[vtkusers] MPI application writing PVTI

Thu Jun 11 16:45:06 EDT 2015

Hi Alejandro,

I will check this out soon. To make sure that I understand, when you write
out the data stored in the trivial producer using vtkXMLPImageDataWriter,
the extent in the pvti file is wrong. Did I get that right?

Best,
-berk

On Thu, Jun 4, 2015 at 7:43 AM, Alejandro Fernández <
alejandro.fernandez at bsc.es> wrote:

>  Hi Berk,
>
> Thanks a lot for your help. Now the whole extent in the .pvti file is
> correct.
>
> However, since I upgraded from VTK 6.0 to VTK 6.2, the extent information
> in the PVTI file contains only the extent information of the piece 0 (since
> only process 0 writes the .pvti file). If I add them manually in the PVTI
> file, paraview opens it perfectly (although the extents have to overlap in
> one point, even if the information in the pieces is completely disjoint,
> otherwise paraview complains).
>
> Here I attach my original .pvti file and the one manually fixed, as well
> as the piece VTI files.
>
> Thank you very much for your time and attention,
>
> --
>
> Alejandro Fernández Suárez
> Computer Science Dept.
> K2M Building - Room 104 - (+34) 934 137 529
> Barcelona Supercomputing Center - CNSwww.bsc.es
>
> On 03/06/2015 16:33, Berk Geveci wrote:
>
> Hi Alejandro,
>
>  (I CCed the mailing list to share the knowledge)
>
>  (Note that you need VTK 6.2 or later for what I am about to describe.)
>
>  What you have is almost correct. You just need a way for the whole
> extent information to get to the writer. So do this:
>
>  vtkNew<vtkTrivialProducer> tp;
> tp->SetOutput(imageData);
> tp->SetWholeExtent(0, msx-1, 0, msy-1, 0, msz-1);
>
>  writer->SetInputConnection(tp->GetOutputPort());
>
>  By the way, SetInputData() does almost exactly this except that it has
> no way of setting the whole extent.
>
>  Best,
> -berk
>
> On Tue, Jun 2, 2015 at 12:28 PM, Alejandro Fernández <
> alejandro.fernandez at bsc.es> wrote:
>
>>  Thanks for your answer!
>>
>> I used the vtkXMLPImageDataWriter to write my .pvti file only with MPI
>> process 0. However, I can not find a way to specify the whole extent of the
>> .pvti file separately from the extent of each piece. My domains are
>> patitioned along the Z axis (third) component. But the writer seems to
>> implicitly partition the Y axis and I do not know how to specify it
>> separately. Please, can you tell me if there is any way to do so? Here is
>> the structure of my code:
>>
>> vtkSmartPointer<vtkImageData> imageData =
>> vtkSmartPointer<vtkImageData>::New();
>> imageData->SetExtent(0, msx-1, 0, msy-1, zstart, zend); // zstart and
>> zend vary depending on MPI process
>> imageData->SetSpacing(hx, hy, hz);
>>
>> vtkSmartPointer<VtkFloatArray> sf = vtkSmartPointer<VtkFloatArray>::New();
>> sf->SetNumberOfComponents(nDims);
>> sf->SetNumberOfTuples(msx*msy*(zend-zstart+1));
>> ... loop
>>             sf->SetTuple(tupleCount++, field_data);
>> ...
>>
>> imageData->GetPointData()->AddArray(sf);
>>
>> vtkSmartPointer<vtkXMLPImageDataWriter> writer =
>> vtkSmartPointer<vtkXMLPImageDataWriter>::New();
>>
>> // I would expect a way to specify the "whole extent" here
>> // This does not work
>> http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_SetWholeExtent
>> if (world->rank() != 0)  writer->WriteSummaryFileOff();
>> writer->SetNumberOfPieces(world->size());
>> writer->SetEndPiece(world->rank());
>> writer->SetStartPiece(world->rank());
>>
>> writer->SetFileName("output.pvti");
>> writer->SetInputData(imageData);
>> writer->Write();
>>
>> Thanks a lot!
>>
>> --
>>
>> Alejandro Fernández Suárez
>> Computer Science Dept.
>> K2M Building - Room 104 - (+34) 934 137 529
>> Barcelona Supercomputing Center - CNSwww.bsc.es
>>
>>   On 01/06/2015 19:52, Shawn Waldon wrote:
>>
>>  One of the key things to realize about the vtkXMLP*Writers is that the
>> writer makes no assumptions when used in parallel.  The P is for Piece not
>> Parallel, so you have to tell it how many pieces total are being written.
>> You also have to tell it the start and end piece numbers for each process
>> (probably just the process id).  Otherwise it defaults to  one total piece
>> and each process thinks it is writing piece 0 so the file gets clobbered
>> when all the processes try to write it.  See the vtkXMLPDataWriter
>> documentation [1] for details on how to set these options.
>>
>>  HTH,
>>  Shawn
>>
>> [1]: http://www.vtk.org/doc/nightly/html/classvtkXMLPDataWriter.html
>>
>> On Mon, Jun 1, 2015 at 1:15 PM, Berk Geveci <berk.geveci at kitware.com>
>> wrote:
>>
>>> The easiest thing is to use vtkXMLPImageDataWriter in parallel to write
>>> an example and then to follow that template.
>>>
>>>  Best,
>>> -berk
>>>
>>> On Thu, May 28, 2015 at 2:20 PM, Alejandro Fernández <
>>> alejandro.fernandez at bsc.es> wrote:
>>>
>>>> Hello everyone,
>>>>
>>>> I have a C++ MPI application that writes the results of a
>>>> domain-decomposed mesh in different VTI files. Each process writes its own
>>>> VTI file with the points corresponding to its domain. In order to group all
>>>> VTI files into a single 3D image in paraview, I want to produce a single
>>>> PVTI file using XMLPImageDataWriter. However, I have not found any example
>>>> and do not know how to achieve this result with just the raw class method
>>>> documentation.
>>>>
>>>> Please, can somebody provide me a C++ example or point me to the
>>>> required documentation?
>>>>
>>>> Thank you very much, your help will be much appreciated.
>>>>
>>>> --
>>>>
>>>> Alejandro Fernández Suárez
>>>> Computer Science Dept.
>>>> K2M Building - Room 104 - (+34) 934 137 529
>>>> Barcelona Supercomputing Center - CNS
>>>> www.bsc.es
>>>>
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