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<div class="moz-cite-prefix">Il 15/07/21 14:26, Matthew Knepley ha
scritto:<br>
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<div dir="ltr">On Thu, Jul 15, 2021 at 8:20 AM Matteo Semplice
<<a href="mailto:matteo.semplice@uninsubria.it" moz-do-not-send="true">matteo.semplice@uninsubria.it</a>>
wrote:<br>
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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" moz-do-not-send="true">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" moz-do-not-send="true">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%7C3a9815038ab445f8246b08d9478bd031%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619488512510053%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=e9a30wOMKKyHI2Ay5xFBaEFznwgzLg%2BxDCrQY75464c%3D&reserved=0" originalsrc="https://www.xdmf.org/index.php/XDMF_Model_and_Format" shash="fOvlJlS+U5T3sYt7/4eCNJkl0Bu2aE+t6R8BNR/crrmG+ZF3tF85LlMq+Kc1Ano3+B96NN9xLUYKEawd+DZflvfRjaGIYjQK9PLfKDysyVfaq5N5j4g2QXyMBepYVMZDAUBUoX5QyzTV/Zd87emFN3/r1BM2msRw2ikr/R/DKQc=" target="_blank" moz-do-not-send="true">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%7C3a9815038ab445f8246b08d9478bd031%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619488512520008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0%2BwxLzRPRupk2klRoxuKSEHpzNVipjkF%2FVU0pq5jn%2B4%3D&reserved=0" originalsrc="https://www.hdfgroup.org/HDF5" shash="scw7dgJ+eqldamtqOxtJecOwNMUnv7jUAacPKs8Q8RcS7TqW/kDXJsDES5VNNJ8JHrDtqIqEGDOVCBJoxoi4W0WL9iPWUjaCJrX/Ybw5GTi1x4nNHH705moBTk/wMHmK4jiur21yM38O6jxDZlgnhhvfghY9SyHv7nOS7XcJuGQ=" target="_blank" moz-do-not-send="true">[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>
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<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>
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<p>Thanks a lot!<br>
</p>
Matteo<br>
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<div> Thanks,</div>
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<div> Matt</div>
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<p>Matteo</p>
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-- <br>
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<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>
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<pre class="moz-signature" cols="72">--
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Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
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