[petsc-users] [petsc-dev] Using PETSc MatIS, how to matmult a global IS matrix and a global vector ?

Tue May 23 06:27:14 CDT 2017

On Tue, May 23, 2017 at 6:23 AM, Stefano Zampini <stefano.zampini at gmail.com>
wrote:

> As I said, the local sizes of the MATIS matrix are NOT the sizes of the
> subdomain problem. As in all PETSc code, the local sizes of the matrix
> correspond to the local size of the non-overlapping right and left vectors
> used in matmult operations. You can use PETSC_DECIDE in place of localsize
> in your call to MatCreateIS. The size of the subdomain problem in MATIS is
> the local size of the l2g map.
>

I just want to make sure that MatIS is really what you want, since its a
little more complex than other options.

MatIS is useful for methods that need unassembled matrices, like domain
decomposition methods which use
Neumann problems on subdomains. If you are fine with assembled sparse
matrices, than the normal AIJ should
be easier to handle. Just checking.

  Thanks,

     Matt

> Il 23 Mag 2017 11:53, "Franck Houssen" <franck.houssen at inria.fr> ha
> scritto:
>
>> The first thing I did was to put 3, not 4 : I got an error thrown in
>> MatCreateIS (see the git diff + stack below). As the error said I used
>> globalSize = numberOfMPIProcessus * localSize : my understanding is that,
>> when using MatIS, the global size needs to be the sum of all local sizes.
>> Correct ?
>>
>> I have a 3x3 global matrix made of two overlapping 2x2 local matrix (=
>> diagonal with 1.). Each local matrix correspond to one domain (each domain
>> is delegated to one MPI proc, so, I have 2 MPI procs because I have 2
>> domains).
>> This is the simplest possible example: I have two 2x2 (local) diag matrix
>> that overlap so that the global matrix built from them is 1, 2, 1 on the
>> diagonal (local contributions add up in the middle).
>> I need to MatMult this global matrix with a global vector filled with 1.
>>
>> Franck
>>
>> Git diff :
>>
>> --- a/matISLocalMat.cpp
>> +++ b/matISLocalMat.cpp
>> @@ -16,7 +16,7 @@ int main(int argc,char **argv) {
>>    int size = 0; MPI_Comm_size(MPI_COMM_WORLD, &size); if (size != 2)
>> return 1;
>>    int rank = 0; MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>>
>> -  PetscInt localSize = 2, globalSize = localSize*2 /*2 MPI*/;
>> +  PetscInt localSize = 2, globalSize = 3;
>>    PetscInt localIdx[2] = {0, 0};
>>    if (rank == 0) {localIdx[0] = 0; localIdx[1] = 1;}
>>    else           {localIdx[0] = 1; localIdx[1] = 2;}
>>
>>
>>
>> Stack error:
>>
>> [0]PETSC ERROR: Nonconforming object sizes
>> [0]PETSC ERROR: Sum of local lengths 4 does not equal global length 3, my
>> local length 2
>> [0]PETSC ERROR: [0] ISG2LMapApply line 17 /home/fghoussen/Documents/INRI
>> A/petsc-3.7.6/src/vec/is/utils/isltog.c
>> [0]PETSC ERROR: [0] MatSetValues_IS line 692
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
>> [0]PETSC ERROR: [0] MatSetValues line 1157 /home/fghoussen/Documents/INRI
>> A/petsc-3.7.6/src/mat/interface/matrix.c
>> [0]PETSC ERROR: [0] MatISSetPreallocation_IS line 95
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
>> [0]PETSC ERROR: [0] MatISSetPreallocation line 80
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
>> [0]PETSC ERROR: [0] PetscSplitOwnership line 80
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/sys/utils/psplit.c
>> [0]PETSC ERROR: [0] PetscLayoutSetUp line 129
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/vec/is/utils/pmap.c
>> [0]PETSC ERROR: [0] MatSetLocalToGlobalMapping_IS line 628
