Unable to visualise XDMF checkpoint in 1D

Rem · October 16, 2019, 9:02am

Hi all,

I’m writing xdmf files with checkpointing with FEniCS. everything works fine in 2D/3D, but 1D fields cannot be visualise in Paraview 5.7 (nor in the previous versions).

Here’s an exemple file:u_checkpoint.h5 (7.7 KB) u_checkpoint.xdmf (1.2 KB)

Does anyone has an idea ?

Thanks in advance!

Rem

mwestphal · October 17, 2019, 2:37am

the Center="Other" attribute in your xdmf file is not supported.

Rem · October 17, 2019, 7:42am

thanks for the reply. how can I check if this attribute is also present in these files ? (these files have been generated with the same FEniCS function but in 3D)

I’d like to know if it’s a FEniCS issue

u_checkpoint.h5 (16.0 KB) u_checkpoint.xdmf (1.2 KB)

mwestphal · October 17, 2019, 7:51am

You can check by reading the .xdmf file.

Rem · October 17, 2019, 7:54am

Cheers. It appears that there is indeed an Center="Other" attribute in this xdmf file.u_checkpoint.h5 (16.0 KB) u_checkpoint.xdmf (1.2 KB)

Yet it’s readeable in Paraview. It must be supported then

mwestphal · October 17, 2019, 7:59am

My bad, the warning I was seeing was a red herring.

Actually, your first file seems to load fine, it just contains 3 cells and 4 points;

Rem · October 17, 2019, 8:18am

I can load but I can’t plot over line.

This is the message I get when loading with paraview
“Finite element function of family CG and degree 1 on Polyline is not supported.
Unable to get number of points for cell type 0”

mwestphal · October 17, 2019, 8:55am

The message is quite self explanatory. Your dataset contains only a line. You can’t plot over line when your dataset is only a line.

Rem · October 17, 2019, 8:59am

Yes I understand that, yet I’ve been able to plot over line with a line dataset before.

See this example :

Same data, generating without checkpointing though. But i’m able to plot over line even though it’s a 1D dataset.

u_normal.h5 (6.9 KB) u_normal.xdmf (660 Bytes)

mwestphal · October 17, 2019, 9:08am

My bad, the reason because you can’t plot over line your first dataset is because it does not contains any data, only geometry.

Rem · October 17, 2019, 11:13am

I’m afraid it does have data in it since I’m able to import it and use it in a FEniCS script.

mwestphal · October 17, 2019, 11:43am

The data is ignored because of the Center="Other" attribute

Rem · October 17, 2019, 11:49am

How come in the 3D case, where the attribute Center="Other" is also present, visualisation is possible ?

mwestphal · October 17, 2019, 11:57am

No idea, this would require investigation. In any case, the bug is in ParaView/VTK side, not FEniCS.

Rem · March 11, 2021, 1:48pm

Hi Mathieu, this bug still occurs in the latest version of Paraview. Any update on the matter ?

Cheers
Rem

mwestphal · March 11, 2021, 1:49pm

Not that I’m aware of. You may want to test with master and then, is the issue still present, open an issue on https://gitlab.kitware.com/paraview/paraview/-/issues.

Rem · March 11, 2021, 2:13pm

I’ve just opened this issue

https://gitlab.kitware.com/paraview/paraview/-/issues/20549

Rem · May 19, 2021, 1:43pm

Hi Mathieu, any chance there’s an update on this bug?

Cheers,
Rem