[Paraview] Time series with Xdmf
Paisa Seeluangsawat
seeluang at mailbox.sc.edu
Tue Nov 17 00:16:22 EST 2009
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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