How to use paraview to open this open source hdf5 file, is the version of the problem?

ParaView Support
1

I would appreciate your help with the following questions!
I am reproducing an open source project on gihub( sukjulian/segnn-hemodynamics: Implementation accompanying our FIMH 2023 paper (github.com)) and the author declares to open its hdf5 dataset with paraview. This is a dataset obtained from CFD simulation, when I open it with paraview, the software only gives two readers, i.e. Visit Chombo Reader and Visit Tetrad Reader. theoretically this dataset belongs to Chombo, but I tried both and the software reports errors, among which the chombo The errors are reported as follows:

ERROR: In C:\glr\builds\paraview\paraview-ci\build\superbuild\paraview\build\Utilities\VisItBridge\databases\vtkVisItChomboReader.cxx, line 135
vtkVisItChomboReader (000002E30FBB3ED0): The selected database type was not correct for the given file.  The message from the database was Cannot be a Chombo file, does not have Chombo_global

ERROR: In C:\glr\builds\paraview\paraview-ci\build\superbuild\paraview\src\VTK\Common\ExecutionModel\vtkExecutive.cxx, line 753
vtkPVCompositeDataPipeline (000002E311D4CCF0): Algorithm vtkFileSeriesReader(000002E318D98620) returned failure for request: vtkInformation (000002E319D29ED0)
  Debug: Off
  Modified Time: 301643
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FORWARD_DIRECTION: 0
  ALGORITHM_AFTER_FORWARD: 1



ERROR: In C:\glr\builds\paraview\paraview-ci\build\superbuild\paraview\src\Utilities\VisItBridge\databases\AvtAlgorithms\vtkAvtSTMDFileFormatAlgorithm.cxx, line 127
vtkVisItChomboReader (000002E30FBB3ED0): Unable to find any meshes

ERROR: In C:\glr\builds\paraview\paraview-ci\build\superbuild\paraview\src\VTK\Common\ExecutionModel\vtkExecutive.cxx, line 753
vtkPVCompositeDataPipeline (000002E311D4CCF0): Algorithm vtkFileSeriesReader(000002E318D98620) returned failure for request: vtkInformation (000002E319D29ED0)
  Debug: Off
  Modified Time: 301643
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FORWARD_DIRECTION: 0
  ALGORITHM_AFTER_FORWARD: 1



ERROR: In C:\glr\builds\paraview\paraview-ci\build\superbuild\paraview\src\Utilities\VisItBridge\databases\AvtAlgorithms\vtkAvtSTMDFileFormatAlgorithm.cxx, line 127
vtkVisItChomboReader (000002E30FBB3ED0): Unable to find any meshes

ERROR: In C:\glr\builds\paraview\paraview-ci\build\superbuild\paraview\src\VTK\Common\ExecutionModel\vtkExecutive.cxx, line 753
vtkPVCompositeDataPipeline (000002E311D4CCF0): Algorithm vtkFileSeriesReader(000002E318D98620) returned failure for request: vtkInformation (000002E319D29ED0)
  Debug: Off
  Modified Time: 301643
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FORWARD_DIRECTION: 0
  ALGORITHM_AFTER_FORWARD: 1

I also used matlab to look at the data structure inside:

Group '/sample-0000' 
        Dataset 'face' 
            Size:  3x43402
            MaxSize:  3x43402
            Datatype:   H5T_IEEE_F32LE (single)
            ChunkSize:  []
            Filters:  none
            FillValue:  0.000000
        Dataset 'inlet_idcs' 
            Size:  1472
            MaxSize:  1472
            Datatype:   H5T_STD_I32LE (int32)
            ChunkSize:  []
            Filters:  none
            FillValue:  0
        Dataset 'lumen_wall_idcs' 
            Size:  18960
            MaxSize:  18960
            Datatype:   H5T_STD_I32LE (int32)
            ChunkSize:  []
            Filters:  none
            FillValue:  0
        Dataset 'outlets_idcs' 
            Size:  1271
            MaxSize:  1271
            Datatype:   H5T_STD_I32LE (int32)
            ChunkSize:  []
            Filters:  none
            FillValue:  0
        Dataset 'pos_tets' 
            Size:  3x236575
            MaxSize:  3x236575
            Datatype:   H5T_IEEE_F32LE (single)
            ChunkSize:  []
            Filters:  none
            FillValue:  0.000000
        Dataset 'pressure' 
            Size:  236575
            MaxSize:  236575
            Datatype:   H5T_IEEE_F32LE (single)
            ChunkSize:  []
            Filters:  none
            FillValue:  0.000000
        Dataset 'surface_idcs' 
            Size:  21703
            MaxSize:  21703
            Datatype:   H5T_STD_I32LE (int32)
            ChunkSize:  []
            Filters:  none
            FillValue:  0
        Dataset 'tets' 
            Size:  4x1402652
            MaxSize:  4x1402652
            Datatype:   H5T_STD_I32LE (int32)
            ChunkSize:  []
            Filters:  none
            FillValue:  0
        Dataset 'velocity' 
            Size:  3x236575
            MaxSize:  3x236575
            Datatype:   H5T_IEEE_F32LE (single)
            ChunkSize:  []
            Filters:  none
            FillValue:  0.000000
        Dataset 'wss' 
            Size:  3x21703
            MaxSize:  3x21703
            Datatype:   H5T_IEEE_F32LE (single)
            ChunkSize:  []
            Filters:  none
            FillValue:  0.000000
2

Please share the dataset you are trying to open, I dont see any in the github link.

3

Sorry, I forgot to upload the dedicated link to the dataset, which is hidden by the author in the github link. I apologize for my ignorance and I greatly appreciate your eagerness to help. Here is the link to the dataset: lumen_tiny.hdf5 - Google Cloud Drive

4

Indeed, HDF5 is not a format, just a container and the github user never specify the format. No idea how it was opened. Ask the person ?

5

Follow the instructions in the Getting started section of segnn-hemodynamics and execute the following command
python main.py --num_epochs 0
This will output

  • visuals_idx_000018.vtu
  • visuals_idx_000019.vtu

which can be loaded into ParaView.

1 Like