[petsc-users] A few questions about hdf5 viewer

[Matthew Knepley]

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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