[Paraview] segfault playing a simulation
Sergi Mateo Bellido
sergi.mateo.bellido at gmail.com
Fri Jul 17 10:21:42 EDT 2015
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
>> <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>
>>>>>
>>>>> _______________________________________________
>>>>> 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:
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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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