[petsc-users] A few questions about hdf5 viewer

[Mohamad M. Nasr-Azadani]

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 ?



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
>
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