[petsc-users] MatGetRow for global rows of a parallel matrix
Matthew Knepley
knepley at gmail.com
Wed Jul 1 06:41:47 CDT 2020
On Wed, Jul 1, 2020 at 7:32 AM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
> I'm sorry but I still can't understand how to put an input as these
> parameters. It is the first time I saw 'const' for IS. If it doesn't
> refer IS, then as a parameter for row and column indices, how should I
> give them as a valid input? It still should be an IS, right?
>
> Lastly, I tried to use in the form:
>
> IS idUi;
> ISCreateStride(PETSC_COMM_WORLD,siz,0,1,&idUi);
> Mat *submat;
> MatCreateSubMatrices(U,nev,&idUi,&idUi,MAT_INITIAL_MATRIX,&submat);
>
You gave n = 4 (you call it nev), but you only have 1 rowIS. You are
supposed to give an array of 4.
Thanks,
Matt
> where nev = 4, siz = 72 and U is 72*4 matrix.
>
> But then, the error becomes about the matrix, U:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Invalid argument
> [1]PETSC ERROR: Wrong type of object: Parameter # 1
> Invalid argument
> [0]PETSC ERROR: Wrong type of object: Parameter # 1
> [0]PETSC ERROR: See
> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [0]PETSC ERROR: Petsc Release Version 3.13.2, Jun 02, 2020
> [0]PETSC ERROR: ./deneme_new_vecscatter_arastep on a
> arch-linux2-c-debug named b342.wls.metu.edu.tr by edaoktay Wed Jul 1
> 14:25:00 2020
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --download-mpich --download-openblas --download-slepc --download-metis
> --download-parmetis --download-chaco --with-X=1
> [1]PETSC ERROR: See
> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> shooting.
> [1]PETSC ERROR: Petsc Release Version 3.13.2, Jun 02, 2020
> [1]PETSC ERROR: [0]PETSC ERROR: #1 ISSorted() line 1777 in
> /home/edaoktay/petsc-3.13.2/src/vec/is/is/interface/index.c
> [0]PETSC ERROR: ./deneme_new_vecscatter_arastep on a
> arch-linux2-c-debug named b342.wls.metu.edu.tr by edaoktay Wed Jul 1
> 14:25:00 2020
> [1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
> --download-mpich --download-openblas --download-slepc --download-metis
> --download-parmetis --download-chaco --with-X=1
> [1]PETSC ERROR: #2 MatCreateSubMatrices_MPIDense_Local() line 104 in
> /home/edaoktay/petsc-3.13.2/src/mat/impls/dense/mpi/mmdense.c
> [0]PETSC ERROR: #3 MatCreateSubMatrices_MPIDense() line 66 in
> /home/edaoktay/petsc-3.13.2/src/mat/impls/dense/mpi/mmdense.c
> #1 ISSorted() line 1777 in
> /home/edaoktay/petsc-3.13.2/src/vec/is/is/interface/index.c
> [1]PETSC ERROR: #2 MatCreateSubMatrices_MPIDense_Local() line 104 in
> /home/edaoktay/petsc-3.13.2/src/mat/impls/dense/mpi/mmdense.c
> [0]PETSC ERROR: #4 MatCreateSubMatrices() line 6758 in
> /home/edaoktay/petsc-3.13.2/src/mat/interface/matrix.c
> [1]PETSC ERROR: #3 MatCreateSubMatrices_MPIDense() line 66 in
> /home/edaoktay/petsc-3.13.2/src/mat/impls/dense/mpi/mmdense.c
> [1]PETSC ERROR: #4 MatCreateSubMatrices() line 6758 in
> /home/edaoktay/petsc-3.13.2/src/mat/interface/matrix.c
>
> Before I used &idUi, I tried to use just idUi (without & sign) and it
> didn't work, so I decided to try using this way, since may be 'const'
> refers this one. But how can my matrix be of wrong type? It is MPI
> Dense.
>
> Thanks!
>
> Eda
>
> Matthew Knepley <knepley at gmail.com>, 1 Tem 2020 Çar, 13:43 tarihinde şunu
> yazdı:
> >
> > On Wed, Jul 1, 2020 at 6:34 AM Eda Oktay <eda.oktay at metu.edu.tr> wrote:
> >>
> >> 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().
> >
> >
> > The 'const' refers to the array, not the IS:
> >
> >
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatCreateSubMatrices.html
> >
> > Thanks,
> >
> > Matt
> >
> >>
> >> 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/
> >> >
> >> >
> >
> >
> >
> > --
> > 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/ <http://www.cse.buffalo.edu/~knepley/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200701/802e088f/attachment-0001.html>
More information about the petsc-users
mailing list