Re: [Paraview] [BUG] segfault playing a simulation

Sun, 02 Aug 2015 09:42:06 -0700 

Hi,
After a few hours debugging ParaView's code I think that I finally found the bug! :) 


The problem is that the meaning of the piece extent changes depending on 
if the piece has the whole dimensions or only a portion of them. For 
example, imagine that we have the following *.pvti file:


<VTKFile type="PImageData"  ... compressor="vtkZLibDataCompressor">
  <PImageData WholeExtent="0 200 0 200 0 200" ...>
    <PPointData>
      <PDataArray type="Float32" ..."/>
    </PPointData>
    <Piece Extent="0 200 0 200 0 101" Source="raw_binary_0_0.vti"/>
    <Piece Extent="0 200 0 200 101 200" Source="raw_binary_0_1.vti"/>
  </PImageData>
</VTKFile>

In this case, the dimensions of the pieces are:
  1st piece -> [0..200], [0..200], [0..101)
  2nd piece -> [0..200], [0..200], [101..200]


Note that the last dimension range of the 1st piece doesn't include the 
101 value which is included in the 2nd piece.



The issue here is that the code is not taking into account this when 
it's computing the dimensions of the current piece. In file 
VTK/IO/XML/vtkXMLPStructuredDataReader.cxx:155 we have the next call to 
'ComputePointDimensions' function:


 this->ComputePointDimensions(this->SubExtent, this->SubPointDimensions);


I printed the values of 'this->SubExtent' and they were the same values 
specified in the Piece Extent field:


(gdb) p SubExtent
$1 = {0, 200, 0, 200, 0, 101}


For these values, the 'ComputePointDimensions' function, which is 
defined in VTK/IO/XML/vtkXMLReader.cxx:916, computed the next dimensions:


(gdb) p this->SubPointDimensions
$2 = {201, 201, 102}


How these values are computed is very simple: upper_bound - lower_bound 
+ 1. Note that the value of the third dimension is wrong: it should be 
101 instead of 102.



Finally, the segfault is produced in the 'CopySubExtent' function, which 
is defined in VTK/IO/XML/vtkXMLPStructuredDataReader.cxx:342, because 
SubPointDimensions information is used to copy the regions and we are 
doing an extra copy (loop defined in 371 line).


Could you confirm me this bug?

Best regards,

Sergi Mateo


PS1: Source references are related to the last version of ParaView's 
source published in your webpage: 
http://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v4.3&type=source&os=all&downloadFile=ParaView-v4.3.1-source.tar.gz



PS2: You can reproduce this bug using one of the examples that I sent 
you in my previous emails.


On 07/24/2015 11:24 AM, Sergi Mateo Bellido wrote:

Hi Cory,


I have been doing some experiments with the encoding formats but I've 
not progressed much.



The elements of my mesh are floats and the mesh dimensions are 
201x201x201 (X,Y,Z). I executed all the experiments with 2 MPI 
processes and the data domain was manually partionated by the Z axis, 
i.e. each process computes half of the cube.



The program basically writes, at each position of the mesh, the 
identifier of the MPI process that computed that position (mpi rank). 
In our case, this means that half of the cube has a '0' whereas the 
other portion has a '1'.



Attached to this email you will  a tarball with 3 outputs, one for 
each different encoding (ASCII, zipped binary, raw binary). The size 
of the mesh is 201x201x201 and the only difference among the 
executions is the encoding format.


I hope you could give me some light.

Thanks!

Sergi

On 07/17/2015 04:21 PM, Sergi Mateo Bellido wrote:

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]>

                _______________________________________________
                Powered by www.kitware.com <http://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

                Follow this link to subscribe/unsubscribe:
                http://public.kitware.com/mailman/listinfo/paraview





            -- 
            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

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview






















					Reply via email to