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HDF5 IO library for OpenFOAM

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Old   February 3, 2014, 11:04
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Håkon Strandenes
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I will try HDF5 1.8.12 myself tomorrow or Wednesday (I am very busy tomorrow) and see what I get. I think I am using HDF5 1.8.11 myself right now. Have you checked that you have write permissions in the folder?
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Old   February 4, 2014, 01:46
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thanks Haakon

sure, with OF22x and Gcc it works
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Old   February 14, 2014, 15:58
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Thanks Håkon for the HDF5 Plugin.

I am currently porting it to the foam-extend-3.0 version. I have modified all the environment variables different from OF-2.2.x and foam-extend-3.0.

I am currently getting the following error in the core hd5Write.H, could you please comment on this error.


Cheers,

Krishna
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Old   January 9, 2015, 06:44
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Eric Paterson
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Have there been further developments since the last post (almost 1 year ago)? This is a pace-setting issue for true HPC (1000+ core) simulations. My HPC admins are demanding that we come up with a solution, and I wanted to check on status before digging in.
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Old   January 9, 2015, 07:53
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The latest update is on Github (https://github.com/hakostra/IOH5Write). It does work on OF 2.3.x as far as I know. As with any software there is some installation problems if your environment is not configured properly. Use a recent HDF5 version. Try to read the installation guidelines.

The "known bugs and limitations" section in the README file (see Github) does still apply. I should also probably emphasize that due to missing support in the XDMF format, polyhedral cells is not supported. I would love to see polyhedral cell support in XDMF, but I doubt that's going to happen any time soon.

One possible workaround for this issue is perhaps to rewrite the whole thing to use CGNS, that has support for polyhedral cells. However, it does not have support for discrete particles, and that was a showstopper for me when I wrote this library, hence the current HDF5+XDMF approach.
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Old   June 23, 2015, 14:57
Default Wrting Boundary Data to HDF5?
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Hi Haakon,

How do we implement to write the boundary data?

Cheers!
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Old   February 3, 2016, 08:43
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Quote:
Originally Posted by haakon View Post
The latest update is on Github (https://github.com/hakostra/IOH5Write). It does work on OF 2.3.x as far as I know. As with any software there is some installation problems if your environment is not configured properly. Use a recent HDF5 version. Try to read the installation guidelines.

The "known bugs and limitations" section in the README file (see Github) does still apply. I should also probably emphasize that due to missing support in the XDMF format, polyhedral cells is not supported. I would love to see polyhedral cell support in XDMF, but I doubt that's going to happen any time soon.

One possible workaround for this issue is perhaps to rewrite the whole thing to use CGNS, that has support for polyhedral cells. However, it does not have support for discrete particles, and that was a showstopper for me when I wrote this library, hence the current HDF5+XDMF approach.
Hi,

It's a great tool you've written! I've been writing on a CGNS exporter my self for a while. I did this since I need polyhedral support. Now ParaView's CGNS reader doesn't support polyhedrals so I had to write my own reader. I got it to work rather well but when I started to implement a parallel version I got into all sorts of trouble with CGNS. Now since CGNS uses HDF5 in the background I've come to the conclusion that it might be better to just stick to HDF5.

Since I need polyhedrals I think I need to develop my own HDF5 writer. My idea is basically to write the mesh fields just as they are and keep a similar structure as OpenFOAM already has. Then I would have to develop a reader or paraview which would read the hdf5-file and use vtkPolyhedron.

Do you see any problems with this approach or can I leverage on some of the work you have done?

Best Regards
Nicolas
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Old   February 10, 2016, 17:51
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I think there is another way.

You could extend the XDMF format to handle polyhedral cells. There is already a bug report concerning this topic and I discussed this recently with some XDMF developers, see here:
http://www.kitware.com/pipermail/xdm...er/000895.html

I would start by modifying XdmfTopologyType.cpp, i.e. add polyhedral cell support similar to the POLYGON implementation. Extending the VTK/ParaView readers to handle shouldn't be too difficult either, since polyhedral cells are already supported in VTK.

You can get the latest XDMF source like this:
git clone git://public.kitware.com/Xdmf2.git

However, I would probably recommend you to implement this directly in VTK, which contains a more or less full copy of the XDMF source tree. You get the latest VTK source from here:
https://gitlab.kitware.com/vtk/vtk
And this is the file, where I would start to implement the polyhedral cell support:
https://gitlab.kitware.com/vtk/vtk/b...gyType.cpp#L70

Hope this helps!

-Armin

Last edited by dkxls; February 13, 2016 at 09:31. Reason: Change link to the public XDMF mailing archive
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Old   February 11, 2016, 04:37
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Quote:
Originally Posted by dkxls View Post
I think there is another way.

You could extend the XDMF format to handle polyhedral cells. There is already a bug report concerning this topic and I discussed this recently with some XDMF developers, see here:
http://www.kitware.com/cgi-bin/mailm...er/000895.html

I would start by modifying XdmfTopologyType.cpp, i.e. add polyhedral cell support similar to the POLYGON implementation. Extending the VTK/ParaView readers to handle shouldn't be too difficult either, since polyhedral cells are already supported in VTK.

You can get the latest XDMF source like this:
git clone git://public.kitware.com/Xdmf2.git

However, I would probably recommend you to implement this directly in VTK, which contains a more or less full copy of the XDMF source tree. You get the latest VTK source from here:
https://gitlab.kitware.com/vtk/vtk
And this is the file, where I would start to implement the polyhedral cell support:
https://gitlab.kitware.com/vtk/vtk/b...gyType.cpp#L70

Hope this helps!

