[Paraview] xdmf with field data in multiple files

[Peter Brady]

So it seems that this can be achieved using spatial grid collections.  
Here's what I have now:

<?xml version="1.0" encoding="utf-8"?><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
<Xdmf Version="2.0">
   <Domain>
     <Topology TopologyType="3DCoRectMesh" Dimensions="64 64 64"/>
     <Topology TopologyType="3DCoRectMesh" Dimensions="64 64 64"/>

     <Geometry GeometryType="Origin_DxDyDz">
       <DataItem Format="XML" NumberType="Float" Dimensions="3">
        -1.000000 -0.500000 -0.500000
       </DataItem>
       <DataItem Format="XML" NumberType="Float" Dimensions="3">
         0.01574803 0.01587301 0.01587301
       </DataItem>
     </Geometry>

     <Geometry GeometryType="Origin_DxDyDz">
       <DataItem Format="XML" NumberType="Float" Dimensions="3">
         0.007874 -0.500000 -0.500000
       </DataItem>
       <DataItem Format="XML" NumberType="Float" Dimensions="3">
         0.01574803 0.01587301 0.01587301
       </DataItem>
     </Geometry>

     <Grid Name="TimeSeries" GridType="Collection" 
CollectionType="Temporal">
       <Time TimeType="List">
         <DataItem Format="XML" NumberType="Float" Dimensions="1">
          0.00000E+00
         </DataItem>
       </Time>
       <Grid Name="0" GridType="Collection" CollectionType="Spatial">
         <Grid Name="Section 1" GridType="Uniform">
           <Topology Reference="/Xdmf/Domain/Topology[1]"/>
           <Geometry Reference="/Xdmf/Domain/Geometry[1]"/>
           <Attribute Name="G" Type="Scalar" Center="Node">
             <DataItem DataType="Float" Precision="8" Dimensions="64 64 
64" Format="Binary">
               G.1.bin
             </DataItem>
           </Attribute>
         </Grid>

         <Grid Name="Section 2" GridType="Uniform">
           <Topology Reference="/Xdmf/Domain/Topology[2]"/>
           <Geometry Reference="/Xdmf/Domain/Geometry[2]"/>
           <Attribute Name="G" Type="Scalar" Center="Node">
             <DataItem DataType="Float" Precision="8" Dimensions="64 64 
64" Format="Binary">
               G.2.bin
             </DataItem>
           </Attribute>
         </Grid>

       </Grid> <!-- End of Spatial Collection 0 -->
     </Grid> <!-- End of Temporal Collection -->
   </Domain>
</Xdmf>

This works decently well but there is a gap of one grid cell between my 
grid sections.  I can make this go away by having each section extend 
their dimensions by 1 in the appropriate directions but is there a 
better way?  Specifically I would like to know if there is a way to 
specify the connectivity between the grids in my collection or if 
something like Subsets are the way to go.

Thanks,
Peter.

On 11/17/2015 01:09 PM, Peter Brady wrote:
> I've been using an xdmf file like the following:
>
> <?xml version="1.0" encoding="utf-8"?><!DOCTYPE Xdmf SYSTEM "Xdmf.dtd">
> <Xdmf Version="2.0">
>   <Domain>
>     <Topology TopologyType="2DCoRectMesh" Dimensions="256 512"/>
>     <Geometry GeometryType="Origin_DxDy">
>       <DataItem Format="XML" NumberType="Float" Dimensions="2">
>        0.00000E+00 0.00000E+00
>       </DataItem>
>       <DataItem Format="XML" NumberType="Float" Dimensions="2">
>        1.22718E-02 1.22959E-02
>       </DataItem>
>     </Geometry>
>     <Grid Name="TimeSeries" GridType="Collection" 
> CollectionType="Temporal">
>       <Time TimeType="List">
>         <DataItem Format="XML" NumberType="Float" Dimensions="2">
>          0.00000E+00 1.00399E-01
>         </DataItem>
>       </Time>
>       <Grid Name="0" GridType="Uniform">
>         <Topology Reference="/Xdmf/Domain/Topology[1]"/>
>         <Geometry Reference="/Xdmf/Domain/Geometry[1]"/>
>         <Attribute Name="density" Type="Scalar" Center="Node">
>           <DataItem DataType="Float" Precision="8" Dimensions="256 
> 512" Format="Binary" Seek="224">
>            rstrt.0000.bin
>           </DataItem>
>         </Attribute>
>         <Attribute Name="temperature" Type="Scalar" Center="Node">
>           <DataItem DataType="Float" Precision="8" Dimensions="256 
> 512" Format="Binary" Seek="0">
>            rstrt.0000.6.bin
>           </DataItem>
>         </Attribute>
>         ...
>       </Grid>
> ...
> </Xdmf>
>
> However, as the simulations have gotten larger, the time to write a 
> single file like "rstrt.0000.bin" in parallel has become obscene. My 
> plan is to have groups of processors write different files where the 
> extents written will be a continuous slab of ijk coordinates. I've 
> looked at the documentation for hyperslabs in xdmf but can't quite see 
> what changes I would need to make to make to my xdmf file.  For 
> example, do I only need to change the innermost "DataItem" or do the 
> changes need to be made higher up?
>
> Some guidance on how to modify my xdmf file would be greatly appreciated.
>
> Thanks,
> Peter.
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at: 
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview