[Paraview] xdmf X_Y_Z format

[Jerry Clarke]

Tobias,

You've run into a bug in Xdmf that has been fixed.
The problem is with XdmfHDF.cxx when not compiled with MPI.
You can :
	1. Compile with MPI - probably not what you want
	2. Edit XdmfHDF.cxx - asking for trouble
	3. Get a current version of XDMF - I think you can go
		into Utilities/Xdmf/libsrc and just "cvd up -d".
Also, just to be picky,
	<Geometry Type="3DSMESH" ...
should really be :
	<Geometry GeometryType="3DSMESH ...

"Type" will work with the Xdmf library but it's really not standard.

Let me know if it works,
Jerry Clarke

Tobias Brandvik wrote:
> Hi,
> 
> I have a program that writes out files in HDF5 format. The geometry is 
> a structured grid and is specified as three arrays, each containing
> one coordinate value for every point. I'm trying to get Paraview to
> read this by using Xdmf, but can't get it to work. Reading the
> following xdmf file with the attached hdf5 file gives the error below.
> If I interleave the coordinates and use the XYZ format instead of
> X_Y_Z then everything is fine. For various reasons though, it is
> inconvenient to change the original program to do this so I would
> prefer to use X_Y_Z.  I'm using serial Paraview 3.2.2 on 64-bit Centos
> 5. Does anyone know what might be wrong?
> 
> Cheers,
> Tobias.
> 
> <Xdmf>
>   <Domain>
>     <Grid GridType="Uniform">
> 
>         <Topology Type="3DSMESH" Dimensions="4 4 4">
> 	</Topology>
> 
> 	<Geometry Type="X_Y_Z">
> 	<DataItem DataType="Float" Precision="4" Dimensions="4 4 4" Format="HDF">
>              test2.hdf5:/block0/bp0
>           </DataItem>
> 	<DataItem DataType="Float" Precision="4" Dimensions="4 4 4" Format="HDF">
>              test2.hdf5:/block0/bp1
>           </DataItem>
> 	<DataItem DataType="Float" Precision="4" Dimensions="4 4 4" Format="HDF">
>              test2.hdf5:/block0/bp2
>           </DataItem>
> 	</Geometry>
> 	
> 
>     </Grid>
>   </Domain>
> </Xdmf>
> 
> 
> XDMF Error in /home/tbrandvik/downloads/ParaView3.2.2/Utilities/Xdmf2/libsrc/XdmfHDF.cxx
> line 679 (DSM Interface is unavailable)
> HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
> Back trace follows.
>   #000: /home/tbrandvik/downloads/ParaView3.2.2/Utilities/hdf5/H5D.c
> line 1072 in H5Dcreate(): not a location ID
>     major(01): Function arguments
>     minor(03): Inappropriate type
>   #001: /home/tbrandvik/downloads/ParaView3.2.2/Utilities/hdf5/H5G.c
> line 2441 in H5G_loc(): invalid object ID
>     major(01): Function arguments
>     minor(05): Bad value
> XDMF Error in /home/tbrandvik/downloads/ParaView3.2.2/Utilities/Xdmf2/libsrc/XdmfHDF.cxx
> line 850 (Can't Create Temp Dataset CORE:XdmfJunk12.h5:/TempData)
> XDMF Error in /home/tbrandvik/downloads/ParaView3.2.2/Utilities/Xdmf2/libsrc/XdmfHDF.cxx
> line 679 (DSM Interface is unavailable)
> HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
> Back trace follows.
>   #000: /home/tbrandvik/downloads/ParaView3.2.2/Utilities/hdf5/H5D.c
> line 1072 in H5Dcreate(): not a location ID
>     major(01): Function arguments
>     minor(03): Inappropriate type
>   #001: /home/tbrandvik/downloads/ParaView3.2.2/Utilities/hdf5/H5G.c
> line 2441 in H5G_loc(): invalid object ID
>     major(01): Function arguments
>     minor(05): Bad value
> XDMF Error in /home/tbrandvik/downloads/ParaView3.2.2/Utilities/Xdmf2/libsrc/XdmfHDF.cxx
> line 850 (Can't Create Temp Dataset CORE:XdmfJunk13.h5:/TempData)
> XDMF Error in /home/tbrandvik/downloads/ParaView3.2.2/Utilities/Xdmf2/libsrc/XdmfHDF.cxx
> line 679 (DSM Interface is unavailable)
> HDF5-DIAG: Error detected in HDF5 library version: 1.6.5 thread 0.
> Back trace follows.
>   #000: /home/tbrandvik/downloads/ParaView3.2.2/Utilities/hdf5/H5D.c
> line 1072 in H5Dcreate(): not a location ID
>     major(01): Function arguments
>     minor(03): Inappropriate type
>   #001: /home/tbrandvik/downloads/ParaView3.2.2/Utilities/hdf5/H5G.c
> line 2441 in H5G_loc(): invalid object ID
>     major(01): Function arguments
>     minor(05): Bad value
> XDMF Error in /home/tbrandvik/downloads/ParaView3.2.2/Utilities/Xdmf2/libsrc/XdmfHDF.cxx
> line 850 (Can't Create Temp Dataset CORE:XdmfJunk14.h5:/TempData)
> 
> 
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