[petsc-users] A few questions about hdf5 viewer

Thu Jan 19 18:00:19 CST 2012

1) What is wrong with more DAs?
Nothing. Just I never needed more than one DA.

2) Get the coordinate vector for one, copy it, and then shift it to get the
others
Well, I played around a bit and I realized that the coordinate vector
returned from DMDAGetCoordinates() is actually of size Nx*Ny*Nz*3 (for DA
3D).
This will double the size of my output file.
What I need is just to add 3 1-D arrays of (x[Nx]+y[Ny]+z[Nz]) including
the grid coordinates to the end of the *.h5 file and then later on, I can
use any visualization software to load the data using those coordinates. I
am using orthogonal grid, that's why I don't need  all the
(x,y,z) coordinates for each cell.

Thanks again,
Mohamad

On Thu, Jan 19, 2012 at 3:30 PM, Matthew Knepley <knepley at gmail.com> wrote:

> 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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