[petsc-users] output DMDA to hdf5 file?

Matthew Knepley knepley at gmail.com
Thu Jul 15 07:15:47 CDT 2021

On Thu, Jul 15, 2021 at 6:39 AM Matteo Semplice <
matteo.semplice at uninsubria.it> wrote:

> 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> 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?
This is slightly more complicated than you would expect. We have two
implementations, one which uses MPI-IO, and one which sends
data from each process to 0, which writes it out. It turns out that MPI-IO
is sometimes poorly supported or badly implemented, so you need
the fallback.



> Matteo
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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