<div dir="ltr"><div dir="ltr">On Thu, Jul 15, 2021 at 6:39 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 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%7Cb7db50b8974544e2f5ed08d9454ce429%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637617019536687302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gBEr%2BY1%2BD4Tw8u8oUdEiqJQgMmsHhqXAKr2Z9xBH8Do%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%7Cb7db50b8974544e2f5ed08d9454ce429%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637617019536697248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=8evP7yBnpwcrxdFeGdAo7PFNIDS7Xn1Q05pVMrHidH4%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>
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<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>
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<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></p></div></blockquote><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><div><br></div><div> Thanks,</div><div><br></div><div> Matt</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>
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<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>