[Paraview] XDMF help (UNCLASSIFIED)

[Leiter, Kenneth (Cont, ARL/CISD)]

Classification:  UNCLASSIFIED 
Caveats: NONE

Hi Christine,

If you are reading in a position array and are unsure of the topology type,
you will probably want to read in the data with Polyvertex topology, which
is a group of unconnected points.

The Topology element must specify the number of elements to read.  In this
case, it would be the number of points = 3751383.

This is what I imagine your Xdmf file should look like:

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
  <Domain>
    <Grid>
      <Topology TopologyType="Polyvertex" Dimensions="3751383"/>
      <Geometry>
        <DataItem Dimensions="3751383 3" NumberType="Float" Precision="8"
Format="HDF">examplefile.h5:/dark/position</DataItem>
      </Geometry>
    </Grid>
  </Domain>
</Xdmf>


- Ken

---------------------------------------------------------
Kenneth Leiter
Scientific Visualization Team
Lockheed Martin / ARL DoD Supercomputing Resource Center
410-278-2580

-----Original Message-----
From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org]
On Behalf Of Christine Corbett Moran
Sent: Monday, August 24, 2009 11:27 AM
To: paraview at paraview.org
Subject: [Paraview] XDMF help

Hi,

I have an existing HDF5 file (which I did not personally create so am not
familiar with other than the info I get from h5dump/h5ls) I'd like to read
in with Paraview. I'm first trying to create the most basic xmf file
possible which allows Paraview to read in the position array from the HDF5
file (based on the documentation here:
http://www.xdmf.org/index.php/XDMF_Model_and_Format). Right now whatever I
try either causes a segfault or reads in data nonsensically. Could anyone
point me in the right direction--e.g. based on the info below are my data
dimensions just off?--or to better documentation? Thanks in advance, it's
hopefully something simple I just missed from the documentation.

More information about the file and what I have tried is below.

*After reading a bit and playing around with the parameters, my current .xmf
attempt segfaults shortly after the server prints "Done Parsing." If I
change TopologyType to 3DSMesh it doesn't segfault but what it manages to
read in (only a single point) is nonsensical. Any of the other TopologyTypes
listed in the documentation I have found likewise produce a segfault. I also
tried various permutations of the Dimensions argument ("11254149 3", "3
11254149", "3751383 3", "3751383 3"), with each possible 3D Topology, these
likewise manage to read in either just a single point or segfault. I didn't
try modifying the precision argument as hd5ls tells me the position array
should be of doubles. This is my current attempt:
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
  <Domain>
    <Grid>
      <Topology TopologyType="3DRectMesh"/>
      <Geometry>
        <DataItem Dimensions="11254149 3" Precision="8"
Format="HDF">examplefile.h5:/dark/position</DataItem>
      </Geometry>
    </Grid>
  </Domain>
</Xdmf>

*About the portion of the file I am trying to read in:
% h5ls -rv examplefile.h5
Opened "examplefile.h5" with sec2 driver.

/dark                    Group
    Attribute: iOrder    {1}

        Type:      native unsigned long
        Data:  0

    Location:  0:1:0:2552
    Links:     1

...
/dark/position           Dataset {11254149/Inf, 3/3}

    Location:  0:1:0:2600
    Links:     1

    Modified:  2008-07-31 04:12:06 CEST
    Chunks:    {32768, 1} 262144 bytes

    Storage:   270099576 logical bytes, 270536736 allocated bytes, 99.84%
utilization
    Filter-0:  fletcher32-3  {}

    Type:      native double
...

*More information about the portion of the file I am trying to read in
obtained from h5dump

%h5dump -x examplefile.h5 > examplefile.xml %grep -A 30 position
examplefile.xml

      <hdf5:Dataset Name="position" OBJ-XID="xid_2600-0" H5Path=
"/dark/position" Parents="xid_2552-0" H5ParentPaths="/dark">

         <hdf5:StorageLayout>
            <hdf5:ChunkedLayout Ndims="2">

               <hdf5:ChunkDimension DimSize="32768" />
               <hdf5:ChunkDimension DimSize="1" />

               <hdf5:RequiredFilter>
                     <hdf5:Fletcher32 />
</hdf5:RequiredFilter>

            </hdf5:ChunkedLayout>
         </hdf5:StorageLayout>

         <hdf5:FillValueInfo FillTime="FillIfSet"
AllocationTime="Incremental">
            <hdf5:FillValue>

                  <hdf5:NoFill/>
            </hdf5:FillValue>

         </hdf5:FillValueInfo>
         <hdf5:Dataspace>

            <hdf5:SimpleDataspace Ndims="2">
               <hdf5:Dimension  DimSize="11254149" MaxDimSize="UNLIMITED"/>

               <hdf5:Dimension  DimSize="3" MaxDimSize="3"/>
            </hdf5:SimpleDataspace>

         </hdf5:Dataspace>
         <hdf5:DataType>

            <hdf5:AtomicType>
               <hdf5:FloatType ByteOrder="LE" Size="8" SignBitLocation="63"
ExponentBits="11" ExponentLocation="52" MantissaBits="52"
MantissaLocation="0" />

            </hdf5:AtomicType>
         </hdf5:DataType>

         <hdf5:Data>
            <hdf5:DataFromFile>

            -0.0117184 -0.00222114 -0.0762903
            -0.0111324 -0.00176135 -0.0765049

            -0.0106262 -0.00136187 -0.0765845
            -0.0112606 -0.00112936 -0.0766193

...
Classification:  UNCLASSIFIED 
Caveats: NONE

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