[petsc-users] MatGetRow for global rows of a parallel matrix

[Eda Oktay]

Der Barry,

ı am trying to use your way but I couldn't understand how I create sub
matrices by using MatCreateSubMatrices() since as input, the function
needs const IS instead of IS and I couldn't understand how to get a
const IS. I tried to use ISCreateStride since this IS should be 0:71
because as you mentioned, the sub matrix should consist of the entire
matrix. However, since ISCreateStride produces IS, not const IS, I
couldn't use it in MatCreateSubMatrices().

Thanks

Eda

Barry Smith <bsmith at petsc.dev>, 10 Haz 2020 Çar, 19:59 tarihinde şunu yazdı:
>
>
>   You can use MatCreateSubMatrices() with each process getting a single sequential dense sub matrix that consists of the entire matrix.
>
>   Use VecDuplicateVecs() to create an array of 72 vectors (create a single seq vector of size 4 as the input to this routine)
>
>   Then use MatDenseGetArrayRead() to access the upper left corner of the new sequential dense matrix
>
>   Loop over the vectors calling VecGetArray()
>      Then loop over the row of the dense array filling up the vector
>
>   Because dense matrices are stored by column, you have to do this looping to fill up the vectors, they can't share the space with the matrix.
>
>   Barry
>
>
>
> On Jun 10, 2020, at 11:36 AM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Wed, Jun 10, 2020 at 12:26 PM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
>>
>> Matthew Knepley <knepley at gmail.com>, 10 Haz 2020 Çar, 19:13 tarihinde
>> şunu yazdı:
>> >
>> > On Wed, Jun 10, 2020 at 12:07 PM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
>> >>
>> >> Der Matt,
>> >>
>> >> When I looked at the results, I found that there are some problems I
>> >> couldn't understand.
>> >>
>> >> First of all, I am working on a 72*4 matrix and as I said before, I
>> >> want to have 72 different vectors having size 4 each, whose elements
>> >> consist of the elements in the same row. And of course, all vectors
>> >> should be in all processors (currently I am using 4 processors).
>> >>
>> >> When I use your scatter code, the output vector is divided into 4
>> >> parts for 4 processors and each vector consists of 18 row vectors
>> >> whose elements are arranged in a way that if I want to find zeroth row
>> >> vector, its elements are located in 0th,18th,36th,54th elements.
>> >
>> >
>> > Was the global size of the vector you wrapped around the dense matrix 72*4?
>>
>> Yes it is. I set up its global size  to 72*4.
>>
>> >
>> > If you use CreateToAll(), it will make a vector on each process which has the global size of the original vector.
>>
>> Although I set 72*4, the size of the vectors in each process is 72.
>
>
> You can understand how it is hard to accept, as this code is tested every night. Can you VecView() the input vector
> to CreateToAll and the output vector,  and send that output?
>
>   Thanks,
>
>      Matt
>
>>
>> Thanks,
>>
>> Eda
>>
>> >
>> >   Thanks,
>> >
>> >     Matt
>> >
>> >>
>> >> So, isn't scatter's goal is to scatter all values to all processors?
>> >>
>> >> Furthermore, I am trying to use my vectors in that way but isn't there
>> >> any possible way that I can reach my goal entirely?
>> >>
>> >> Thanks so much for your help,
>> >>
>> >> Eda
>> >>
>> >> Matthew Knepley <knepley at gmail.com>, 10 Haz 2020 Çar, 18:11 tarihinde
>> >> şunu yazdı:
>> >> >
>> >> > On Wed, Jun 10, 2020 at 10:09 AM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
>> >> >>
>> >> >> Dear Matt,
>> >> >>
>> >> >> I have one last question I believe. Up to creating a dense matrix I
>> >> >> did what you've suggested. Thank you so much for that.
>> >> >>
>> >> >> I created a new dense matrix. Now, how should I wrap each vector in a
>> >> >> MatDense again? I mean, what is wrapping vectors in a matrix? To put
>> >> >> each of them again as rows?
>> >> >
>> >> >
>> >> > I thought you need a dense matrix for something, since you started with one. If you
>> >> > do not, just do VecGetArray() on the vector from CreateToAll and use the values.
