[Paraview] CoProcessing
Andy Bauer
andy.bauer at kitware.com
Fri Aug 13 10:42:35 EDT 2010
On Fri, Aug 13, 2010 at 3:39 AM, Jacques Papper <jacques.papper at gmail.com>wrote:
> I found the problem... I was inserting PointData instead of CellData :) ,,,
> Anyway it seems to be starting to work now.. 2 things though :
>
> -> Whenever I try to run directly a python script exported from paraview
> (Through the Coprocessing export state) it won't run until I remove all
> references to LIC and all lines containing Null...
>
> Now that you mention it, I didn't put in anything special for plugins.
Setting the plugins to auto-load may work but my guess is that it won't.
I'll look into the plugin thing and the best way to do it in the script
generator.
What do you mean by Null? I don't know what that is so you'll have to
explain it to me.
> For the LIC, is it because the python script doesn't automatically load the
> LIC plugin ?
> For the Null, do you have this problem as well ?
>
> -> Is the Live Source Data code already available in git ? I'd love to test
> it out even if it is not robust yet.
>
We don't yet have permission to release the Live Source Data code yet but I
think it should be available in the next couple of months.
>
> Best,
> Jacques
>
>
> 2010/8/12 Andy Bauer <andy.bauer at kitware.com>
>
>> You probably want to add the field data to the specific grids in the
>> multiblock data set and not just the block itself. As an example:
>>
>> create multiblock
>> for each grid:
>> create grid points and cells
>> add point and cell data to grid
>> add grid to block
>>
>> Note that in parallel for coprocessing that the block must have the same
>> structure on each process but whether a leaf node is empty or not can
>> change. For example:
>>
>> proc 0 mutliblock:
>> block 0 -> unstructured grid
>> block 1 -> uniform grid
>> block 2 -> NULL
>> proc 1 multiblock:
>> block 0 -> NULL
>> block 1 -> NULL
>> block 2 -> unstructured grid
>>
>> I'm not sure of all of the details but what I do is that I set a block to
>> only be non-NULL on a single process.
>>
>> Hope this helps,
>> Andy
>>
>>
>> On Thu, Aug 12, 2010 at 2:38 PM, Jacques Papper <jacques.papper at gmail.com
>> > wrote:
>>
>>> Hi All,
>>>
>>> I am making some more progress on this. Everything was working until I
>>> tried adding field data... I now get an explosion :
>>>
>>> #2 ?? in "/lib64/libc.so.6"
>>> #3 vtkDataArrayTemplate<double>::ComputeScalarRange(int) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCommon.so.pv3.9"
>>> #4 vtkDataArray::ComputeRange(int) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCommon.so.pv3.9"
>>> #5 vtkPVArrayInformation::CopyFromObject(vtkObject*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #6
>>> vtkPVDataSetAttributesInformation::CopyFromDataSetAttributes(vtkDataSetAttributes*)
>>> in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #7 vtkPVDataInformation::CopyFromDataSet(vtkDataSet*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #8 vtkPVDataInformation::CopyFromObject(vtkObject*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #9 vtkPVCompositeDataInformation::CopyFromObject(vtkObject*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #10 vtkPVDataInformation::CopyFromCompositeDataSet(vtkCompositeDataSet*)
>>> in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #11 vtkPVDataInformation::CopyFromObject(vtkObject*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #12 vtkSelfConnection::GatherInformation(unsigned int,
>>> vtkPVInformation*, vtkClientServerID) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #13 vtkSynchronousMPISelfConnection::GatherInformation(unsigned int,
>>> vtkPVInformation*, vtkClientServerID) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerCommon.so"
>>> #14 vtkSMOutputPort::GatherDataInformation() in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
>>> #15 vtkSMOutputPort::GetDataInformation() in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
>>> #16 vtkSMDataTypeDomain::IsInDomain(vtkSMSourceProxy*, int) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
>>> #17 vtkSMDataTypeDomain::IsInDomain(vtkSMProperty*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
>>> #18 vtkSMProperty::IsInDomains() in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
>>> #19 vtkSMRenderViewProxy::CreateDefaultRepresentation(vtkSMProxy*, int)
>>> in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVServerManager.so"
>>> #20 ?? at vtkSMRenderViewProxyPython.cxx:0
>>> #21 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #22 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #23 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #24 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #25 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #26 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #27 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #28 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #29 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #30 PyEval_EvalFrameEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #31 PyEval_EvalCodeEx in "/usr/lib64/libpython2.6.so.1.0"
>>> #32 PyEval_EvalCode in "/usr/lib64/libpython2.6.so.1.0"
>>> #33 ?? in "/usr/lib64/libpython2.6.so.1.0"
>>> #34 PyRun_StringFlags in "/usr/lib64/libpython2.6.so.1.0"
>>> #35 PyRun_SimpleStringFlags in "/usr/lib64/libpython2.6.so.1.0"
>>> #36 vtkPVPythonInterpretor::RunSimpleString(char const*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkPVPythonInterpretor.so"
>>> #37 vtkCPPythonScriptPipeline::CoProcess(vtkCPDataDescription*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCoProcessor.so"
>>> #38 vtkCPProcessor::CoProcess(vtkCPDataDescription*) in
>>> "/users/boreas01/jacques/PARAVIEW/ParaView-bin/bin/libvtkCoProcessor.so"
>>>
>>> Any ideas where this can be coming from ?
