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

Tue May 23 11:46:34 CDT 2017

On Tue, May 23, 2017 at 11:28 AM, Franck Houssen <franck.houssen at inria.fr>
wrote:

> OK, thanks. This is helpfull... But I really think the doc should be more
> verbose about that: this is really confusing and I didn't find any simple
> example to begin with which make all this even more confusing (personal
> opinion).
>

Did you respond to my other question (how are you using them)? That would
help me understand how to phrase it.

  Thanks,

    Matt

> Franck
>
>
> ------------------------------
>
> *De: *"Matthew Knepley" <knepley at gmail.com>
> *À: *"Franck Houssen" <franck.houssen at inria.fr>
> *Cc: *"Stefano Zampini" <stefano.zampini at gmail.com>, "PETSc" <
> petsc-users at mcs.anl.gov>, "PETSc" <petsc-dev at mcs.anl.gov>
> *Envoyé: *Mardi 23 Mai 2017 13:21:21
> *Objet: *Re: [petsc-dev] Using PETSc MatIS, how to matmult a global IS
> matrix and a global vector ?
>
> On Tue, May 23, 2017 at 4:53 AM, Franck Houssen <franck.houssen at inria.fr>
> wrote:
>
>> 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 ?
>>
>
> No. MatIS means that the matrix is not assembled. The easiest way (for me)
> to think of this is that processes do not have
> to hold full rows. One process can hold part of row i, and another
> processes can hold another part. However, there are still
> the same number of global rows.
>
> 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).
>>
>
> So the global size is 3. The local size here is not the size of the local
> IS block, since that is a property only of MatIS. It is the
> size of the local piece of the vector you multiply. This allows PETSc to
> understand the parallel layout of the Vec, and how it
> matched the Mat.
>
> This is somewhat confusing because FEM people mean something different by
> "local" than we do here, and in fact we use this
> other definition of local when assembling operators.
>
>    Matt
>
>
>> 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/
>> INRIA/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/
>> INRIA/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/
>> INRIA/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/
>
>
>

-- 
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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