<div dir="ltr"><div dir="ltr">On Thu, Jul 15, 2021 at 8:20 AM Matteo Semplice <<a href="mailto:matteo.semplice@uninsubria.it">matteo.semplice@uninsubria.it</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div>Il 15/07/21 14:15, Matthew Knepley ha
scritto:<br>
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<div dir="ltr">On Thu, Jul 15, 2021 at 6:39 AM Matteo Semplice
<<a href="mailto:matteo.semplice@uninsubria.it" target="_blank">matteo.semplice@uninsubria.it</a>>
wrote:<br>
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<div>Il 12/07/21 17:51, Matthew Knepley ha scritto:<br>
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<div dir="ltr">On Mon, Jul 12, 2021 at 11:40 AM Matteo
Semplice <<a href="mailto:matteo.semplice@uninsubria.it" target="_blank">matteo.semplice@uninsubria.it</a>>
wrote:<br>
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<p>Dear all,</p>
<p> I am experimenting with hdf5+xdmf output.
At <a href="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%7Cfb0d540c87a64e4ea51d08d9478a4e9b%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619481622608977%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=sOQskFoMTHdOwjOec0d9npdw%2BiAVbar1SXBuU%2BH8xKc%3D&reserved=0" target="_blank">https://www.xdmf.org/index.php/XDMF_Model_and_Format</a>
I read that "XDMF uses XML to store Light data
and to describe the data Model. Either HDF5<a rel="nofollow" href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.hdfgroup.org%2FHDF5&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7Cfb0d540c87a64e4ea51d08d9478a4e9b%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619481622618934%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=akFyfHE4BULSscevnO0MxjMhEByT3USoJFQKsikJSzg%3D&reserved=0" target="_blank">[3]</a>
or binary files can be used to store Heavy
data. The data Format is stored redundantly in
both XML and HDF5."</p>
<p>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?<br>
</p>
<p>Here below is what I have tried.</p>
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<div>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</div>
<div>without putting anything in the HDF5. We could
write metadata so that the XML could be
autogenerated, but we have not done that.</div>
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<p>Thanks for the clarification. It shouldn't be hard to
produce the XML from my code.<br>
</p>
<p>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?<br>
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<div>This is slightly more complicated than you would expect.
We have two implementations, one which uses MPI-IO, and one
which sends</div>
<div>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</div>
<div>the fallback.</div>
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<p>Thanks!<br>
</p>
<p>On my machine I am compiling from the git repo with
--download-hdf5, so I have some control, but on clusters I prefer
to use the available petsc.<br>
</p>
Is there a simple way to check which implementation is begin used in
a run?</div></blockquote><div> </div><div>You have to check the configure output. We never gather everything to one process, so you should not have to worry about it.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>
<p>Matteo</p></div></blockquote></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>