[vtkusers] Different behavior of vtkXMLPUnstructuredGridWriter in VTK 7.1

Andy Bauer andy.bauer at kitware.com
Mon Feb 19 07:38:58 EST 2018 

If you haven't used the SetStartPiece(), SetEndPiece() and
SetNumberOfPieces() methods in serial that's what is probably missing. In
serial you should be able to use vtkDummyController.



On Mon, Feb 19, 2018 at 4:59 AM, Andrew Parker <
andy.john.parker at googlemail.com> wrote:

> Andy,
>
> I can confirm this now works for my parallel code.  However, I have a
> separate stand-alone serial code (has never had a communicator) which still
> calls the vtkXMLPUnstructuredGridWriter and produces several part/piece
> meshes and one global pvtu file.  This now fails with 7.1.1, same error
> before, only one entry in the pvtu.  I have tried to make the changes noted
> in your demo file (which have worked for my parallel code) but in this
> instance they do not work in my serial code.  I have also tried the
> vtkDummyController as a well as vtkmpicontroller, and have also tried
> explicitly setting the number of (fake) processors: vtk_mpi_controller->
> SetNumberOfProcesses(4);
>
> Could I ask what the recommended way to now use the vtkXMLPUnstructuredGridWriter
> is from a completely serial code where I still wish to write out piece
> meshes (and a corresponding pvtu) and do not have a communicator?  I should
> add this is not threaded code either.  The vtk 7.1.1 build is the same one
> that is now working correctly in my mpi parallel code.
>
> Cheers again,
> Andy
>
> On 6 February 2018 at 13:48, Andy Bauer <andy.bauer at kitware.com> wrote:
>
>> My guess is that you've forgotten:
>>
>> controller->SetGlobalController(controller);
>>
>> Could you also verify that VTK was built with MPI enabled? If you try my
>> example file does that work properly for you with both VTK versions?
>>
>>
>> On Tue, Feb 6, 2018 at 4:49 AM, Andrew Parker <
>> andy.john.parker at googlemail.com> wrote:
>>
>>> Andy,
>>>
>>> To follow up.  So this is a direct copy of my source for writing vtu in
>>> parallel via mpi, no edits:
>>>
>>> vtkSmartPointer<vtkXMLPUnstructuredGridWriter> pwriter =
>>> vtkSmartPointer<vtkXMLPUnstructuredGridWriter>::New();
>>> std::stringstream sss;
>>> sss << outputDirectory << "/";
>>> sss << outputPrefix;
>>> sss << "Parts";
>>> sss << ".pvtu";
>>>
>>> pwriter->SetFileName(sss.str().c_str());
>>> pwriter->SetNumberOfPieces(comms.Size());
>>> if(comms.IsParallel())
>>>   pwriter->SetGhostLevel(1);
>>> pwriter->SetStartPiece(comms.Rank());
>>> pwriter->SetEndPiece(comms.Rank());
>>> pwriter->SetInputData(cellGrid);
>>> // pwriter->SetDataModeToAscii();
>>> pwriter->SetDataModeToBinary();
>>> pwriter->SetCompressorTypeToZLib();
>>> pwriter->Write();
>>>
>>> and for vtp files in parallel via mpi, no edits:
>>>
>>> vtkSmartPointer<vtkXMLPPolyDataWriter> pwriter =
>>> vtkSmartPointer<vtkXMLPPolyDataWriter>::New();
>>> std::stringstream sss;
>>> sss << outputDirectory << "/";
>>> sss << outputPrefix;
>>> sss << bcName << "_";
>>> sss << prefix;
>>> sss << ".pvtp";
>>> std::cout << "Output file name: " << sss.str().c_str() << std::endl;
>>>
>>> pwriter->SetFileName(sss.str().c_str());
>>> pwriter->SetNumberOfPieces(comms->Size());
>>> if(comms->IsParallel())
>>>   pwriter->SetGhostLevel(1);
>>> pwriter->SetStartPiece(comms->Rank());
>>> pwriter->SetEndPiece(comms->Rank());
>>> pwriter->SetInputData(boundingFaceGrids[i]);
>>> pwriter->SetDataModeToBinary();
>>> //pwriter->SetDataModeToAscii();
>>> pwriter->SetCompressorTypeToZLib();
>>> pwriter->Write();
>>>
>>> I initialise the vtk-comms object in an identical way to your demo code,
>>> after my own mpi-comms, and I finalize before I finalize mine.  In between
>>> those calls the above source is called.  All processors partake in all
>>> calls both to init the vtk-mpi and in the above writing.
