[Paraview] Time series with Xdmf
Dominik Szczerba
dominik at itis.ethz.ch
Wed Nov 18 18:16:17 EST 2009
I experience similar problems, it takes too long to load.
What I do is to generate an xmf file with only Nth timestep to be able
to work reasonably fast.
One thing is that XML is ASCII - but lots of redundant information in
the xmf file makes it even worse. For (my) example: I have hundreds of
timesteps from flow simulations but on a rigid mesh. Each time a new
timestep is requested the whole mesh is re-loaded in vein. With large
meshes tets it starts being unfeasible.
Dominik
Paisa Seeluangsawat wrote:
> Hi Jerry,
>
> Thanks for the response. Earlier I used Paraview 3.6.1. Today, I
> tried the CVS version. The "apply" button now works instantly.
> Loading the Xdmf file still takes 40 seconds (compare to 50 secs in
> 3.6.1).
>
> The time it takes to load an Xdmf file seems to grow quadraticly
> with number of timesteps.
>
> # of timesteps : 500 1000 2000
>
> Loadtime (sec) : 10 40 160
>
> Back to the issue of having to repeat the same data descriptions
> 1000 times. Is it a fundamental limitation of XDMF file format?
> Is there a better way to get Paraview to read a time series of HDF5
> files?
>
> Paisa
>
>
>
> Jerry Clarke <clarke at arl.army.mil> wrote:
>
>> 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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