Re: [Paraview] segfault playing a simulation

Fri, 17 Jul 2015 07:22:20 -0700 

Hi again,
I've just tried storing the data as a binary and It crashes. In this case we are not using the offset field either. 

May the problem be related to the data compression?

Best,
Sergi

On 07/17/2015 03:38 PM, Sergi Mateo Bellido wrote:

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 
<[email protected] 
<mailto:[email protected]>> 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
    <[email protected]
    <mailto:[email protected]>> 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
        <[email protected]
        <mailto:[email protected]>> 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
            <[email protected]
            <mailto:[email protected]>> 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
                [email protected]
                <mailto:[email protected]>

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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.





_______________________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

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