[petsc-users] A few questions about hdf5 viewer

[Matthew Knepley]

On Thu, Jan 19, 2012 at 5:19 PM, Mohamad M. Nasr-Azadani
<mmnasr at gmail.com>wrote:

> Thanks Mat,
> Use the DA coordinate mechanism and you can get the coordinates as a
> parallel Vec.
>
> well, that won't be working for me since although I use one DA and the
> parallel vectors derived from same DA, yet I am using staggered grid
> formulation. So, there the coordinates could be different for different
> vectors.
> Is there any other way around this ?
>

I do not understand what you mean, be more specific.

   Matt


> On Thu, Jan 19, 2012 at 6:59 AM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Thu, Jan 19, 2012 at 2:50 AM, Mohamad M. Nasr-Azadani <
>> mmnasr at gmail.com> wrote:
>>
>>> Hi guys,
>>>
>>> I have compiled petsc to use HDF5 package.
>>>
>>> I like to store the data from a parallel vector(s) (obtained from
>>> structured DA in 3 dimensions) to file using VecView() in conjunction with PetscViewerHDF5Open().
>>>
>>> I followed the example here
>>> http://www.mcs.anl.gov/petsc/petsc-current/src/dm/examples/tutorials/ex10.c.html
>>> and everything looks fine.
>>>
>>> However, I had a couple questions:
>>>
>>> 1- When I am done writing the parallel vector obtained from the DA (and
>>> PETSC_COMM_WORLD),
>>>
>>> // Create the HDF5 viewer
>>> PetscViewerHDF5Open<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5Open.html#PetscViewerHDF5Open>
>>> (PETSC_COMM_WORLD<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PETSC_COMM_WORLD.html#PETSC_COMM_WORLD>
>>> ,"gauss.h5",FILE_MODE_WRITE,&H5viewer);
>>> // Write the H5 file
>>>    VecView<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecView.html#VecView>
>>> (gauss,H5viewer);
>>> // Cleaning stage
>>> PetscViewerDestroy<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerDestroy.html#PetscViewerDestroy>
>>> (&H5viewer);
>>>
>>> how can I add data that are just simple 1-D numbers stored on local
>>> arrays.
>>>  Easier said, I would like to add the structured grid coordinates (first
>>> all x's, then all y's, and then all z's) at the end (or to the beginning)
>>> of each data (*.h5) file. But the grid coordinates are stored locally on
>>> each machine and not derived from any parallel vectors or DA. I was
>>> thinking about creating vectors and viewers using PETSC_COMM_SELF but i am
>>> not sure if that is the right approach since that vector is created on all
>>> processors locally.
>>>
>>
>> Use the DA coordinate mechanism and you can get the coordinates as a
>> parallel Vec.
>>
>>
>>> 2- When using VecView() and HDF5 writer, what is the status of data
>>> compression?
>>> The reason that I am asking is that, I used the same example above and
>>> comparing two files saved via two different PetscViewers, i.e. (just)
>>> Binary and HDF5 (Binary) the size is not reduced in the (*.h5) case.
>>> In fact, it is slightly bigger than pure binary file!!
>>> Is there any command we have to set in Petsc to tell HDF5 viewer to use
>>> data compression?
>>>
>>
>> We do not support it. We are happy to take patches that enable this.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thanks for your patience,
>>>  Best,
>>> Mohamad
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> 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
>>
>
>


-- 
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
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