[petsc-users] SNES ex12 visualization

[Kong, Fande]

On Thu, Sep 14, 2017 at 9:47 AM, Matthew Knepley <knepley at gmail.com> wrote:

> 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.
>

I have slightly different things here. We tried the serial output, it looks
really slow for large-scale problems, and the first processor often runs
out of memory because of gathering all data from other processor cores. The
parallel IO runs smoothly and much faster than I excepted. We have done
experiments with ten thousands  of cores for a problem with 1 billion of
unknowns. I did not see any concern so far.


Fande,


>
>   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/
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.caam.rice.edu_-7Emk51_&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4ts7XKfj2opmiCY&m=4H_Jl8Ex4tyDDtEJRWDYBqSUWZTlt2N0nDQD6_nPQn0&s=v0mwIWnPBNUdE0PYg8qYZ40fhnBA5I5AqDVWOpe2wdU&e=>
>>>
>>
>>
>>
>> --
>> 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/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.caam.rice.edu_-7Emk51_&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=DUUt3SRGI0_JgtNaS3udV68GRkgV4ts7XKfj2opmiCY&m=4H_Jl8Ex4tyDDtEJRWDYBqSUWZTlt2N0nDQD6_nPQn0&s=v0mwIWnPBNUdE0PYg8qYZ40fhnBA5I5AqDVWOpe2wdU&e=>
>
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