>> >> >
>> >> >   Thanks,
>> >> >
>> >> >      Matt
>> >> >
>> >> >>
>> >> >> Thanks!
>> >> >>
>> >> >> Eda
>> >> >>
>> >> >> Matthew Knepley <knepley at gmail.com>, 10 Haz 2020 Çar, 16:16 tarihinde
>> >> >> şunu yazdı:
>> >> >> >
>> >> >> > On Wed, Jun 10, 2020 at 9:08 AM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
>> >> >> >>
>> >> >> >> Dear Matt,
>> >> >> >>
>> >> >> >> Matthew Knepley <knepley at gmail.com>, 10 Haz 2020 Çar, 16:03 tarihinde
>> >> >> >> şunu yazdı:
>> >> >> >> >
>> >> >> >> > On Wed, Jun 10, 2020 at 8:56 AM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
>> >> >> >> >>
>> >> >> >> >> Hi all,
>> >> >> >> >>
>> >> >> >> >> I am trying to get all the rows of a parallel matrix as individual
>> >> >> >> >> vectors. For instance, if I have 72*4 matrix, I want to get 72
>> >> >> >> >> different vectors having size 4.
>> >> >> >> >>
>> >> >> >> >> As far as I understood, MatGetRow is only for local rows, so
>> >> >> >> >> MatGetOwnershipRange is used, however, when I tried this one, I
>> >> >> >> >> couldn't get the whole and desired row vectors.
>> >> >> >> >>
>> >> >> >> >> In MatGetRow explanation, it is written that I should use
>> >> >> >> >> MatCreateSubMatrices first, then use MatGetRow. But I couldn't
>> >> >> >> >> understand to which extent I should create submatrices. I just need to
>> >> >> >> >> have all 72 rows as 72 different vectors each having 4 elements.
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > 1) For sparse matrices, the storage is always divided by row, so that values can only be retrieved for local rows with MatGetRow()
>> >> >> >> >
>> >> >> >> > 2) Is this matrix sparse? It sounds like it is dense.
>> >> >> >>
>> >> >> >> Matrix is dense.
>> >> >> >>
>> >> >> >> >
>> >> >> >> > 3) Are you asking to get all matrix values on all processes? If so, I think the easiest thing to do is first wrap a Vec around the
>> >> >> >> >     values, then use VecScatterToAll(), then wrap each one in a MatDense again.
>> >> >> >>
>> >> >> >> Yes, I want all row vectors on all processes. In a dense matrix,
>> >> >> >> should I still wrap a Vec around the values? I know I should use
>> >> >> >> scatter but I couldn't even wrap a Vec around them.
>> >> >> >
>> >> >> >
>> >> >> > I would do
>> >> >> >
>> >> >> >   MatGetSize(&N);
>> >> >> >   MatGetLocalSize(&m);
>> >> >> >   https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatDenseGetArray.html
>> >> >> >   <create vector of local size m*N>
>> >> >> >   https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecPlaceArray.html
>> >> >> >   https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecScatterCreateToAll.html
>> >> >> >   <do scatter>
>> >> >> >   https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecResetArray.html#VecResetArray
>> >> >> >   https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatCreateDense.html
>> >> >> >   <use it>
>> >> >> >   <destroy matrix>
>> >> >> >   <destroy vector from CreateToAll>
>> >> >> >
>> >> >> >   Thanks,
>> >> >> >
>> >> >> >      Matt
>> >> >> >
>> >> >> >>
>> >> >> >> Thanks so much!
>> >> >> >>
>> >> >> >> Eda
>> >> >> >>
>> >> >> >> >
>> >> >> >> >   Thanks,
>> >> >> >> >
>> >> >> >> >      Matt
>> >> >> >> >
>> >> >> >> >>
>> >> >> >> >> Thanks!
>> >> >> >> >>
>> >> >> >> >> Eda
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > 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
>> >> >> >> >
>> >> >> >> > https://www.cse.buffalo.edu/~knepley/
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > 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
>> >> >> >
>> >> >> > https://www.cse.buffalo.edu/~knepley/
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > 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
>> >> >
>> >> > https://www.cse.buffalo.edu/~knepley/
>> >
>> >
>> >
>> > --
>> > 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
>> >
>> > https://www.cse.buffalo.edu/~knepley/
>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
>
>