[Paraview] Error reading timeseries with spatial grid collection with XDMF
Joachim Pouderoux
joachim.pouderoux at kitware.com
Sun Nov 12 23:15:49 EST 2017
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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