[Paraview] xdmf X_Y_Z format

[Tobias Brandvik]

Jerry,

Thanks for your help. I compiled it with MPI support and everything works fine.

Tobias.

On Fri, Jun 13, 2008 at 1:21 PM, Jerry Clarke <clarke at arl.army.mil> wrote:
> 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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>>
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