [(libvtkCommonExecutionModel-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd98fa7f :
>>>> vtkPVDataRepresentation::ProcessViewRequest(vtkInformationRequestKey*,
>>>> vtkInformation*, vtkInformation*)
>>>> [(libvtkPVClientServerCoreRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd973d79 :
>>>> vtkGeometryRepresentation::ProcessViewRequest(vtkInformationRequestKey*,
>>>> vtkInformation*, vtkInformation*)
>>>> [(libvtkPVClientServerCoreRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd975d71 :
>>>> vtkGeometryRepresentationWithFaces::ProcessViewRequest(vtkInformationRequestKey*,
>>>> vtkInformation*, vtkInformation*)
>>>> [(libvtkPVClientServerCoreRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd9bd388 :
>>>> vtkPVView::CallProcessViewRequest(vtkInformationRequestKey*,
>>>> vtkInformation*, vtkInformationVector*)
>>>> [(libvtkPVClientServerCoreRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd9bd552 : vtkPVView::Update()
>>>> [(libvtkPVClientServerCoreRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54cd9acb78 : vtkPVRenderView::Update()
>>>> [(libvtkPVClientServerCoreRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54d780ac30 : vtkPVRenderViewCommand(vtkClientServerInterpreter*,
>>>> vtkObjectBase*, char const*, vtkClientServerStream const&,
>>>> vtkClientServerStream&, void*)
>>>> [(libvtkPVServerManagerApplication-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e135e0 : vtkClientServerInterpreter::CallCommandFunction(char
>>>> const*, vtkObjectBase*, char const*, vtkClientServerStream const&,
>>>> vtkClientServerStream&) [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e18393 :
>>>> vtkClientServerInterpreter::ProcessCommandInvoke(vtkClientServerStream
>>>> const&, int) [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e16832 :
>>>> vtkClientServerInterpreter::ProcessOneMessage(vtkClientServerStream const&,
>>>> int) [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e16ced :
>>>> vtkClientServerInterpreter::ProcessStream(vtkClientServerStream const&)
>>>> [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b26cec :
>>>> vtkPVSessionCore::ExecuteStreamInternal(vtkClientServerStream const&, bool)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b26958 : vtkPVSessionCore::ExecuteStream(unsigned int,
>>>> vtkClientServerStream const&, bool)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b25203 : vtkPVSessionBase::ExecuteStream(unsigned int,
>>>> vtkClientServerStream const&, bool)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54cdcae44f : vtkSMViewProxy::Update()
>>>> [(libvtkPVServerManagerRendering-pv4.3.so.1) ???:-1]
>>>> 0x7f54cdf2f6f7 : vtkSMAnimationScene::TickInternal(double, double,
>>>> double) [(libvtkPVAnimation-pv4.3.so.1) ???:-1]
>>>> 0x7f54cf415cab : vtkAnimationCue::Tick(double, double, double)
>>>> [(libvtkCommonCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54cdf23268 : vtkAnimationPlayer::Play()
>>>> [(libvtkPVAnimation-pv4.3.so.1) ???:-1]
>>>> 0x7f54d7851619 :
>>>> vtkSMAnimationSceneCommand(vtkClientServerInterpreter*, vtkObjectBase*,
>>>> char const*, vtkClientServerStream const&, vtkClientServerStream&, void*)
>>>> [(libvtkPVServerManagerApplication-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e135e0 : vtkClientServerInterpreter::CallCommandFunction(char
>>>> const*, vtkObjectBase*, char const*, vtkClientServerStream const&,
>>>> vtkClientServerStream&) [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e18393 :
>>>> vtkClientServerInterpreter::ProcessCommandInvoke(vtkClientServerStream
>>>> const&, int) [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e16832 :
>>>> vtkClientServerInterpreter::ProcessOneMessage(vtkClientServerStream const&,
>>>> int) [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d4e16ced :
>>>> vtkClientServerInterpreter::ProcessStream(vtkClientServerStream const&)
>>>> [(libvtkClientServer-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b436d4 : vtkSIProperty::ProcessMessage(vtkClientServerStream&)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b4377e : vtkSIProperty::Push(paraview_protobuf::Message*, int)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b4459e : vtkSIProxy::Push(paraview_protobuf::Message*)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b2884a :
>>>> vtkPVSessionCore::PushStateInternal(paraview_protobuf::Message*)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b27484 :
>>>> vtkPVSessionCore::PushState(paraview_protobuf::Message*)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5b2514d :
>>>> vtkPVSessionBase::PushState(paraview_protobuf::Message*)
>>>> [(libvtkPVServerImplementationCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d5d859b7 : vtkSMProxy::UpdateProperty(char const*, int)
>>>> [(libvtkPVServerManagerCore-pv4.3.so.1) ???:-1]
>>>> 0x7f54d6d8aa07 : pqVCRController::onPlay()
>>>> [(libvtkpqComponents-pv4.3.so.1) ???:-1]
>>>> 0x7f54cfa98258 : QMetaObject::activate(QObject*, QMetaObject const*,
>>>> int, void**) [(libQtCore.so.4) ???:-1]
>>>> 0x7f54d01102f2 : QAction::triggered(bool) [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d0111710 : QAction::activate(QAction::ActionEvent)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d04fd514 : ??? [(???) ???:-1]
>>>> 0x7f54d04fd7ab : QAbstractButton::mouseReleaseEvent(QMouseEvent*)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d05d15ea : QToolButton::mouseReleaseEvent(QMouseEvent*)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d0175ac1 : QWidget::event(QEvent*) [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d04fca3f : QAbstractButton::event(QEvent*) [(libQtGui.so.4)
>>>> ???:-1]
>>>> 0x7f54d05d422d : QToolButton::event(QEvent*) [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d011759e : QApplicationPrivate::notify_helper(QObject*, QEvent*)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d011e533 : QApplication::notify(QObject*, QEvent*)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54cfa802f3 : QCoreApplication::notifyInternal(QObject*, QEvent*)
>>>> [(libQtCore.so.4) ???:-1]
>>>> 0x7f54d011a656 : QApplicationPrivate::sendMouseEvent(QWidget*,
>>>> QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d019ca94 : ??? [(???) ???:-1]
>>>> 0x7f54d019b877 : QApplication::x11ProcessEvent(_XEvent*)
>>>> [(libQtGui.so.4) ???:-1]
>>>> 0x7f54d01c4805 : ??? [(???) ???:-1]
>>>> 0x7f54cfa7f375 :
>>>> QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)
>>>> [(libQtCore.so.4) ???:-1]
>>>> 0x7f54cfa7f748 :
>>>> QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) [(libQtCore.so.4)
>>>> ???:-1]
>>>> 0x7f54cfa8414b : QCoreApplication::exec() [(libQtCore.so.4) ???:-1]
>>>> 0x407785 : main [(paraview) ???:-1]
>>>> 0x7f54ce06cec5 : __libc_start_main [(libc.so.6) ???:-1]
>>>> 0x4074da : QMainWindow::event(QEvent*) [(paraview) ???:-1]
>>>> =========================================================
>>>>
>>>> Thanks,
>>>>
>>>> Sergi Mateo
>>>> sergi.mateo.bellido at gmail.com
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>  --
>>> Cory Quammen
>>> R&D Engineer
>>> Kitware, Inc.
>>>
>>>
>>>
>>
>>
>>  --
>> Cory Quammen
>> R&D Engineer
>> Kitware, Inc.
>>
>>
>>
>
>
>  --
> Cory Quammen
> R&D Engineer
> Kitware, Inc.
>
>
>

-- 
Cory Quammen
R&D Engineer
Kitware, Inc.
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