[petsc-users] output DMDA to hdf5 file?

Matteo Semplice matteo.semplice at uninsubria.it
Thu Jul 15 05:38:59 CDT 2021

Il 12/07/21 17:51, Matthew Knepley ha scritto:
> On Mon, Jul 12, 2021 at 11:40 AM Matteo Semplice 
> <matteo.semplice at uninsubria.it <mailto:matteo.semplice at uninsubria.it>> 
> wrote:
>     Dear all,
>         I am experimenting with hdf5+xdmf output. At
>     https://www.xdmf.org/index.php/XDMF_Model_and_Format
>     <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.xdmf.org%2Findex.php%2FXDMF_Model_and_Format&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7Cb7db50b8974544e2f5ed08d9454ce429%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637617019536687302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gBEr%2BY1%2BD4Tw8u8oUdEiqJQgMmsHhqXAKr2Z9xBH8Do%3D&reserved=0>
>     I read that "XDMF uses XML to store Light data and to describe the
>     data Model. Either HDF5[3]
>     <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.hdfgroup.org%2FHDF5&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7Cb7db50b8974544e2f5ed08d9454ce429%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637617019536697248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=8evP7yBnpwcrxdFeGdAo7PFNIDS7Xn1Q05pVMrHidH4%3D&reserved=0>
>     or binary files can be used to store Heavy data. The data Format
>     is stored redundantly in both XML and HDF5."
>     However, if I call DMView(dmda,hdf5viewer) and then I run h5ls or
>     h5stat on the resulting h5 file, I see no "geometry" section in
>     the file. How should I write the geometry to the HDF5 file?
>     Here below is what I have tried.
> The HDF5 stuff is only implemented for DMPlex since unstructured grids 
> need to be explicitly stored. You can usually just define the 
> structured grid in the XML
> without putting anything in the HDF5. We could write metadata so that 
> the XML could be autogenerated, but we have not done that.

Thanks for the clarification. It shouldn't be hard to produce the XML 
from my code.

Just another related question: if I call VecView in parallel with the 
HDF5 viewer, I get a single output file. Does this mean that data are 
gathered by one process and written or it handles it smartly by 
coordinating the output of all processes to a single file?


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