-Armin
Hi Armin,

Thanks for the insight. However I don't really see the benefit of going via XDMF. It could be that I'm just not enlightened. Since we already have to write a reader why not skip XDMF. That was my main lesson learned when I implemented the cgns reader writer. It took quite some time of going through the docs. And in the end I discoverer that the standard is so free it is near impossible to write a general reader. So I decided that my reader would have to be specific to my foamwriter. And then I had problems compiling cgns for parallel applications. It was to obvious that I should ditch the CGNS standard. And just go with HDF5. Which is what CGNS uses in the background any ways.

Now as I see it the benefit with not using XDMF is that we could make a reader that can read while the simulation is running. And we can make it smart on how to read the results in parallel since would keep the decomposition. And there would be no need have an intermediate step between simulation and postprocessing.

Now I've only started to work with it, will see how much I get done. It's a spare time project so it will take a while.

If you or some one else is working on something similar or want to pich in I'm happy to discuss the details!

Nicolas
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Old   February 11, 2016, 06:34
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Thanks for elaborating your view.
I certainly agree that the CGNS standard is "too free" and writing a general reader is and rather big task. However, the XDMF standard, is far more specific and there exist already readers for VTK/ParaView and VisIt.
So, in my opinion, the XDMF standard is very well suited for CFD applications.

I have a few comments below to further the discussion.

Quote:
Originally Posted by nsf View Post
Now as I see it the benefit with not using XDMF is that we could make a reader that can read while the simulation is running. And we can make it smart on how to read the results in parallel since would keep the decomposition. And there would be no need have an intermediate step between simulation and postprocessing.
There is nothing that holds you back from reading the HDF5/XDMF result file while the simulation is running. With Håkon's HDF5 writer, you just have to run the python utility in-between, but that's a detail specific to the current implementation. Alternatively, one could write the XDMF file directly during run time, always overwriting the previous XDMF file or something more sophisticated.
Concerning the VTK/ParaView XDMF reader: I think they are already quite smart concerning the parallel data handling, but I have no general overview of that.

Quote:
Originally Posted by nsf View Post
If you or some one else is working on something similar or want to pich in I'm happy to discuss the details!
I actually have implemented an HDF5 surface (i.e. cutplanes, isosurfaces, ...) writer for OpenFOAM similarly to Håkon's IO library. Meaning, I'm writing HDF5 files with during runtime and generate the XDMF file with a python script afterwards.
It's not (yet) publicly available, but I'm happy to share it if you are interested in. (I actually should just put it to some public git repo.)

-Armin
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Old   February 11, 2016, 07:17
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Quote:
Originally Posted by dkxls View Post

I actually have implemented an HDF5 surface (i.e. cutplanes, isosurfaces, ...) writer for OpenFOAM similarly to Håkon's IO library. Meaning, I'm writing HDF5 files with during runtime and generate the XDMF file with a python script afterwards.
It's not (yet) publicly available, but I'm happy to share it if you are interested in. (I actually should just put it to some public git repo.)

-Armin
Hi,

If it includes patches I would definitely be interested! Even if I don't choose to go with xdmf it would be interesting to see how you solved some of the issues I currently have. Right now if I use my function object from a custom app "foamToHDF5" then everything is fine. I can write in parallel and see no issues. However if I include my function object in say icoFoam I get and segmentation fault when when icoFoam does "finalize". The writing goes fine. It's just a bit unclean to exit on a segmenation fault. The only difference I can see is that my app includes hdf5.h and dynamically links libhdf5.so at compile time while icoFoam would do it at runtime. Is it something you've seen?

Another point I have is that by organizing the data very close to how foam already does simplifies converting back. We would have faces, owners, neighbours, points exactly as they are now. Is it possible with XDMF?

The link you posted to the discussion of polyhedral cells for XDF is private so I can't see it.

I can offer one point of experience from CGNS. At least in CGNS you can't mix polyhedral cells with structured types. For structured types (tetras, hexas and so on). All you need is a list of points for each cell. (it's actually slightly more complicated but not much). But for a polyhedral you need two lists. One defining all the faces in the mesh and one list defining the cells. (Although I've come to realize that defining the faces i a separate list is redundant.) In any case that makes merging a polyhedral reader with the current CGNS reader difficult since the structure is totally different. I suspect we might run in to similar issues if we implement polyhedrals in XDMF. But I have no experince of XDMF so I don't really know.

Best Regards
Nicolas
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Old   February 13, 2016, 09:29
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Just a few quick comments now, I will get back to you concerning the XDMF surface writer for OpenFOAM.

Quote:
Originally Posted by nsf View Post
The link you posted to the discussion of polyhedral cells for XDF is private so I can't see it.
The mailing list archives are now public, here the new link (I also changed the link in the original post):
http://www.kitware.com/pipermail/xdm...er/000895.html

Quote:
Originally Posted by nsf View Post
I can offer one point of experience from CGNS. At least in CGNS you can't mix polyhedral cells with structured types.
...
I suspect we might run in to similar issues if we implement polyhedrals in XDMF. But I have no experince of XDMF so I don't really know.
In XDMF you can actually mix different cell types by using TopologyType="Mixed", so there is no problem on that end. For more information see here:
http://www.xdmf.org/index.php/XDMF_Model_and_Format

Cheers,
Armin
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