[petsc-users] Matrix and vector type selection & memory allocation for efficient matrix import?

[Matthew Knepley]

On Fri, Apr 20, 2018 at 11:05 AM, Klaus Burkart <k_burkart at yahoo.com> wrote:

> I think I understood the matrix structure for parallel computation with
> the rows, diagonal (d) and off-diagonal (o) structure, where I have
> problems is how to do the setup including memory allocation in PETSc:
>
> Lets assume, I use a 16 core workstation (=16 processes) and the number of
> nonzeros varies in each row for both d and o and the number of rows
> assigned to each process differs too - at least for the nth process.
>
> Looking at the manual and http://www.mcs.anl.gov/petsc/petsc-current/docs/
> manualpages/Mat/MatCreateAIJ.html#MatCreateAIJ, I don't understand how to
> enter a global matrix when n is NOT the same for each process as e.g. in
> MatSetSizes(A, m,n,M,N); n and m are integers, not arrays?
>

This is SPMD programming, so the call on each process gives a different n,
and collectively you have 16 different n values.

"Using MPI" is a great book for understanding this.

  Thanks,

    Matt


>     MatCreate(...,&A);
>
>     MatSetType(A,MATMPIAIJ);
>
>     MatSetSizes(A, m,n,M,N); // seems to assume n and m are the same for
> each process which isn't even the case in the example on the page mentioned
> above?!
>
>     MatMPIAIJSetPreallocation(A,...);
>
>
> How can I enter the parallel global-local matrix structure?
>
> How can the memory preallocation be done?
>
> Klaus
>
> Am Donnerstag, 19. April 2018, 01:47:59 MESZ hat Smith, Barry F. <
> bsmith at mcs.anl.gov> Folgendes geschrieben:
>
>
>
>
> > On Apr 18, 2018, at 4:42 PM, k_burkart at yahoo.com wrote:
> >
> > So, practically speaking, l should invent routines to decompose the
> matrix e.g. into a block matrix structure to be able to make real use of
> PETSc ie. be able to solve a linear system using more than one process/core?
>
>   To really use PETSc efficiently/effectively you need to generate your
> matrix in parallel.
>
>   Barry
>
> >
> > Klaus
> >
> > Von meinem Huawei-Mobiltelefon gesendet
> >
> >
> > -------- Originalnachricht --------
> > Betreff: Re: [petsc-users] Matrix and vector type selection & memory
> allocation for efficient matrix import?
> > Von: "Smith, Barry F."
> > An: Klaus Burkart
> > Cc: PETSc Users List
> >
> >
> >
> > If you can only generate the nonzero allocation sequentially you can
> only solve sequentially which means your matrix is MATSEQAIJ and your
> vector is VECSEQ and your communicator is PETSC_COMM_SELF.
> >
> > If you pass and array for nnz, what you pass for nz is irrelevant, you
> might as well pass 0.
> >
> > Barry
> >
> >
> > > On Apr 18, 2018, at 10:48 AM, Klaus Burkart wrote:
> > >
> > > More questions about matrix and vector type selection for my
> application:
> > >
> > > My starting point is a huge sparse matrix which can be symmetric or
> asymmetric and a rhs vector. There's no defined local or block structure at
> all, just row and column indices and the values and an array style rhs
> vector together describing the entire linear system to be solved. With
> quite some effort, I should be able to create an array nnz[N] containing
> the number of nonzeros per row in the global matrix for memory allocation
> which would leave me with MatSeqAIJSetPreallocation(M, 0, nnz); as the only
> option for efficient memory allocation ie. a MATSEQAIJ matrix and VECSEQ. I
> assume here, that 0 indicates different numbers of nonzero values in each
> row, the exact number being stored in the nnz array. Regarding this detail
> but one example assume a constant number of nz per row so I am not sure
> whether I should write 0 or NULL for nz?
> > >
> > > I started with:
> > >
> > > MatCreate(PETSC_COMM_WORLD, &M);
> > > MatSetSizes(M, PETSC_DECIDE, PETSC_DECIDE, N, N);
> > > MatSetFromOptions(M);
> > >
> > > taken from a paper and assume, the latter would set the matrix type to
> MATSEQAIJ which might conflict with PETSC_COMM_WORLD. Maybe
> decompositioning took place at an earlier stage and the authors of the
> paper were able to retrieve the local data and structure.
> > >
> > > What type of matrix and vector should I use for my application e.g.
> MATSEQAIJ and VECSEQ to be able to use MatSeqAIJSetPreallocation(M, 0,
> nnz); for efficient memory allocation?
> > >
> > > In this case, where would the decompositioning / MPI process
> allocation take place?
> >
>



-- 
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.caam.rice.edu/~mk51/>
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