>>>
>>> Do you have any further thoughts as to the problem?  Problem goes away
>>> if I use 6.3....
>>>
>>> Cheers,
>>> Andy
>>>
>>>
>>> On 5 February 2018 at 18:40, Andrew Parker <
>>> andy.john.parker at googlemail.com> wrote:
>>>
>>>> Andy,
>>>>
>>>> My own code. I’ve always had those Piece lines in my src from day one,
>>>> and always used it via mpi, so don’t need added. All procs call all lines
>>>> in my file writer. There is no if-master-section.  Literally just a vtk
>>>> version number change that causes the problem. Can’t get the data files or
>>>> the cut down source until tomorrow.
>>>>
>>>> I shared the other two links as those in addition to this post are the
>>>> only places I can find that reference such a major change to the library
>>>> that is undocumented and causes such a significant change to user code. Are
>>>> there any further references on this change that I can read about to try to
>>>> resolve this?
>>>>
>>>> I find it strange that this has not come up more. It would mean all
>>>> users of 7.1 without the additional vtkmpicontroller lines would fail when
>>>> calling a parallel writer from a parallel mpi-user-code....
>>>>
>>>> Cheers,
>>>> Andy
>>>>
>>>> On Mon, 5 Feb 2018 at 18:07, Andy Bauer <andy.bauer at kitware.com> wrote:
>>>>
>>>>> Are you using libMesh or another simulation code? You'll definitely
>>>>> need the following to tell each process what piece it has:
>>>>> pwriter->SetNumberOfPieces(nprocs);
>>>>>
>>>>> pwriter->SetStartPiece(rank);
>>>>>
>>>>> pwriter->SetEndPiece(rank);
>>>>>
>>>>> pwriter->Write();
>>>>>
>>>>> Can you share the portion of your code that uses
>>>>> vtkXMLPUnstructuredGridWriter? Also, looking at the data files from 6.3 and
>>>>> 7.1.1 may help.
>>>>>
>>>>> Thanks,
>>>>> Andy
>>>>>
>>>>>
>>>>> On Mon, Feb 5, 2018 at 12:08 PM, Andrew Parker <
>>>>> andy.john.parker at googlemail.com> wrote:
>>>>>
>>>>>> Andy,
>>>>>>
>>>>>> Just moved from vtk 6.3.0 to vtk 7.1.1.  Cannot for the life of me
>>>>>> get your modifications to work from your vtk_test.C.  I've included the
>>>>>> vtkmpiController stuff after I init mpi myself.  I found the migration
>>>>>> problem mentioned here:
>>>>>>
>>>>>> https://github.com/libMesh/libmesh/issues/1179
>>>>>>
>>>>>> and here:
>>>>>>
>>>>>> https://gitlab.kitware.com/vtk/vtk/issues/16924
>>>>>>
>>>>>> as well as this post.  My parallel unstructured grid now only
>>>>>> contains one source within the piece section of the pvtu, as opposed to
>>>>>> n-processor sources (all processors have real data to write and this is not
>>>>>> a case of empty meshes on these processors).  I can re-link and recompile
>>>>>> against 6.3 and the problem goes away and I get the correct number of
>>>>>> sources written to the pvtu file as before.  Can you help?  I make
>>>>>> extensive use of pvtu files from my mpi-based code and now all grid files
>>>>>> (pvtu and pvtp) have stopped working just by moving to 7.1.1 (which has
>>>>>> been built with mpi-enabled).
>>>>>>
>>>>>> Any thoughts?
