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Intro_paraview.md

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Introduction to ParaView

  • Visualization program
  • Developed by Kitware
  • OpenSource
  • Competing with VisIt (developed by LLNL)
  • For POST-processing
    • Not for pre-processing: Not mesher!
  • Multiple processor support
    • mpiexec is included in binary distribution
    • But not for multiple nodes
  • Batch job capability
    • pvbatch/pvpython

Feature

  • All kinds of plotting
    • 2D bar/line/histogram chart
    • 2D/3D Mesh
      • Mesh data from commercial/open source FEM/FVM
    • Particle Data
      • Not rendered as sphere image
  • User customization
    • Paraview must be built from source package
  • Can generation movie/animation

VTK file format

  • Standard files for ParaView
  • Supported in many other visualization programs as well
  • ASCII or binary
  • Can define particles, meshes of 2D/3D
  • VTM
    • Multi-block version of VTK
      • This is different from legacy VTK
      • XML format
      • Actual data are stored in the linked VTU or other partitioned files
    • VTU
      • XML VTK file format for unstructured grid
  • Examples - Read some data (xmf or CAS) then save as vtm in Paraview using ASCII format
$ more ccc.vtm
<VTKFile type="vtkMultiBlockDataSet" version="1.0" byte_order="LittleEndian" header_type="UInt64">
  <vtkMultiBlockDataSet>
    <Piece index="0" name="Grid_2">
      <DataSet index="0" file="ccc/ccc_0_0.vtu">
      </DataSet>
      <DataSet index="1" file="ccc/ccc_0_1.vtu">
      </DataSet>
    </Piece>
  </vtkMultiBlockDataSet>
</VTKFile>
$ more ccc/ccc_0_0.vtu 
<VTKFile type="UnstructuredGrid" version="2.0" byte_order="LittleEndian" header_type="UInt64">
  <UnstructuredGrid>
    <Piece NumberOfPoints="5000" NumberOfCells="5000">
      <PointData Scalars="dmg" GlobalIds="___D3___GlobalNodeIds">
        <DataArray type="Float64" Name="dmg" format="ascii" RangeMin="0" RangeMax="0">
          0 0 0 0 0 0
          0 0
        </DataArray>
        <DataArray type="UInt8" Name="vtkGhostType" format="ascii" RangeMin="0" RangeMax="0">
…

Multi-core visualization

  • Settings -> General -> Multi-core support -> Adjust core numbers
  • Close paraview and restart
  • Load file. Then go to Filters -> D3
  • Some file formats might not be supported

Tracing

  • Similar to VB in Excel or journaling in FEM packages
  • Edit the script and rerun as pvbatch --use-offscreen-rendering batch.py
    • pvbatch is a customized python by ParaView, enclosed in the pre-built package
    • 4.0 has a bug and re-locate “WriteImage()” function to the bottom

Batch/distributed visualization

  • Not recommended but use it at your own risk
    • VisIt would be recommended for batch distributed visualization
  • Recompilation of source might be necessary
  • Add server/connect allows only one node connection
  • For multiple nodes connection, write a pvsc file and “load servers”
    • Submit a batch script running mpirun -np $SLURM_NPROCS pvserver
    • Prepare .pvsc file and add the name of computing nodes. Then “load servers”
<Servers>
<Server name="case1" resource="cs://server1.aaa.bbb//server2.ccc.ddd">
    <ManualStartup />
 </Server>
</Servers>
  • Open a paraview from a separate terminal. When paraview is terminated or disconnects the computing node, the batch job will be terminated as well

Running mpi from GUI

  • Edit-> Setting -> adjust mpi rank number. Restart paraview
  • Now paraview will use multiple ranks
  • However, loading large scale models may trigger the violation of 32bit integer limit
    • Visualizing small models might be beneficial
    • For large scale models, use pvserver on localhost
    • From a separate terminal, run mpirun -np 8 pvserver
    • On Paraview GUI, connect server -> localhost
      • Now large scale model can be visualized successfully