[Paraview] Import of XDMF/HDF5:Cell centered attribute of 2D Rectangular grid

Fri Mar 6 18:24:56 EST 2015

Don't forget to reply to the list -- 

Without seeing errors or images of what was wrong about it, there isn't much we can do to help. The file I sent does work and PV reads it just fine. The coordinate axes in this case is Y-Z, but ultimately those are just names since it's 2D right? It doesn't matter if I call it X-Y, Y-Z, or X-Z so long as I have 2 orthogonal coordinates. 

The axes are specified in reverse order when you list them the way it is done there. So the first dataitem is always Z, the second is always Y and the third, if you have one, is always X. This also comes up when you specify the multi-dimensional data items in the attribute section because you have to remember it uses C memory layout (row major), which is different from the Fortran layout (column major) . 

We use XDMF for massive multiblock structured simulations and we store our coordinates in hdf5 files in full 3D arrays (so what something like the meshgrid function returns in Matlab/Numpy) and I've put an example at the end of my email here. In this case, we have a grid which in Fortran would have coordinates X(I,J,K) where I = 1, 83; J = 1, 83; K = 1, 4. Note that the indexing is flipped when we specify it in the XDMF file. It is also flipped from what one would expect coming from Fortran when you look at the h5dump (after the XDMF example). Our strategy is to specify our grid points as an array of vectors and we create that array of vectors using the JOIN function. 

The XDMF documentation isn't always as helpful as I'd like sometimes. It took a lot of trial and error on our part to get this working (and it's made more complicated because we use hyperslabs a lot to only display portions of our data). The PV release binaries are also not helpful in understanding the problems sometimes -- very often, it will just segfault or crash with a glibc double-linked list error or something. Building PV yourself with debug options may help if you are really stuck. 

But what you seem to be trying to do is fully supported and you just need to keep working at it to understand why it doesn't work. And if you are having problems, posting images of what it looks like when you import the data would really help if the issue is just that it doesn't seem to be what you think it should be. 

Tim 

<Topology TopologyType="3DSMesh" Dimensions="4 83 83 3"/> 
<Geometry GeometryType="XYZ" Units="m"> 
<DataItem ItemType="Function" Function="JOIN($0, $1, $2)" Dimensions="4 83 83 3"> 
<DataItem Dimensions="6 85 85" NumberType="Float" Precision="8" Format="HDF">&gridpath;/grid.h5:/Domain_00001/x</DataItem> 
<DataItem Dimensions="6 85 85" NumberType="Float" Precision="8" Format="HDF">&gridpath;/grid.h5:/Domain_00001/y</DataItem> 
<DataItem Dimensions="6 85 85" NumberType="Float" Precision="8" Format="HDF">&gridpath;/grid.h5:/Domain_00001/z</DataItem> 
</DataItem> 
</DataItem> 
</Geometry> 
<Attribute AttributeType="Scalar" Center="Cell" Name="Temperature [K]"> 
<DataItem NumberType="Float" Dimensions="3 82 82" Precision="8" Format="HDF">&outputpath;/RESTS/REST_00000.h5:/FlowData/temperature</DataItem> 

GROUP "/" { 
GROUP "Domain_00001" { 
DATASET "x" { 
DATATYPE H5T_IEEE_F64LE 
DATASPACE SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) } 
} 
DATASET "y" { 
DATATYPE H5T_IEEE_F64LE 
DATASPACE SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) } 
} 
DATASET "z" { 
DATATYPE H5T_IEEE_F64LE 
DATASPACE SIMPLE { ( 6, 85, 85 ) / ( 6, 85, 85 ) } 
} 
} 

----- Original Message -----

From: "Canis Major" <canismajorwuff at gmail.com> 
To: "tim gallagher" <tim.gallagher at gatech.edu> 
Sent: Friday, March 6, 2015 6:05:43 PM 
Subject: Re: [Paraview] Import of XDMF/HDF5:Cell centered attribute of 2D Rectangular grid 

Tim, thank you for your concerns. But of course I tried the configuration like this, it is most intuitive way of description. But unfortunately, it does not work with paraview. In this case the wrong geometry is being created, I do not know how to more clearly describe what is wrong with it. First of all, there is nothing in X direction anymore, but in Y-Z plane, and the geometry shape is wrong, I do not know. 