>>>>>>
>>>>>> Thanks,
>>>>>> Andy
>>>>>>
>>>>>>
>>>>>> On 6 December 2016 at 16:12, Andy Bauer <andy.bauer at kitware.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi John,
>>>>>>>
>>>>>>> The issue is indeed due to changes that I mentioned before (i.e.
>>>>>>> only data sets that have data get written out and the .pvtu file is
>>>>>>> adjusted accordingly). With this change though interprocess communication
>>>>>>> is required which is done the the vtkMultiProcessController::GetGlobalController()
>>>>>>> object which essentially acts as MPI_COMM_WORLD within VTK. You need to
>>>>>>> create a vtkMPIController which derives from vtkMultiProcessController. See
>>>>>>> the attached files for how that is done. This should also be backwards
>>>>>>> compatible but if it isn't, please let us know.
>>>>>>>
>>>>>>> Best,
>>>>>>> Andy
>>>>>>>
>>>>>>> ps. Ignore the ADIOS stuff in there (it's commented out). I was
>>>>>>> trying to do two things at once and that's why the ADIOS stuff is in the
>>>>>>> CMakeLists.txt.
>>>>>>>
>>>>>>> On Mon, Dec 5, 2016 at 6:06 PM, John Peterson <jwpeterson at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Dec 5, 2016 at 12:45 PM, Andy Bauer <andy.bauer at kitware.com
>>>>>>>> > wrote:
>>>>>>>>
>>>>>>>>> Beyond this I can't think of any change off the top of my head
>>>>>>>>> that would cause your issue. I looked at the repo but can't figure out the
>>>>>>>>> VTK configurations from that. If you can share a simple test case which
>>>>>>>>> demonstrates the issue I may be able to easily diagnose it.
>>>>>>>>>
>>>>>>>>
>>>>>>>> Here's a standalone test code that reproduces the issue for me:
>>>>>>>>
>>>>>>>> https://gist.github.com/jwpeterson/92f4b8422d6fbb1056e848c9b14ee1d7
>>>>>>>>
>>>>>>>> Run on two procs with: mpiexec -np 2 and I get the following
>>>>>>>> test.pvtu file:
>>>>>>>>
>>>>>>>> <?xml version="1.0"?>
>>>>>>>>> <VTKFile type="PUnstructuredGrid" version="0.1"
>>>>>>>>> byte_order="LittleEndian" header_type="UInt32"
>>>>>>>>> compressor="vtkZLibDataCompressor">
>>>>>>>>>   <PUnstructuredGrid GhostLevel="1">
>>>>>>>>>     <PPointData>
>>>>>>>>>       <PDataArray type="Float64" Name="u"/>
>>>>>>>>>     </PPointData>
>>>>>>>>>     <PCellData>
>>>>>>>>>       <PDataArray type="Int32" Name="elem_id"/>
>>>>>>>>>       <PDataArray type="Int32" Name="subdomain_id"/>
>>>>>>>>>       <PDataArray type="Int32" Name="processor_id"/>
>>>>>>>>>     </PCellData>
>>>>>>>>>     <PPoints>
>>>>>>>>>       <PDataArray type="Float64" Name="Points"
>>>>>>>>> NumberOfComponents="3"/>
>>>>>>>>>     </PPoints>
>>>>>>>>>     <Piece Source="test_0.vtu"/>
>>>>>>>>>   </PUnstructuredGrid>
>>>>>>>>> </VTKFile>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> As you can see, only one "Piece Source" is listed, but the output
>>>>>>>> of the program is actually all 3 files (test.pvtu, test_0.vtu, test_1.vtu)
>>>>>>>> and both the _0 and _1 files have nodes in them.  Furthermore, if I simply
>>>>>>>> add a second "Piece Source" line corresponding to "test_1.vtu", the whole
>>>>>>>> thing opens up just fine in Paraview.  I am a novice VTK programmer so it's
>>>>>>>> very possible I'm doing something wrong, but this code definitely worked in
>>>>>>>> VTK 6.x, and 7.0.
>>>>>>>>
>>>>>>>> Thanks for your help,
>>>>>>>> John
>>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
>>>>>
>>>
>>
>
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