[petsc-users] A few questions about hdf5 viewer

[Mohamad M. Nasr-Azadani]

Sorry for the confusion.
I use only one DA parallel layout for my problem in spite of the fact that
I use MAC-staggered grid (I added one extra cell to the end of the domain
in each direction so that I overcome the difficulty of one extra cell
associated with each velocity in the corresponding direction, i.e. one
extra u-grid exists in x-direction or one extra v-grid exists in
y-direction).
So, the vectors (global and locals) are derived from same DA but they do
not refer to the same physical location.
I could fix this if I create DA for each velocity and scalar components and
set the coordinates for each of them separately, but I would rather not do
this at this point.

I hope I was clear.
Best,
Mohamad




On Thu, Jan 19, 2012 at 3:20 PM, Matthew Knepley <knepley at gmail.com> wrote:

> 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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