Also I think there is no such geometry type as VXVY. I have not seen it in Xmdf specification. 

I suppose Armin tried it too and, as he said, failed. 

With Best Regards, 
Slava 

On Fri, Mar 6, 2015 at 11:54 PM, Tim Gallagher < tim.gallagher at gatech.edu > wrote: 

Hi guys, 

So the problems you're having are due to specifying inconsistent data here. You are specifying a 2DRectMesh grid but then giving it 3 vectors for the points. I don't have your HDF5 files so I made a light data XMF file that works for me on all versions going back to 3.14. I have attached it here for you to test. 

This all works fine. I've also created a 3DRectMesh. For that, you need to give it 2 points in the 3rd direction for the grid because you are specifying cell centered data. If you only give it 1 point in the 3rd direction, there is no "cell" anymore in which to specify the data. 

I'll leave adding the 3rd dimension as an exercise for you to work with. Once you figure out how it needs to work using the light data format, then switch over to using the heavy data format and get it working again. 

Hope that helps, 

Tim 

----- Original Message ----- 
From: dkxls23 at gmail.com 
To: canismajorwuff at gmail.com 
Cc: paraview at paraview.org 
Sent: Friday, March 6, 2015 4:55:37 PM 
Subject: Re: [Paraview] Import of XDMF/HDF5:Cell centered attribute of 2D Rectangular grid 

I have had similar problems with 2D structured grids and XDMF in the past. 
I never got them to work in ParaView. 

I solved the problem by using 3D grids and set the first dimension (i.e. the slowest varying) one to 1, the same way as you have done it with VXVYVZ. 
You just have to adjust your data arrays accordingly, i.e. dimensions 1 82 221 in your example. 

I can send you a working xdmf file when back in the office. 

I believe the computational overhead from 2D to 3D grids with effectively 2 dimensions is rather small. 

Maybe the next-generation XDMF reader in ParaView works better for 2D structued grids or somebody with the knowledge explains us how to write them correctly. :) 

-Armin 

On Fri Mar 6 23:17:52 2015 GMT+0200, Canis Major wrote: 
> I have troubles importing xdmf output to paraview. 
> 
> This is an example of xdmf of 0th iteration. 
> 
> <?xml version="1.0" ?> 
> <Xdmf> 
> <Domain> 
> <Grid Name="Grid" GridType="Uniform"> 
> <Topology TopologyType="2DRectMesh" Dimensions="1 82 221"/> 
> <Geometry GeometryType="VXVYVZ"> 
> 
> <DataItem Dimensions="1" NumberType="Float" Precision="4" Format="HDF"> 
> xdmf2d.h5:/Z 
> </DataItem> 
> 
> <DataItem Dimensions="83" NumberType="Float" Precision="4" Format="HDF"> 
> xdmf2d.h5:/Y </DataItem> 
> 
> <DataItem Dimensions="221" NumberType="Float" Precision="4" Format="HDF"> 
> xdmf2d.h5:/X </DataItem> </Geometry> 
> 
> <Attribute Name="pressure" AttributeType="Scalar" Center="Cell"> 
> <DataItem Dimensions="82 220" NumberType="Float" Precision="4" 
> Format="HDF"> 
> xdmf2d.0.h5:/pressure 
> </DataItem> 
> </Attribute> 
> 
> </Grid> 
> </Domain> 
> </Xdmf> 
> 
> 
> I have an error that paraview failed to import attribute. What could 
> be wrong? I have played around the parameters nothing helps. 
> 

-- 
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