[petsc-users] A few questions about hdf5 viewer

[Matthew Knepley]

On Thu, Jan 19, 2012 at 5:26 PM, Mohamad M. Nasr-Azadani
<mmnasr at gmail.com>wrote:

> 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.
>

1) What is wrong with more DAs?

2) Get the coordinate vector for one, copy it, and then shift it to get the
others

   Matt


> 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
>>
>
>


-- 
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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