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/impls/is/matis.c
>> [0]PETSC ERROR: [0] MatSetLocalToGlobalMapping line 1899
>> /home/fghoussen/Documents/INRIA/petsc-3.7.6/src/mat/interface/matrix.c
>> [0]PETSC ERROR: [0] MatCreateIS line 986 /home/fghoussen/Documents/INRI
>> A/petsc-3.7.6/src/mat/impls/is/matis.c
>>
>>
>>
>> ------------------------------
>>
>> *De: *"Stefano Zampini" <stefano.zampini at gmail.com>
>> *À: *"Matthew Knepley" <knepley at gmail.com>
>> *Cc: *"Franck Houssen" <franck.houssen at inria.fr>, "PETSc" <
>> petsc-users at mcs.anl.gov>, "PETSc" <petsc-dev at mcs.anl.gov>
>> *Envoyé: *Dimanche 21 Mai 2017 23:02:37
>> *Objet: *Re: [petsc-dev] Using PETSc MatIS, how to matmult a global IS
>> matrix and a global vector ?
>>
>> Franck,
>>
>> PETSc takes care of doing the matrix-vector multiplication properly using
>> MatIS.  As Matt said, the layout of the vectors is the usual parallel
>> layout.
>> The local sizes of the MatIS matrix (i.e. the local size of the left and
>> right vectors used in MatMult) are not the sizes of the local subdomain
>>  matrices in MatIS.
>>
>>
>> On May 21, 2017, at 6:47 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Sun, May 21, 2017 at 11:26 AM, Franck Houssen <franck.houssen at inria.fr
>> > wrote:
>>
>>> Using PETSc MatIS, how to matmult a global IS matrix and a global vector
>>> ? Example is attached : I don't get what I expect that is a vector such
>>> that proc0 = [1, 2] and proc1 = [2, 1]
>>>
>>
>> 1) I think the global size of your matrix is wrong. You seem to want 3,
>> not 4
>>
>> 2) Global vectors have a non-overlapping row partition. You might be
>> thinking of local vectors
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>
>>
>> --
>> 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
>>
>> http://www.caam.rice.edu/~mk51/
>>
>>
>> ------------------------------
>>
>> *De: *"Stefano Zampini" <stefano.zampini at gmail.com>
>> *À: *"Matthew Knepley" <knepley at gmail.com>
>> *Cc: *"Franck Houssen" <franck.houssen at inria.fr>, "PETSc" <
>> petsc-users at mcs.anl.gov>, "PETSc" <petsc-dev at mcs.anl.gov>
>> *Envoyé: *Dimanche 21 Mai 2017 23:02:37
>> *Objet: *Re: [petsc-dev] Using PETSc MatIS, how to matmult a global IS
>> matrix and a global vector ?
>>
>> Franck,
>>
>> PETSc takes care of doing the matrix-vector multiplication properly using
>> MatIS.  As Matt said, the layout of the vectors is the usual parallel
>> layout.
>> The local sizes of the MatIS matrix (i.e. the local size of the left and
>> right vectors used in MatMult) are not the sizes of the local subdomain
>>  matrices in MatIS.
>>
>>
>> On May 21, 2017, at 6:47 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Sun, May 21, 2017 at 11:26 AM, Franck Houssen <franck.houssen at inria.fr
>> > wrote:
>>
>>> Using PETSc MatIS, how to matmult a global IS matrix and a global vector
>>> ? Example is attached : I don't get what I expect that is a vector such
>>> that proc0 = [1, 2] and proc1 = [2, 1]
>>>
>>
>> 1) I think the global size of your matrix is wrong. You seem to want 3,
>> not 4
>>
>> 2) Global vectors have a non-overlapping row partition. You might be
>> thinking of local vectors
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> Franck
>>>
>>
>>
>>
>> --
>> 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
>>
>> http://www.caam.rice.edu/~mk51/
>>
>>
>>
>>

-- 
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

http://www.caam.rice.edu/~mk51/
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