Xdmf output files crash Paraview

Question

Xdmf output files crash Paraview

jedbrown opened this issue 7 years ago · 10 comments

I've been able to visualize using VisIt, but not Paraview. Additionally, the files fail to validate with Xdmf.dtd.

xmllint --noout --valid --dtdvalid Xdmf.dtd u.xmf

This may be a deficiency of Xdmf.dtd because many examples from the Xdmf documentation also fail to validate, but could also be the reason for crashes with Paraview. I'm using Paraview-5.4.1 on Linux.

Neither 'Type' nor 'TopologyType' found in itemProperties in XdmfTopologyType::New
terminate called after throwing an instance of 'XdmfError'
  what():  Neither 'Type' nor 'TopologyType' found in itemProperties in XdmfTopologyType::New
Aborted (core dumped)

Answer 1 · 2018-04-24T02:35:53.000Z

Thank you, @jedbrown.

The DTD file does not have all elements and attributes mentioned in either XDMF2 or XDMF3 format. So maybe this DTD file is not complete. For example, in the documentation, it says

Any element in XDMF can have a Name attribute or have a Reference attribute.

But in the DTD file, Topology element doesn't have Name attribute, and only DataItem element can have attribute Reference.

However, we did manage to follow the DTD file with some workarounds. The XDMF files now should pass the validation. And this indeed makes ParaView able to read the XDMF files. The followings are the main changes:

1. Use `3DRectMesh` and `VXVYVZ` for both 2D and 3D cases

There is no VXVY geometry type in the DTD file. This probably means ParaView doesn't handle 2DRectMesh well because it doesn't know how to handle VXVY. So we use 3DRectMesh and VXVYVZ for all cases regardless 2D or 3D. In 2D, therefore, we add dummy z-axis.

2. Use `ENTITY` definition instead of `Reference` for topologies and geometries

We use entity definitions to handle repeating Topology and Geometry in each XDMF file. We used to use Reference skill. But according to the DTD file, Topology and Geometry elements don't have attribute Reference, so we now use entity definitions as the trick to avoid DTD validation failure.

The modification can be found in the commit c6fcfef.

We also added information about ParaView to documentation in doc/markdowns/runpetibm.md.

Answer 2 · 2018-04-24T02:41:31.000Z

That's great. I'll test in the morning. What do you think about filing a bug report (or PR) with Xdmf to fix their Xdmf.dtd? (I know this is outside the scope of the JOSS review, but it evidently needs to be done.)

Answer 3 · 2018-04-25T16:55:04.000Z

When I tried to create an issue in XDMF's GitLab repo, I found there is already an issue for that from two months ago: https://gitlab.kitware.com/xdmf/xdmf/issues/12 And this issue is now on the top of the issue list, so I think currently we don't have to create a new one for the same problem.

Answer 4 · 2020-03-09T11:28:10.000Z

Hi, guys,

I met the same problem when trying to open u.xmf file created by petibm-createxdmf using ParaView-5.6.0. I also have OpenFOAM 7 installed, so this ParaView version is installed automatically as a third-party package.

When I opened the u.xmf file and clicked the Apply button, the ParaView gave loads of errors.

BTW, I used the last case of the 2D examples: unsteady flow past a cylinder at Re=550.

Can you guys help to have a look what the problem is?

Thanks a lot.

Kind regards;

Guangyu

Answer 5 · 2020-03-09T11:31:26.000Z

Hi, guys,

Here are the errors reported by ParaView-5.6.0