[vtkusers] how to avoid overlapping (ghost) layer in *.pvti files

[Berk Geveci]

Dear Kaya,

We need nodes overlapping for visualization purposes. We need to be able to
interpolate the field on each partition all the way to a shared boundary to
prevent gaps. Think of operations such as slicing or iso-surfacing. You can
verify this by loading several vti files individually, grouping them and
then applying slice. You'll see the gap at the boundary. There are various
way of fixing this. One would be to use a format such as hdf5 and write to
a single 3D array. Another would be to do the data movement to close the
gaps in ParaView. We currently don't have a filter that does this out of
box so using a Python programmable with mpi4py would be the simplest way to
go there. Then there is the option of doing it in the code before
outputting of course. From a developer perspective, this may be the
simplest one for you to do but may introduce an overhead that may not be
acceptable if you are running on thousands of codes and cannot exploit some
sort of locality.

Best,
-berk

On Fri, Nov 6, 2015 at 4:43 AM, Kaya Onur Dag <kaya.onur.dag at gmail.com>
wrote:

> I have my own cfd solver in which I was using *.vti for paraview input but
> decided to use parallel data write with *.pvti format and do node
> parallelisation.
>
> My *.pvti file is like :
>
> <?xml version="1.0"?>
> <VTKFile type="PImageData" version="1.0" byte_order="LittleEndian"
> header_type="UInt64">
>   <PImageData WholeExtent=[/QUOTE][/QUOTE]"       0      31       0
>  31       0      31" Origin="  0.000000000000E+00  0.000000000000E+00
>  0.000000000000E+00" Spacing="  0.196349540849E+00  0.196349540849E+00
>  0.645161290323E-01" GhostLevel="0">
>       <PPointData Scalars="u v w">
>     <PDataArray type="Float64" Name="u" NumberOfComponents="1"
> format="appended"/>
> <PDataArray type="Float64" Name="v" NumberOfComponents="1"
> format="appended"/>
> <PDataArray type="Float64" Name="w" NumberOfComponents="1"
> format="appended"/>
> </PPointData>
> <Piece Extent="0 31 0 31 0 15" Source="data0_0.vti"/>
> <Piece Extent="0 31 0 31 16 31" Source="data0_1.vti"/>
> </PImageData></VTKFile>
>
>
> The problem I am facing is I am having a gap in between z-axis 15-16 -
> which paraview complains.
>
> I know that the solution is to have a ghost (overlapping) layer (can't
> understand why since I am using point data?), and the issue is that my code
> is not capable of generating overlapping nodes, unless I code it up and
> manually transfer ghost layers at each data output stage for the sake of
> being able to write data in parallel but it feels like an overkill...
>
> Any suggestions?
>
> Thanks in advance.
> Kaya
>
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