>>> When I do not add the field data it just complains about missing fields
>>> so I know that the code is not completely wrong...
>>> I am adding the data to the first block of my multiblockdataset... Is
>>> that a problem ?
>>>
>>>
>>>
>>> Thanks !
>>> Jacques
>>>
>>>
>>> 2010/8/12 Jacques Papper <jacques.papper at gmail.com>
>>>
>>> Hi Andy, Pat,
>>>>
>>>> I have the skeleton of the coprocessing working (for the moment I just
>>>> tried by populating the point field - no cells, no data).
>>>> I am trying to figure out the most efficient way of transferring my data
>>>> structure to VTK with minimal copying and looping...
>>>> I would like to use the vtkUnstructuredGrid::SetCells() method, which
>>>> means I probably need to use the vtkCellArray::SetCells() method, and
>>>> therefore the vtkIdType::SetArray() method...
>>>> The problem is I am not sure what the format of the array should be ?
>>>> I am dealing with unstructured polyhedra cells (most of which are known
>>>> types like hex prism etc..).
>>>>
>>>> Of course, I could also use the InsertNextCell() methods, but I was
>>>> wondering if there wasn't a more efficient way...
>>>>
>>>> Best,
>>>> Jacques
>>>>
>>>>
>>>> 2010/8/9 Andy Bauer <andy.bauer at kitware.com>
>>>>
>>>> Hi Jacques,
>>>>>
>>>>> I put an example on the wiki based on Pat's example for running a
>>>>> coprocessing. It's at:
>>>>> http://paraview.org/Wiki/Coprocessing_example#Python_Scripts
>>>>> Let me know if you have any problems with it so that I can fix any
>>>>> errors that I have.
>>>>>
>>>>> Also, I just made changes so that the coprocessing library gets
>>>>> installed properly.
>>>>>
>>>>> Thanks,
>>>>> Andy
>>>>>
>>>>>
>>>>> On Wed, Aug 4, 2010 at 7:21 PM, Jacques Papper <
>>>>> jacques.papper at gmail.com> wrote:
>>>>>
>>>>>> Thanks Pat,
>>>>>>
>>>>>> I am trying to compile my first attempt.
>>>>>> Although I do find the headers I need, I am having some trouble
>>>>>> identifying which libraries I need to link to.
>>>>>> For example, I assume that I should be linking to libvtkCoProcessor.so
>>>>>> ... Although I find this library in the compilation folder (under bin), I do
>>>>>> not find it in the make installed version under lib...
>>>>>> Is this normal ?
>>>>>>
>>>>>> Best,
>>>>>> Jacques
>>>>>>
>>>>>> 2010/8/4 pat marion <pat.marion at kitware.com>
>>>>>>
>>>>>> Below is a simple cxx program I have used for testing. It creates one
>>>>>>> sphere per process, positions the sphere as a function of the process id,
>>>>>>> and the spheres grow/shrink over time.
>>>>>>>
>>>>>>> Pat
>>>>>>>
>>>>>>> #include "vtkCPProcessor.h"
>>>>>>> #include "vtkCPPythonScriptPipeline.h"
>>>>>>> #include "vtkMultiProcessController.h"
>>>>>>> #include "vtkXMLUnstructuredGridReader.h"
>>>>>>> #include "vtkUnstructuredGrid.h"
>>>>>>> #include "vtkCPDataDescription.h"
>>>>>>> #include "vtkCPInputDataDescription.h"
>>>>>>> #include "vtkSmartPointer.h"
>>>>>>> #include "vtkPolyData.h"
>>>>>>> #include "vtkSphereSource.h"
>>>>>>>
>>>>>>> #include <stdio.h>
>>>>>>> #include <string>
>>>>>>> #include <sstream>
>>>>>>>
>>>>>>> static unsigned int procId;
>>>>>>>
>>>>>>> void myprint(const std::string& str)
>>>>>>> {
>>>>>>> printf("driver (%u): %s\n", procId, str.c_str());
>>>>>>> }
>>>>>>>
>>>>>>> class DataGenerator {
>>>>>>> public:
>>>>>>>
>>>>>>> DataGenerator()
>>>>>>> {
>>>>>>> this->Sphere = vtkSmartPointer<vtkSphereSource>::New();
>>>>>>> this->Sphere->SetThetaResolution(30);
>>>>>>> this->Sphere->SetPhiResolution(30);
>>>>>>> this->Sphere->SetCenter(procId*4.0, 0, 0);
>>>>>>> this->Index = 0;
>>>>>>> }
>>>>>>>
>>>>>>> vtkSmartPointer<vtkPolyData> GetNext()
>>>>>>> {
>>>>>>> double radius = fabs(sin(0.1 * this->Index));
>>>>>>> this->Index++;
>>>>>>> this->Sphere->SetRadius(1.0 + radius);
>>>>>>> this->Sphere->Update();
>>>>>>> vtkSmartPointer<vtkPolyData> ret =
>>>>>>> vtkSmartPointer<vtkPolyData>::New();
>>>>>>> ret->DeepCopy(this->Sphere->GetOutput());
>>>>>>> return ret;
>>>>>>> }
>>>>>>>
>>>>>>> protected:
>>>>>>>
>>>>>>> int Index;
>>>>>>> vtkSmartPointer<vtkSphereSource> Sphere;
>>>>>>>
>>>>>>>
>>>>>>> };
>>>>>>>
>>>>>>> int main(int argc, char* argv[])
>>>>>>> {
>>>>>>> if (argc < 3)
>>>>>>> {
>>>>>>> printf("Usage: %s <cp python file> <number of steps>\n",
>>>>>>> argv[0]);
>>>>>>> return 1;
>>>>>>> }
>>>>>>>
>>>>>>> std::string cpPythonFile = argv[1];
>>>>>>> int nSteps = atoi(argv[2]);
>>>>>>>
>>>>>>> myprint("starting coprocessor");
>>>>>>>
>>>>>>> vtkCPProcessor* processor = vtkCPProcessor::New();
>>>>>>> processor->Initialize();
>>>>>>> vtkCPPythonScriptPipeline* pipeline =
>>>>>>> vtkCPPythonScriptPipeline::New();
>>>>>>>
>>>>>>> // mpi was initialized when we called
>>>>>>> vtkCPPythonScriptPipeline::New()
>>>>>>> procId =
>>>>>>> vtkMultiProcessController::GetGlobalController()->GetLocalProcessId();
>>>>>>>
>>>>>>>
>>>>>>> // read the coprocessing python file
>>>>>>> myprint("loading pipeline python file: " + cpPythonFile);
>>>>>>> int success = pipeline->Initialize(cpPythonFile.c_str());
>>>>>>> if (!success)
>>>>>>> {
>>>>>>> myprint("aborting");
>>>>>>> return 1;
>>>>>>> }
>>>>>>>
>>>>>>> processor->AddPipeline(pipeline);
>>>>>>> pipeline->Delete();
>>>>>>>
>>>>>>> if (nSteps == 0)
>>>>>>> {
>>>>>>> return 0;
>>>>>>> }
>>>>>>>
>>>>>>> // create a data source
>>>>>>> DataGenerator generator;
>>>>>>>
>>>>>>> // do coprocessing
>>>>>>> double tStart = 0.0;
>>>>>>> double tEnd = 1.0;
>>>>>>> double stepSize = (tEnd - tStart)/nSteps;
>>>>>>>
>>>>>>> vtkCPDataDescription* dataDesc = vtkCPDataDescription::New();
>>>>>>> dataDesc->AddInput("input");
>>>>>>>
>>>>>>> for (int i = 0; i < nSteps; ++i)
>>>>>>> {
>>>>>>>
>>>>>>> double currentTime = tStart + stepSize*i;
>>>>>>> std::stringstream timeStr;
