[petsc-dev] MatCopy to zero preallocated matrix

[Matthew Knepley]

On Thu, Mar 1, 2012 at 5:14 PM, Vaclav Hapla <vaclav.hapla at vsb.cz> wrote:

> **
> This is what I used before for a long time until now when I updated PETSc
> and it started to complain "New nonzero caused a malloc!" when I wanted to
> add
>

You can turn off this message using MatSetOption(). We put it there so
people know when allocation is being done since it
can be slow.

  Thanks,

    Matt


> some new nonzero outside of the original nnz-pattern. MatDuplicate is
> always retaining the pattern, isn't it?
> Vaclav
>
> On 03/02/2012 12:06 AM, Matthew Knepley wrote:
>
> On Thu, Mar 1, 2012 at 5:03 PM, Vaclav Hapla <vaclav.hapla at vsb.cz> wrote:
>
>> Dear PETSc team,
>> why I am not able to do this:
>>
>> ...
>> MatCreate(PETSC_COMM_SELF, &Kreg);
>> MatSetSizes(Kreg,m,n,m,n);
>> MatSetType(Kreg, MATSEQAIJ);
>> MatSeqAIJSetPreallocation(Kreg,0,nnz);
>> MatAssemblyBegin(Kreg, MAT_FINAL_ASSEMBLY);
>> MatAssemblyEnd(   Kreg, MAT_FINAL_ASSEMBLY);
>> PetscFree(nnz);
>> {
>>    PetscInt nz_Kreg;
>>    MatGetRow(Kreg, 0, &nz_Kreg, PETSC_IGNORE, PETSC_IGNORE);
>>    PetscPrintf(PETSC_COMM_SELF, "nnz %d  Kreg %d\n", nnz[0], nz_Kreg);
>>  // prints nnz 11  Kreg 0 !!!
>> }
>> MatCopy(K_loc, Kreg, DIFFERENT_NONZERO_PATTERN); //fails: New nonzero at
>> (0,0) caused a malloc!
>>
>
>  I think you want
>
>
> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatDuplicate.html
>
>  which does it in one line.
>
>     Matt
>
>
>>
>> PETSc complains about new nonzero - not surprisingly because
>> MatAssemblyBegin/End filters zeros as I understand.
>> But when I comment out MatAssemblyBegin/End, MatCopy complains that it is
>> only for assembled matrices.
>>
>> I think that to call MatSetValues on all allocated nonzeros just to make
>> them survive MatAssemblyBegin/End or to replace MatCopy call by loop over
>> raw array is both quite awkward.
>> Maybe one should be able to turn the filter in MatAssemblyBegin/End off.
>> Or is there any other way out?
>>
>> BTW, what I need is to make a copy Kreg of given matrix K_loc but with
>> few additional preallocated positions which are filled later. Is there some
>> other convenient solution?
>>
>> Cheers,
>> Vaclav Hapla
>>
>
>
>
>  --
> 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
>
>
>
> --
>
> Vaclav Hapla
> Research assistant
> SPOMECH project <http://spomech.vsb.cz/>
> Centre of Excellence IT4Innovations <http://www.it4i.eu/>
>
> tel.: (+420) 59 732 6291
> VSB-Technical University of Ostrava
> 17.listopadu 15/2172
> 708 33 Ostrava-Poruba
> Czech Republic
>



-- 
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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