Il 15/07/21 14:26, Matthew Knepley ha scritto:
On Thu, Jul 15, 2021 at 8:20 AM Matteo Semplice
<[email protected] <mailto:[email protected]>>
wrote:
Il 15/07/21 14:15, Matthew Knepley ha scritto:
On Thu, Jul 15, 2021 at 6:39 AM Matteo Semplice
<[email protected]
<mailto:[email protected]>> wrote:
Il 12/07/21 17:51, Matthew Knepley ha scritto:
On Mon, Jul 12, 2021 at 11:40 AM Matteo Semplice
<[email protected]
<mailto:[email protected]>> wrote:
Dear all,
I am experimenting with hdf5+xdmf output. At
https://www.xdmf.org/index.php/XDMF_Model_and_Format
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I read that "XDMF uses XML to store Light data and to
describe the data Model. Either HDF5[3]
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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.
Thanks!
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.
Is there a simple way to check which implementation is begin used
in a run?
You have to check the configure output. We never gather everything to
one process, so you should not have to worry about it.
Thanks a lot!
Matteo
Thanks,
Matt
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/
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--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como