>>>>>>> timeStr << "time(" << i << ", " << currentTime << ")";
>>>>>>>
>>>>>>>
>>>>>>> dataDesc->SetTimeData(currentTime, i);
>>>>>>>
>>>>>>> myprint("call RequestDataDescription, " + timeStr.str());
>>>>>>> int do_coprocessing =
>>>>>>> processor->RequestDataDescription(dataDesc);
>>>>>>>
>>>>>>> if (do_coprocessing)
>>>>>>> {
>>>>>>> myprint("calling CoProcess, " + timeStr.str());
>>>>>>>
>>>>>>> vtkSmartPointer<vtkDataObject> dataObject =
>>>>>>> generator.GetNext();
>>>>>>>
>>>>>>>
>>>>>>> dataDesc->GetInputDescriptionByName("input")->SetGrid(dataObject);
>>>>>>> processor->CoProcess(dataDesc);
>>>>>>> }
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>> myprint("finalizing");
>>>>>>> dataDesc->Delete();
>>>>>>> processor->Finalize();
>>>>>>> processor->Delete();
>>>>>>>
>>>>>>> return 0;
>>>>>>>
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Aug 4, 2010 at 12:14 PM, Andy Bauer <andy.bauer at kitware.com>wrote:
>>>>>>>
>>>>>>>> Hi Jacques,
>>>>>>>>
>>>>>>>> There is a polyhedra cell type in VTK now --
>>>>>>>> http://www.vtk.org/doc/nightly/html/classvtkPolyhedron.html
>>>>>>>> As far as I know it works with all of the proper filters but since I
>>>>>>>> haven't tried it yet I won't promise that. The good news is that Will
>>>>>>>> Schroeder had a high interest in it and probably worked on some of it so I'd
>>>>>>>> assume that it's working quite well right now.
>>>>>>>>
>>>>>>>> As for Phasta, it does run in parallel (as props to their developers
>>>>>>>> it was a finalist for the 2009 Gordon Bell prize). The grid is already
>>>>>>>> partitioned and each process runs the adaptor and creates an unstructured
>>>>>>>> grid from its portion of the partitioned mesh. Thus, there isn't any need
>>>>>>>> for mpi calls in the adaptor code. If you had ghost cell information in
>>>>>>>> your partitioned mesh and wanted to get fancy you should be able to add that
>>>>>>>> to your partitioned grid to make some of the filters faster but I haven't
>>>>>>>> tried that.
>>>>>>>>
>>>>>>>> Andy
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Aug 4, 2010 at 11:58 AM, Jacques Papper <
>>>>>>>> jacques.papper at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Thanks a lot Andy, Takuya,
>>>>>>>>>
>>>>>>>>> I'm using the PhastaAdaptor, and the FortranAdaptorAPI as a guide
>>>>>>>>> for the moment.
>>>>>>>>> I know there were talks of getting POLYHEDRAL cell support in VTK.
>>>>>>>>> Do you know if this is there yet?
>>>>>>>>> My dataset is multiregion unstructured polyhedral mesh domain
>>>>>>>>> decomposed amongst each processor.
>>>>>>>>>
>>>>>>>>> Is the Phasta code parallelized ? If so, I do not see any MPI
>>>>>>>>> statements in the adaptor code ?
>>>>>>>>>
>>>>>>>>> Jacques
>>>>>>>>>
>>>>>>>>> 2010/8/4 Andy Bauer <andy.bauer at kitware.com>
>>>>>>>>>
>>>>>>>>> Hi Jacques,
>>>>>>>>>>
>>>>>>>>>> What type of data set do you have? Even though the PHASTA adaptor
>>>>>>>>>> ( ParaView/CoProcessing/Adaptors/FortranAdaptors/PhastaAdaptor) is for
>>>>>>>>>> fortran code it may give you an idea. Also stepping through the example in
>>>>>>>>>> ParaView/CoProcessing/CoProcessor/Testing/Cxx/PythonScriptCoProcessingExample.cxx
>>>>>>>>>> may help as well.
