[Paraview] problem in defining vtkStructuredGrid in MPI

Fri Jun 26 09:56:51 EDT 2015

Hi,

Thanks for your help. Actually, every processor has its own data and i am
just using the interior regions (so, it does not overlap, no ghost or halo
regions). Anyway, after my initial mail, i changed the SetExtent part of
the code as

  sg->SetExtent (*nxstart-2, *nxend-2, *nystart-2, *nyend-2, 0, 0);

because it was starting from 1 in each direction, now it starts from zero.
This modification fixes the mismatch problem in the number of points comes
from Paraview and seen in the C++ code. On the other hand, the Paraview
still complains about the following extents (seems that the inner boundary
of the 2 x 2 decomposition elements, like ghost region).

    0 140  57 58  0 0
    70 71  0 57  0 0
    70 71  58 114  0 0

You can find the data in the attached file (data_00.tar.gz).

Then, i tried to put the individual parts of the structured grid into the
vtkMultiBlockDataSet using following code

  //
  // Create multi block grid
  //
  vtkMultiBlockDataSet* grid = vtkMultiBlockDataSet::New ();
  grid->SetNumberOfBlocks(*mpiSize);
  grid->SetBlock (*mpiRank, sg.GetPointer());

and write the grid information to the file (data_01.tar.gz). In this case,
Paraview could open the *.vtm file without any message. So, i could not be
sure about the grid. It seems fine if i look at multi block data file
(vtm) but not in pvts file.

Regards,

--ufuk

> Do you have a node partitioning of your grid? If you do you really need a
> cell partitioning of the grid which will have multiple points a the
> partition overlap.
>
> Can you share your data?
>
> On Fri, Jun 26, 2015 at 5:58 AM, <u.utku.turuncoglu at be.itu.edu.tr> wrote:
>
>> Hi,
>>
>> I am trying to create structured grid in an MPI application and i am
>> using
>> following C++ code to implement it
>>
>> extern "C" void createstgrid_(double* y, double* x,
>>                               int* nxstart, int* nxend, int* nystart,
>> int*
>> nyend,
>>                               int* nx, int* ny, int* nz, int* mpiSize,
>> int* mpiRank) {
>>   //
>>   // Create structured grid
>>   //
>>   vtkSmartPointer<vtkStructuredGrid> sg =
>> vtkSmartPointer<vtkStructuredGrid>::New();
>>   sg->SetExtent (*nxstart-1, *nxend-1, *nystart-1, *nyend-1, 0, 0);
>>
>>   //
>>   // Create data structure to store grid coordinates
>>   //
>>   int pnx = ((*nxend)-(*nxstart))+1;
>>   int pny = ((*nyend)-(*nystart))+1;
>>   vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
>>
>>   //
>>   // Insert grid coordinate data as points
>>   //
>>   k = 0;
>>   for (int j = 0; j < pny; j++) {
>>     for (int i = 0; i < pnx; i++) {
>>       points->InsertPoint(k, x[i+j*pnx], y[i+j*pnx], 0);
>>       k = k+1;
>>     }
>>   }
>>   sg->SetPoints(points);
>>
>>   //
>>   // Set grid
>>   //
>>
>> vtkCPPythonAdaptorAPI::GetCoProcessorData()->GetInputDescriptionByName("input")->SetGrid(sg);
>>
>> vtkCPPythonAdaptorAPI::GetCoProcessorData()->GetInputDescriptionByName("input")->SetWholeExtent(0,
>> *nx-1, 0, *ny-1, 0, 0);
>> }
>>
>> so, when i run the code with grid writer, it creates the individual file
>> (*.vts) for each processor and one extra for the combination (*.pvts).
>> Anyway, the individual files looks fine in Paraview but if i open the
>> file
>> with pvts extension, i am getting following error,
>>
>> ERROR: In
>>
>> /Users/turuncu/Qsync/progs/paraview-4.3.1/src/VTK/IO/XML/vtkXMLPStructuredDataReader.cxx,
>> line 461
>> vtkXMLPStructuredGridReader (0x7f961c0910a0): No available piece
>> provides
>> data for the following extents:
>> 0 140  0 1  0 0
>> 0 1  1 58  0 0
>> 0 140  58 59  0 0
>> 0 1  59 114  0 0
>> 71 72  1 58  0 0
>> 71 72  59 114  0 0
>>
>> The UpdateExtent cannot be filled.
>>
>> What is the meaning of this message? It means that some of the grid data
>> (or points) are not filled by the code. I also check the loop in the C++
>> code and print out the number of points for each processor
>>
>> 0 number of points = 4118
>> 1 number of points = 4047
>> 2 number of points = 4060
>> 3 number of points = 3990
>>
>> and the total is 16215, which is consistent with the size of the grid
>> but
>> if i check the individual vts files from the Paraview, the files shows
>> different number of points for each file
>>
>> 0 number of points = 4118
>> 1 number of points = 3976
>> 2 number of points = 4002
>> 3 number of points = 3864
>>
>> So, only first file matchs with the C++ code but others not. I am not
>> sure
>> what is happening in there and if you have any suggestion that will be
>> great.
>>
>> Anyway, in this case i did not use vtkMultiBlockDataSet but after having
>> correct representation of the grid, i am planing use SetBlock method of
>> vtkMultiBlockDataSet to assign decomposition elements as individual
>> blocks.
>>
>> Regards,
>>
>> --ufuk
>>
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