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-boun...@paraview.org [mailto:paraview-boun...@paraview.org] On Behalf Of Christine Corbett Moran Sent: Monday, August 24, 2009 11:27 AM To: paraview@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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