>>>>>>>>>>
>>>>>>>>>> I'll spend some time this week putting up a skeleton of a
>>>>>>>>>> simulation code on the coprocessing wiki that should hopefully be easier to
>>>>>>>>>> follow. I'll let you know when it's done.
>>>>>>>>>>
>>>>>>>>>> Andy
>>>>>>>>>>
>>>>>>>>>> On Wed, Aug 4, 2010 at 8:02 AM, Jacques Papper <
>>>>>>>>>> jacques.papper at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi All,
>>>>>>>>>>>
>>>>>>>>>>> Sorry for my last post, I figured out that I had wrongly set my
>>>>>>>>>>> PYTHONPATH..
>>>>>>>>>>> All the tests work ok now. Still interested in CoProcessing
>>>>>>>>>>> adaptors examples though :)
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>> Jacques
>>>>>>>>>>>
>>>>>>>>>>> 2010/8/4 Jacques Papper <jacques.papper at gmail.com>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Hi All,
>>>>>>>>>>>>
>>>>>>>>>>>> I'm starting to look into the ParaView CoProcessing libraries.
>>>>>>>>>>>> I just pulled from git today, and compiled it all up following
>>>>>>>>>>>> the guidelines in :
>>>>>>>>>>>> http://www.paraview.org/Wiki/CoProcessing
>>>>>>>>>>>> I didn't find :
>>>>>>>>>>>> *BUILD_PYTHON_COPROCESSING_ADAPTOR
>>>>>>>>>>>> *but instead :
>>>>>>>>>>>> PARAVIEW_BUILD_PLUGIN_CoProcessingScriptGenerator
>>>>>>>>>>>> anyway the compilation went through without any issues.
>>>>>>>>>>>> I then tried :
>>>>>>>>>>>>
>>>>>>>>>>>> ctest -R CoProcessing
>>>>>>>>>>>> Test project /users/boreas01/jacques/PARAVIEW/ParaView-bin
>>>>>>>>>>>> Start 491: CoProcessingTestPythonScript
>>>>>>>>>>>> 1/3 Test #491: CoProcessingTestPythonScript ...........
>>>>>>>>>>>> Passed 0.45 sec
>>>>>>>>>>>> Start 492: CoProcessingPythonScriptGridPlot
>>>>>>>>>>>> 2/3 Test #492: CoProcessingPythonScriptGridPlot
>>>>>>>>>>>> .......***Failed 0.09 sec
>>>>>>>>>>>> Start 493: CoProcessingPythonScriptPressurePlot
>>>>>>>>>>>> 3/3 Test #493: CoProcessingPythonScriptPressurePlot
>>>>>>>>>>>> ...***Failed 0.09 sec
>>>>>>>>>>>>
>>>>>>>>>>>> 33% tests passed, 2 tests failed out of 3
>>>>>>>>>>>>
>>>>>>>>>>>> Total Test time (real) = 0.68 sec
>>>>>>>>>>>>
>>>>>>>>>>>> The following tests FAILED:
>>>>>>>>>>>> 492 - CoProcessingPythonScriptGridPlot (Failed)
>>>>>>>>>>>> 493 - CoProcessingPythonScriptPressurePlot (Failed)
>>>>>>>>>>>> Errors while running CTest
>>>>>>>>>>>>
>>>>>>>>>>>> Is this a problem in my current installation or on the master
>>>>>>>>>>>> branch ?
>>>>>>>>>>>>
>>>>>>>>>>>> Finally, I would like to start writing an adaptor to a C++
>>>>>>>>>>>> parallelised code. Can you tell me what is the closest code I can inspire
>>>>>>>>>>>> myself from ?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you,
>>>>>>>>>>>> Jacques
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> PS sorry mixed up the subjects..
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>> Powered by www.kitware.com
>>>>>>>>
>>>>>>>> Visit other Kitware open-source projects at
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>>>>>>>> Please keep messages on-topic and check the ParaView Wiki at:
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>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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