[Paraview] Structured 3D data with xdmf

[Tobias Brandvik]

Hi,

I've got a simple 3D grid stored in an hdf5 file which I want to view
in Paraview 3.2 using the xdmf reader, but I'm having some problems
getting it to read it. I haven't been able to find any examples that
show how to do this when the geometry data is in the hdf5 file itself,
so I was hoping someone on the list might be able to help me. The
Paraview/HDF5 error message, the xdmf file and the output from h5dump
are included below.


HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
Back trace follows.
  #000: /home/berk/Work/ReleaseBuilds/ParaView3/Utilities/hdf5/H5S.c
line 856 in H5Sget_simple_extent_ndims(): not a data space
    major(01): Function arguments
    minor(03): Inappropriate type
HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
Back trace follows.
  #000: /home/berk/Work/ReleaseBuilds/ParaView3/Utilities/hdf5/H5S.c
line 949 in H5Sget_simple_extent_dims(): not a dataspace
    major(01): Function arguments
    minor(03): Inappropriate type



<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" [
<!ENTITY InitialHeavyData "test.hdf5">
]>

<Xdmf Version="2.0">
<Domain>
<Grid>
<Topology Type="3DSmesh" Dimensions="2 2 2"/>

<Geometry Type="X_Y_Z">
<DataItem Name="bp0" Format="HDF" Dimensions="2 2 2">
test.hdf5:/block0
</DataItem>
<DataItem Name="bp1" Format="HDF" Dimensions="2 2 2">
test.hdf5:/block0
</DataItem>
<DataItem Name="bp2" Format="HDF" Dimensions="2 2 2">
test.hdf5:/block0
</DataItem>
</Geometry>

</Grid>
</Domain>
</Xdmf>



HDF5 "/mnt/pvfs2/test.hdf5" {
   GROUP "block0" {
      DATASET "bp0" {
         DATATYPE  H5T_IEEE_F32BE
         DATASPACE  SIMPLE { ( 2, 2, 2 ) / ( 2, 2, 2 ) }
         DATA {
         (0,0,0): 0, 0.5,
         (0,1,0): 0, 0.5,
         (1,0,0): 0, 0.5,
         (1,1,0): 0, 0.5
         }
      }
      DATASET "bp1" {
         DATATYPE  H5T_IEEE_F32BE
         DATASPACE  SIMPLE { ( 2, 2, 2 ) / ( 2, 2, 2 ) }
         DATA {
         (0,0,0): 0, 0,
         (0,1,0): 0, 0,
         (1,0,0): 1.5, 1.5,
         (1,1,0): 1.5, 1.5
         }
      }
      DATASET "bp2" {
         DATATYPE  H5T_IEEE_F32BE
         DATASPACE  SIMPLE { ( 2, 2, 2 ) / ( 2, 2, 2 ) }
         DATA {
         (0,0,0): 0, 0,
         (0,1,0): 1, 1,
         (1,0,0): 0, 0,
         (1,1,0): 1, 1
         }
      }
   }
}
}

Cheers,
Tobias.

---
Tobias Brandvik
PhD Student
Whittle Laboratory
1 JJ Thomson Avenue
Cambridge CB3 0DY, UK