Hi Ken, Thanks! That worked, I had only tried structured topologies which was my mistake.
Cheers, Christine On Mon, Aug 24, 2009 at 5:57 PM, Leiter, Kenneth (Cont, ARL/CISD) < [email protected]> wrote: > 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: [email protected] [mailto:[email protected]] > On Behalf Of Christine Corbett Moran > Sent: Monday, August 24, 2009 11:27 AM > To: [email protected] > 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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