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

Tue May 23 12:02:28 CDT 2017

On Tue, May 23, 2017 at 11:51 AM, Franck Houssen <franck.houssen at inria.fr>
wrote:

> Not sure to know what question you're talking about ?!...
> I use MatIS to test some kind of domain decomposition methods. I define my
> own preconditioner for that: in the apply callback, I need to matmult my
> (matIS) matrix with the incoming vector.
>

Okay. I will create an example using your suggestion.

  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 18:46:34
> *Objet: *Re: [petsc-dev] Using PETSc MatIS, how to matmult a global IS
> matrix and a global vector ?
>
> 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/
>
>
>

-- 
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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