[Paraview] segfault playing a simulation
Sergi Mateo Bellido
sergi.mateo.bellido at gmail.com
Fri Jul 17 09:38:52 EDT 2015
Hi Cory,
Your intuition was right: the problem is related in some way with the
offset. I've changed the DataMote to ASCII and everything worked :)
Note that in this mode the offset field is not used, instead of that VTK
generates a DataArray.
I would like to know how the offset is computed since I can't find any
relation between the offset value and my data.
Thanks!
Sergi
On 07/13/2015 03:51 AM, Cory Quammen wrote:
> 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 <mailto: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
>> <mailto: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
>>> <mailto: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
>>>> <mailto: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
>>>> <mailto: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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