[petsc-users] SNES ex12 visualization

[Matthew Knepley]

On Thu, Sep 14, 2017 at 11:43 AM, Adriano Côrtes <adrimacortes at gmail.com>
wrote:

> Dear Matthew,
>
> Thank you for your return. It worked, but this prompts another question.
> So why PetscViewer does not write both files (.h5 and .xmf) directly,
> instead of having to post-proc the .h5 file (in serial)?
>

1) Maintenance: Changing the Python is much easier than changing the C you
would add to generate it

2) Performance: On big parallel system, writing files is expensive so I
wanted to minimize what I had to do.

3) Robustness: Moving 1 file around is much easier than remembering 2. I
just always regenerate the xdmf when needed.


> And what about big 3D simulations? PETSc always serialize the output of
> the distributed dmplex? Is there a way to output one .h5 per mesh
> partition?
>

Given the way I/O is structured on big machines, we believe the multiple
file route is a huge mistake. Also, all our measurements
say that sending some data on the network is not noticeable given the disk
access costs.

  Thanks,

    Matt


> Best regards,
> Adriano.
>
>
> 2017-09-14 12:00 GMT-03:00 Matthew Knepley <knepley at gmail.com>:
>
>> On Thu, Sep 14, 2017 at 10:30 AM, Adriano Côrtes <adrimacortes at gmail.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> I am running the SNES ex12  and I'm passing the options -dm_view
>>> hdf5:sol.h5 -vec_view hdf5:sol.h5::append to generate an output file. The
>>> .h5 file is generated, but I'm not being able to load it in Paraview
>>> (5.4.0-64bits). Paraview recognizes the file and offers severel options to
>>> read it, here is the complete list
>>>
>>> Chombo Files
>>> GTC Files
>>> M3DC1 Files
>>> Multilevel 3D Plasma Files
>>> PFLOTRAN Files
>>> Pixie Files
>>> Tetrad Files
>>> UNIC Files
>>> VizSchema Files
>>>
>>> The problem is none of the options above work :(
>>> I'm using the configure option '-download-hdf5' and it installs hdf5
>>> version 1.8.18
>>> Any hint of how to fix it and have the visualization working?
>>>
>>
>> Yes, Paraview does not directly read HDF5. It needs you to tell it what
>> the data in the HDF5 file means. You do
>> this by creating a *.xdmf file, which is XML. We provide a tool
>>
>>   $PETSC_DIR/bin/petsc_gen_xdmf.py <HDF5 file>
>>
>> which should automatically produce this file for you. Let us know if it
>> does not work.
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>>
>>> Best regards,
>>> Adriano.
>>>
>>> --
>>> Adriano Côrtes
>>> =================================================
>>> *Campus Duque de Caxias and*
>>> *High-performance Computing Center (NACAD/COPPE)*
>>> Federal University of Rio de Janeiro (UFRJ)
>>>
>>
>>
>>
>> --
>> 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
>>
>> http://www.caam.rice.edu/~mk51/
>>
>
>
>
> --
> Adriano Côrtes
> =================================================
> *Campus Duque de Caxias and*
> *High-performance Computing Center (NACAD/COPPE)*
> Federal University of Rio de Janeiro (UFRJ)
>



-- 
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

http://www.caam.rice.edu/~mk51/
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