[petsc-users] output DMDA to hdf5 file?

Matteo Semplice matteo.semplice at uninsubria.it
Thu Jul 15 07:53:43 CDT 2021

Il 15/07/21 14:26, Matthew Knepley ha scritto:
> On Thu, Jul 15, 2021 at 8:20 AM Matteo Semplice 
> <matteo.semplice at uninsubria.it <mailto:matteo.semplice at uninsubria.it>> 
> wrote:
>     Il 15/07/21 14:15, Matthew Knepley ha scritto:
>>     On Thu, Jul 15, 2021 at 6:39 AM Matteo Semplice
>>     <matteo.semplice at uninsubria.it
>>     <mailto: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
>>>         <mailto: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%7C3a9815038ab445f8246b08d9478bd031%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619488512510053%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=e9a30wOMKKyHI2Ay5xFBaEFznwgzLg%2BxDCrQY75464c%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%7C3a9815038ab445f8246b08d9478bd031%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619488512520008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0%2BwxLzRPRupk2klRoxuKSEHpzNVipjkF%2FVU0pq5jn%2B4%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.
>     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!

>    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/ 
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cse.buffalo.edu%2F~knepley%2F&data=04%7C01%7Cmatteo.semplice%40uninsubria.it%7C3a9815038ab445f8246b08d9478bd031%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C637619488512520008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=73lAI16uLTsAuFedTXerJQ0jn63UspjPLLRRpb7Uw0E%3D&reserved=0>

Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210715/d6dc9106/attachment.html>

More information about the petsc-users mailing list