HDF5File visualization

Question

Which is the currently suggested approach to save in file HDF5 format?

I wish in particular to save multiple functions and multiple time steps to a single file. It seems to me that this is supported looking at the source in dolfin/io/HDF5File.h, e.g.

HDF5File.write(const Function& u, const std::string name, double timestamp)

However, I am not able to visualize the resulting .h5 file in Paraview or Visit. Which viewer do you suggest?

I was used to use the File('u.xdmf') interface, but if I understand correctly the advanced functionality of HDF5File are not supported with this.

I had a look also to the unit tests in dolfin/test/io, but I cannot visualize the resulting .h5 files in paraview. I suppose I miss something. May someone help?

Corrado

Answer 1

You can timestamp files in XDMFFile:

File("u.xdmf") << (u,t)

You will not find a viewer to view output from HDF5File directly This is stored in a special way that will allow for loading of data into dolfin, but not compatible with any viewer.

In short:
- To store data for viewing, use xdmf
- To store data for reloading, use HDF5
- To store data for viewing and reloading, use xdmf and HDF5

Comments

Thanks,

Is there a reason for which the same functionalities as in HDF5File are not supported with the xdmf wrapper? Is this an expected development?

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I'm not sure which functionality you are referring to? The naming of functions in XDMFFile is taken directly from Function, so if you specify your Function as

u = Function(V, name="Velocity")

before storing u to XDMF, this will be reflected in the XDMF-file (instead of default names such as f_48).

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Thanks,

I was referring to the possibility of writing multiple functions to a single file with File("u.xdmf") << (u,t)

If I do it with it with xdmf, the resulting file is not supported by Paraview. Here the message that I obtain in Paraview when I open a file created saving multiple functions:

ERROR: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,

line 754
vtkPVCompositeDataPipeline (0x123558ea0): Algorithm vtkXdmfReader(0x123566640) returned failure for request:
vtkInformation (0x11b3d7a80)
Debug: Off
Modified Time: 856062
Reference Count: 1
Registered Events: (none)
Request: REQUEST_DATA
ALGORITHM_AFTER_FORWARD: 1
FROM_OUTPUT_PORT: 0
FORWARD_DIRECTION: 0




Warning: In /Users/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/Xdmf2/vtkXdmfReader.cxx,
line 407
vtkXdmfReader (0x10e3e2660): Data type generated (vtkMultiBlockDataSet) does not match data type expected
(vtkUnstructuredGrid). Reader may not produce valid data.

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Are you trying to write Functions from different FunctionSpaces/Mesh to the same xdmf file?

If not, it should work fine. The following works for me

mesh = UnitSquareMesh(4,4)
V = FunctionSpace(mesh, "DG", 2)
ufile = File("u.xdmf")
ufile << (Function(V), 0.0)
ufile << (Function(V), 0.1)
ufile << (Function(V), 0.2)
del ufile # Delete file object (or exit program) to avoid data corruption

Using XDMFFile directly will give you access to XDMFFile.parameters, to get better control of the writing.

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Yes, I have one function from a scalar-valued field and one function from a vector-valued field, on the same mesh. Is it supposed to be supported?

I delete the file object, otherwise I have a segfault coming from the hdf5 library.

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This could be supported, or at least throw an exception.

Please report an issue on https://bitbucket.org/fenics-project/dolfin.

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I reported an issue here

There is a problem even with two fields of the same FunctionSpace

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Apparently, an XDMFFile doesn't accept the << operator anymore (in Python at least). One has to use the write function, namely

file.write(u, t)