[vtkusers] Different behavior of vtkXMLPUnstructuredGridWriter in VTK 7.1
Andy Bauer
andy.bauer at kitware.com
Mon Feb 19 08:47:42 EST 2018
You need to have a single call to pwriter->Write() with all of the pieces
set in a single pass, otherwise the .pvtu file will overwrite each time.
This looks like:
pwriter->SetNumberOfPieces((int)nparts);
pwriter->SetGhostLevel(1);
pwriter->SetStartPiece(0);
pwriter->SetEndPiece((int)part-1);
If you're not generating pieces in your pipeline then you'll probably need
to merge your pieces into a single unstructured grid before calling the
XMLPUnstructuredGridWriter.
On Mon, Feb 19, 2018 at 7:51 AM, Andrew Parker <andrew.parker at cantab.net>
wrote:
> I'm using the following in the serial code:
>
> pwriter->SetNumberOfPieces((int)nparts);
> pwriter->SetGhostLevel(1);
> pwriter->SetStartPiece((int)part);
> pwriter->SetEndPiece((int)part);
>
> My writer function in which the above code is called is called "nparts"
> times, where part goes from 0->(nparts-1).
>
> For the dummy controller, and nparts=4, I have:
>
> vtkSmartPointer<vtkDummyController> vtk_mpi_controller;
> vtk_mpi_controller = vtkSmartPointer<vtkDummyController>::New();
> vtk_mpi_controller->Initialize(&argc, &argv, 1);
> vtk_mpi_controller->SetGlobalController(vtk_mpi_controller);
> vtk_mpi_controller->SetNumberOfProcesses(4);
> ....
> vtk_mpi_controller->Finalize(1);
>
> resulting bottom half of the pvtu reads:
>
> </PCellData>
> <PPoints>
> <PDataArray type="Float64" Name="Points" NumberOfComponents="3"/>
> </PPoints>
> <Piece Source="input_3.vtu"/>
> </PUnstructuredGrid>
> </VTKFile>
>
> Any thoughts?
> Cheers,
> Andy
>
>
> On 19 February 2018 at 12:38, Andy Bauer <andy.bauer at kitware.com> wrote:
>
>> 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/92f4b8422d6fbb1056e848c9b
>>>>>>>>>> 14ee1d7
>>>>>>>>>>
>>>>>>>>>> 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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