[Paraview] Time series with Xdmf
Jerry Clarke
clarke at arl.army.mil
Mon Nov 16 10:20:26 EST 2009
Paisa,
Are you using the CVS version ? The vtkXdmfReader has been significantly
improved and the XML parsing is much faster.
The only other thing I can think of is to write out each timestep to a
separate XML file and use XIncude to build the collection; that way you
could load a single timestep individually if needed.
Jerry Clarke
Paisa Seeluangsawat wrote:
> Hi,
>
> I have about 10 scalar fields and 10 vector fields on 17*17*17 datapoints
> at 1000 time steps. Each time step occupies one h5 file. I wrote an Xdmf
> file, which works fine in Paraview.
>
> My problem is, my Xdmf file is about 4 MB. It takes 50 seconds to load.
> The "apply" properties button, takes another 15 seconds. This happens on
> a moderately new consumer computer (AMD Phenom 9600 quad core, 4 GB memory).
> Am I doing it wrong? How can I speed this up?
>
> My Xdmf file (truncated) follows below. Time step 0 is special. Time steps
> 1..1000 have the same data format. I repeat the same data description 1000
> times. It seems redundant, but I don't know how else to do it.
>
> Thank you,
>
> Paisa
>
>
>
> <?xml version="1.0" ?>
> <!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
> <Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
> <Information Name="SampleLocation" Value="4"/>
> <Domain>
> <Grid Name="My Collection" GridType="Collection" CollectionType="Temporal">
> <Grid Name="My Uniform Grid" GridType="Uniform">
> <Topology Name="Main Topology" TopologyType="3DCORECTMesh" Dimensions="17 17 17"/>
> <Geometry Name="Main Geometry" GeometryType="ORIGIN_DXDYDZ">
> <DataItem Dimensions="3" NumberType="Float" Precision="4" Format="XML">
> 0 0 0
> </DataItem>
> <DataItem Dimensions="3" NumberType="Float" Precision="4" Format="XML">
> 1 1 1
> </DataItem>
> </Geometry>
>
>
> <Time Value="0000" />
> <Attribute Name="40 s" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0000.h5:/40 s</DataItem>
> </Attribute>
> <Attribute Name="50 p" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0000.h5:/50 p</DataItem>
> </Attribute>
> <Attribute Name="50 v" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0000.h5:/50 v</DataItem>
> </Attribute>
> <Attribute Name="60 phi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0000.h5:/60 phi</DataItem>
> </Attribute>
> <Attribute Name="70 c" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0000.h5:/70 c</DataItem>
> </Attribute>
> </Grid>
>
>
> <Grid Name="Structured Grid" GridType="Uniform">
> <Topology Reference="//Topology[@Name='Main Topology']" />
> <Geometry Reference="//Geometry[@Name='Main Geometry']" />
> <Time Value="0001" />
> <Attribute Name="08 eta" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/08 eta</DataItem>
> </Attribute>
> <Attribute Name="09 Ra/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/09 Ra</DataItem>
> </Attribute>
> <Attribute Name="09 Rb/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/09 Rb</DataItem>
> </Attribute>
> <Attribute Name="09 Rc/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/09 Rc</DataItem>
> </Attribute>
> <Attribute Name="09 R/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/09 R</DataItem>
> </Attribute>
> <Attribute Name="10 F" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/10 F</DataItem>
> </Attribute>
> <Attribute Name="10 -G" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/10 -G</DataItem>
> </Attribute>
> <Attribute Name="20 u" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/20 u</DataItem>
> </Attribute>
> <Attribute Name="20 -grad_psi" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/20 -grad_psi</DataItem>
> </Attribute>
> <Attribute Name="30 div_u" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/30 div_u</DataItem>
> </Attribute>
> <Attribute Name="30 -div_grad_psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/30 -div_grad_psi</DataItem>
> </Attribute>
> <Attribute Name="30 -lap_psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/30 -lap_psi</DataItem>
> </Attribute>
> <Attribute Name="30 div_u + lap_psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/30 div_u + lap_psi</DataItem>
> </Attribute>
> <Attribute Name="40 psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/40 psi</DataItem>
> </Attribute>
> <Attribute Name="40 s" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/40 s</DataItem>
> </Attribute>
> <Attribute Name="50 p" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/50 p</DataItem>
> </Attribute>
> <Attribute Name="50 v" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0001.h5:/50 v</DataItem>
> </Attribute>
> <Attribute Name="50 div_v" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/50 div_v</DataItem>
> </Attribute>
> <Attribute Name="55 phi_" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/55 phi_</DataItem>
> </Attribute>
> <Attribute Name="60 phi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/60 phi</DataItem>
> </Attribute>
> <Attribute Name="70 c" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0001.h5:/70 c</DataItem>
> </Attribute>
> </Grid>
>
>
> <Grid Name="Structured Grid" GridType="Uniform">
> <Topology Reference="//Topology[@Name='Main Topology']" />
> <Geometry Reference="//Geometry[@Name='Main Geometry']" />
> <Time Value="0002" />
> <Attribute Name="08 eta" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/08 eta</DataItem>
> </Attribute>
> <Attribute Name="09 Ra/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/09 Ra</DataItem>
> </Attribute>
> <Attribute Name="09 Rb/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/09 Rb</DataItem>
> </Attribute>
> <Attribute Name="09 Rc/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/09 Rc</DataItem>
> </Attribute>
> <Attribute Name="09 R/eta_a" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/09 R</DataItem>
> </Attribute>
> <Attribute Name="10 F" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/10 F</DataItem>
> </Attribute>
> <Attribute Name="10 -G" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/10 -G</DataItem>
> </Attribute>
> <Attribute Name="20 u" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/20 u</DataItem>
> </Attribute>
> <Attribute Name="20 -grad_psi" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/20 -grad_psi</DataItem>
> </Attribute>
> <Attribute Name="30 div_u" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/30 div_u</DataItem>
> </Attribute>
> <Attribute Name="30 -div_grad_psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/30 -div_grad_psi</DataItem>
> </Attribute>
> <Attribute Name="30 -lap_psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/30 -lap_psi</DataItem>
> </Attribute>
> <Attribute Name="30 div_u + lap_psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/30 div_u + lap_psi</DataItem>
> </Attribute>
> <Attribute Name="40 psi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/40 psi</DataItem>
> </Attribute>
> <Attribute Name="40 s" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/40 s</DataItem>
> </Attribute>
> <Attribute Name="50 p" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/50 p</DataItem>
> </Attribute>
> <Attribute Name="50 v" AttributeType="Vector" Center="Node">
> <DataItem Dimensions="17 17 17 3" NumberType="Float" Precision="8" Format="HDF">0002.h5:/50 v</DataItem>
> </Attribute>
> <Attribute Name="50 div_v" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/50 div_v</DataItem>
> </Attribute>
> <Attribute Name="55 phi_" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/55 phi_</DataItem>
> </Attribute>
> <Attribute Name="60 phi" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/60 phi</DataItem>
> </Attribute>
> <Attribute Name="70 c" AttributeType="Scalar" Center="Node">
> <DataItem Dimensions="17 17 17" NumberType="Float" Precision="8" Format="HDF">0002.h5:/70 c</DataItem>
> </Attribute>
> </Grid>
>
>
> .... This repeats until time step 1000 ....
>
>
> </Grid>
> </Domain>
> </Xdmf>
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