­

How to write VTK files in parallel

By 5:24 AM , , , , , , , ,



Writing a VTK file in Serial mode tutorials can be found on VTK example page and many various websites. However, a detailed example on how to output solution files in parallel (i.e. MPI) is almost nonexistent. The only related example can be found on VTK Wiki page, but it is incomplete and misleading. So we wanted share a tutorial on this post. If you find this example too basic or trivial, please contact us for more complex examples. We will be sharing an updated version of this post with our in-house developed library "PAVLOV" in the future.

The following example shows how to write an unstructured grid VTK file (.pvtu) in parallel using MPI:
In this tutorial, the goal is to output a data file in VTK format where each processor generates its own data from its partition. (4 processors were used) .

We start with initializing MPI as usual;

int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
view raw vtk_1.cpp hosted with ❤ by GitHub

Then each processor defines its own point and cell array as if it is in serial mode. Then while writing its own grid file from its partition in ".vtu" format, the naming convention becomes important. The figures below show each vtu file separately.






 


















    

      

        

  

    
    


        



  


  

        

          
            if(mpi_rank==0){
        

        

          
            writer->SetFileName("Voxel_0.vtu");
        

        

          
            }
        

        

          
            if(mpi_rank==1){
        

        

          
            writer->SetFileName("Voxel_1.vtu");
        

        

          
            }
        

        

          
            if(mpi_rank==2){
        

        

          
            writer->SetFileName("Voxel_2.vtu");
        

        

          
            }
        

        

          
            if(mpi_rank==3){
        

        

          
            writer->SetFileName("Voxel_3.vtu");
        

        

          
            }
        

        

          
          #if VTK_MAJOR_VERSION <= 5
        

        

          
            writer->SetInput(unstructuredGrid);
        

        

          
          #else
        

        

          
            writer->SetInputData(unstructuredGrid);
        

        

          
          #endif
        

        

          
            writer->Write();
        

  





    


  




      

      

        view raw
        
          vtk_2.cpp
        
        hosted with ❤ by GitHub
      

    





Here each processor should give a file name with "filename_(mpi_rank).vtu" which will hint the "filename.pvtu" in which files it should merge while visualizing in an visualization software (i.e. Paraview, VisIt). 








Finally, the most important step is the writing the ".pvtu" file by a single processor (which can be root, where mpi_rank=0), which help to "stitch" all individual files into a unified handler and used as the main file to be opened by the visualization software. 










 



    

      

        

  

    
    


        



  


  

        

          
            if(mpi_rank==0){
        

        

          
            vtkSmartPointer pwriter = vtkSmartPointer::New();
        

        

          
            pwriter->SetFileName("Voxel.pvtu");
        

        

          
            pwriter->SetNumberOfPieces(mpi_size);
        

        

          
            #if VTK_MAJOR_VERSION <= 5
        

        

          
            pwriter->SetInput(unstructuredGrid);
        

        

          
            #else
        

        

          
            pwriter->SetInputData(unstructuredGrid);
        

        

          
            #endif
        

        

          
            pwriter->Write();
        

        

          
            }
        

  





    


  




      

      

        view raw
        
          vtk_3.cpp
        
        hosted with ❤ by GitHub
      

    





After importing the main ".pvtu" file, one can see below that all the partitions show up as single unified mesh.






















As a final remark, the main motivation behind writing the output files in parallel comes down to Amdahl's law which states that the maximum speedup a parallel software can achieve is limited by the fraction of serial portion it has. Thus, parallel VTK effectively decreases this serial portion of a software (which is usually non-negligible) and helps it to scale up better.









We are including all the source file that is used to generate this example on our github page (click DOWNLOAD , follow the link and click download on the github page). Once downloaded, please refer to the readme inside the tarball for compile and run instructions.















































,
,
,
,
,
,
,
,

















You Might Also Like




















11
comments












  1. IkeJuly 29, 2013 at 7:01 PM
    Hi, Naoki 

    Could you share all the modifications you made on the code?

    Thanks,
    ReplyDelete
  2. AnonymousDecember 13, 2013 at 5:40 AM
    Hi, 

    Thank you for the impressive example. I want to know whether the same thing can be used for vtk image data just be replacing the unstructured vtk header files with vtk image data headers ?
    ReplyDelete
  3. AnonymousOctober 21, 2014 at 4:36 AM
    Hi,

    Thank you very much! This was very helpful.
    ReplyDelete
  4. UnknownDecember 10, 2015 at 8:52 PM
    Hi, 

    Great tutorial, just wanted to let you know you can also achieve this with the parallel file writers that vtk provides (i.e. vtkXMLPUnstructuredGridWriter)
    ReplyDelete
  5. AlexanderJanuary 26, 2016 at 6:39 AM
    Hello!
    I could not download the source. 
    Could you please re enable it?
    Thank you! 
    ReplyDelete
  6. AnonymousFebruary 19, 2016 at 9:01 PM
    Hi,

    I have a question that how to build VTK with CMake for parallel computing?

    Thank you!
    ReplyDelete
  7. KubaApril 26, 2016 at 9:21 AM
    Hi,
    Could you please refresh a link for download source code?
    Regards
    Kuba
    ReplyDelete
  8. AnonymousNovember 27, 2024 at 11:56 AM
    Cool and that i have a tremendous give: Who Repairs House Windows remodel old house
    ReplyDelete