[Paraview] Error reading timeseries with spatial grid collection with XDMF

David E DeMarle dave.demarle at kitware.com
Mon Nov 20 14:14:23 EST 2017 

It might be that the reader doesn't like or want that both of your times
are 0.0.
...
<Time TimeType="Single" Value="0.0"/>
...
<Time TimeType="Single" Value="0.0"/>
...
but your third case doesn't fit that hypothesis.

Otherwise your file looks ok at first glance. I'ld have to debug the reader
on your data to figure out what is going wrong.

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Sun, Nov 12, 2017 at 11:15 PM, Joachim Pouderoux <
joachim.pouderoux at kitware.com> wrote:

> Nikos,
>
> It looks like you are using the Xdmf2 based reader.
> Did you give a chance to the one based on Xdmf3?
> What version of ParaView are you using?
> Can you provide a full dataset we could use to reproduce the issue?
>
> Best,
>
>
> *Joachim Pouderoux*, PhD
>
> *Technical Expert - Scientific Computing Team*
> *Kitware SAS <http://www.kitware.fr>*
>
>
> 2017-11-11 19:31 GMT+01:00 Nikolaos Beratlis <nikos.beratlis at gmail.com>:
>
>> Hi,
>>
>> I have a cartesian structured grid made of two sub-domains and a two snap
>> shots in a time that I would like to read in Paraview. The data and grid
>> files are stored in HDF5 file and I use a XDMF file to read them in a
>> Paraview. The XDMF files looks like this:
>>
>> <?xml version="1.0" ?>
>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>> <Xdmf Version="2.2">
>> <Domain Name="Bump">
>> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
>>
>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>> <Time TimeType="Single" Value="0.0"/>
>>
>> <Grid GridType="Uniform" Name="GridZone0001">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> </DataItem>
>> </Attribute>
>> </Grid>
>>
>> <Grid GridType="Uniform" Name="GridZone0002">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  268"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  268" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  268" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0002
>> </DataItem>
>> </Attribute>
>> </Grid>
>> </Grid>
>>
>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>> <Time TimeType="Single" Value="0.0"/>
>>
>> <Grid GridType="Uniform" Name="GridZone0001">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> </DataItem>
>> </Attribute>
>> </Grid>
>>
>> <Grid GridType="Uniform" Name="GridZone0002">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  268"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  268" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  268" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0002:/zone0002
>> </DataItem>
>> </Attribute>
>> </Grid>
>>
>> </Grid>
>>
>> </Grid>
>> </Domain>
>> </Xdmf>
>>
>> The file is read in Paraview. When I advance in to the second instant in
>> time I get the following error:
>>
>> Failed to read attribute data.
>>
>> Paraview shows data from the first subset (zone0001), it can't read the
>> data from the second subset (zone0002).
>>
>>
>> When I read only on instant in time like this:
>>
>> <?xml version="1.0" ?>
>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>> <Xdmf Version="2.2">
>> <Domain Name="Bump">
>> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
>>
>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>> <Time TimeType="Single" Value="0.0"/>
>>
>> <Grid GridType="Uniform" Name="GridZone0001">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> </DataItem>
>> </Attribute>
>> </Grid>
>>
>> <Grid GridType="Uniform" Name="GridZone0002">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  268"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  268" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  268" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0002
>> </DataItem>
>> </Attribute>
>> </Grid>
>> </Grid>
>>
>> </Grid>
>> </Domain>
>> </Xdmf>
>>
>> the file is read successfully and no errors show up.
>>
>> Also when I read two time instants but with only one subset (zone0001)
>> Paraview doesn't throw any errors.
>>
>> <?xml version="1.0" ?>
>> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
>> <Xdmf Version="2.2">
>> <Domain Name="Bump">
>> <Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
>>
>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>> <Time TimeType="Single" Value="0.0"/>
>>
>> <Grid GridType="Uniform" Name="GridZone0001">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> </DataItem>
>> </Attribute>
>> </Grid>
>>
>> <Grid Name="0" GridType="Collection" CollectionType="Spatial">
>> <Time TimeType="Single" Value="0.0"/>
>>
>> <Grid GridType="Uniform" Name="GridZone0001">
>> <Topology TopologyType="3DRectMesh" Dimensions="    2  202  267"/>
>> <Geometry GeometryType="VXVYVZ">
>> <DataItem Dimensions="  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> </DataItem>
>> <DataItem Dimensions="  202" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> </DataItem>
>> <DataItem Dimensions="    2" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> </DataItem>
>> </Geometry>
>> <Attribute Name="Q" AttributeType="Scalar" Center="Node">
>> <DataItem Dimensions="    2  202  267" NumberType="Float" Precision="4"
>> Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> </DataItem>
>> </Attribute>
>> </Grid>
>>
>> </Grid>
>>
>> </Grid>
>> </Domain>
>> </Xdmf>
>>
>>
>> Does anyone see the problem in the code?
>>
>> Kind regards,
>>
>> Nikos
>>
>>
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>
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