[petsc-users] Creating SBAIJ matrix using 1-based csr arrays ia, ja and acsr

[Kirill Voronin]

Thank you for the prompt answer!

I shifted the indices but when calling MatSeqSBAIJSetPreallocationCSR got
the error - nnz cannot be greater than block row length: local row 0 value
8 rowlength 1.

Can anyone please make a bit more clear some details of block AIJ format
in PETSC?

My code looks like:
-----------------------------------------------------
  ierr = MatCreate(comm,&Afromcsr);CHKERRQ(ierr);
  ierr = MatSetType(Afromcsr,"sbaij"); CHKERRQ(ierr);
  ierr = MatSetSizes(Afromcsr,dim,dim,dim,dim);CHKERRQ(ierr);
  ierr = MatSetFromOptions(Afromcsr);CHKERRQ(ierr);

  printf("fill in for values of acsr \n");

  for (i = 0; i <= dim; i++)
	ia[i] -= 1;
  for (i = 0; i < ia[dim]; i++)
	ja[i] -= 1;
  ierr = MatSeqSBAIJSetPreallocationCSR(Afromcsr, dim, ia, ja, acsr);
CHKERRQ(ierr);
-----------------------------------------------------------
The questions:

1) Why no MatMPISBAIJSetPreaalocationCSR? Or should
MatCreateMPISBAIJWithArrays be used instead?
2) What is block size and why it is assumed to be 1 (according to the
error I got).
3) What is a local row when I call MatSeqSBAIJSetPreallocationCSR?
4) Can I consider my matrix as a single block when calling
MatSeqSBAIJSetPreallocationCSR ?
5) Can I put my acsr array (with values of nonzero elements of the matrix)
as the argument v[] in the MatSeqSBAIJSetPreallocationCSR? The manual
pages told me that v[] should be of the form v[nnz][bs][bs] and I don't
get why not only v[nnz]?

Sorry for that set of questions but I missed an example of usage for a
symmetric CSR matrix.

Maybe a few lines of code for getting a symmetric (with upper part only
stored) matrix from ia, ja and a arrays (usual CSR format) would help me
to get the whole idea of PETSC matrix creating.

Thanks in advance!


Best regards,

Kirill Voronin


> On Tue, Nov 25, 2014 at 9:07 AM, Kirill Voronin
> <kvoronin at labchem.sscc.ru>
> wrote:
>
>
>>
>> Hello!
>>
>>
>> I am trying to create a matrix for solving Ax = b with PETSC with given
>>  1-based(!) indexed ia, ja and acsr arrays for a symmetric (only upper
>> part is stored) complex matrix.
>>
>> Without memory preallocation it takes too long to fill in all the
>> values of acsr into my Mat A object.
>>
>> But I failed to call
>> ierr = MatSeqSBAIJSetPreallocationCSR(Afromcsr, dim, iaHSS, jaHSS,
>> acHSS); because of the 1 based indexing. And I didn't find an option how
>> to handle this issue.
>>
>> From the manual:
>> "By default the internal data representation for the AIJ formats employs
>>  zero-based indexing. For compatibility with standard Fortran storage,
>> thus enabling use of external Fortran software packages such as SPARSKIT,
>> the option -mat_aij_oneindex enables one-based indexing, where the
>> stored row and column indices begin at one, not zero. All user calls to
>> PETSc routines,
>> regardless of this option, use zero-based indexing."
>>
>> So, what can you recommend to do? I obviously don't want to double the
>> memory for storing ia and ja arrays in 0-based indexing. I don't want to
>>  change the indexing everywhere to 0-based since I use a piece of
>> external code which works only for 1-based indexing as a preconditioner
>> in PETSC KSP solver.
>>
>>
>
> Just decrement ja, make the call, and increment ja.
>
>
> Thanks,
>
>
> Matt
>
>
>
>> Thanks in advance!
>>
>>
>> With best regards,
>>
>>
>> Kirill Voronin
>>
>>
>>
>>
>>
>
>
> --
> 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
>
>


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