On Dec 6, 2011, at 10:26 PM, Xiangdong Liang wrote:
> Hello everyone,
>
> Can anyone help on the usage of MAT_IGNORE_ZERO_ENTRIES? Suppose I
> want to have a 10-by-10 sparse matrix, where each row has maximum two
> nonzeros. I would like to have petsc ignore the 0.0 values by not
> allocating space for 0.0 values. In my problem, the nonzero pattern of
> sparse matrix will never change. I hope the ignore of zero entries
> will save lots of operations when I am doing matrix-vector product or
> spare-direct decomposition .
>
> Below is my script. When I check the mat_view_info, I have
>
> Matrix Object:
> type=mpiaij, rows=10, cols=10
> total: nonzeros=20, allocated nonzeros=40
> not using I-node (on process 0) routines
>
> Is there a way to have nonzeros=10, and allocated nonzeros=10, since
> the number of real nonzeros=10? Thanks.
Those "extra" nonzeros are not actually in the sparse matrix so they do not
cause extra multiples. You can safely ignore them.
Barry
>
> Xiangdong
>
> -----------------------------------------------------------
> Mat A; int N=10, i, ns,ne;
>
> ierr=MatCreateMPIAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,N,N,2,NULL,2,NULL,&A);CHKERRQ(ierr);
> ierr = MatGetOwnershipRange(A, &ns, &ne); CHKERRQ(ierr);
> for (i=ns;i<ne;i++) { ierr=MatSetValue(A,i, i, 1.0,
> ADD_VALUES); CHKERRQ(ierr); ierr=MatSetValue(A,i, (i+1)%N, 0.0,
> ADD_VALUES); CHKERRQ(ierr); }
> MatSetOption(A,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE); ierr =
> MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr); ierr =
> MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
>
> --------------------------------------------------------
>
>
> On Thu, Dec 1, 2011 at 10:01 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>
>> The checks in the code are lines like
>>
>> if (value == 0.0 && ignorezeroentries && (is == ADD_VALUES)) continue;
>>
>> hence changing the source code to ignore small values is not difficult.
>> But I think this is a terribly cheesy hack and would hope people would not
>> do this.
>>
>> Barry
>>
>>
>>
>> On Dec 1, 2011, at 8:42 PM, Mohamad M. Nasr-Azadani wrote:
>>
>>> I was always wondering how difficult it would be to define a constant say,
>>> ZERO_DROP_TOLERANCE so that when the matrix is setup,
>>> MatAssemblyBegin()/End(), it automatically ignores the values below this
>>> threshold?
>>> I understand the for the matrices that might change in successive
>>> iterations, that might not be a good idea since the memory reallocation
>>> could be very slow, but for a lot of cases which a constant matrix, that
>>> could be simply helpful.
>>>
>>> Best,
>>> Mohamad
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Dec 1, 2011 at 5:00 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>
>>> On Dec 1, 2011, at 6:44 PM, Xiangdong Liang wrote:
>>>
>>>> Hello everyone,
>>>>
>>>> I have a question about whether zeros will change the sparse pattern.
>>>> Suppose I am generating two sparse matrices A and B. A is generated
>>>> with exactly number of nonzeros, say 10 nnz per row. When I generate
>>>> matrix B, I specify 12 nonzeros, but two of them are given zero values
>>>> by MatSetValue. Will A and B have same sparsity patterns and
>>>> performance ? In other words, will PETSc simply ignore these zeros
>>>> entries? I output these A and B in matlab, and it seems that these
>>>> zeros entries are ignored. I just want to double check on this.
>>>>
>>>> Is the option MAT_IGNORE_ZERO_ENTRIES on by default?
>>>
>>> No, by default PETSc will insert the zero values thus increasing the
>>> nonzero pattern. If you set that option to the matrix then inserting values
>>> it will not introduce an increase in the pattern.
>>>
>>>
>>> BTW: if you then load the matrix via a binary file to MATLAB it may be
>>> that MATLAB silently removes those locations so you don't see them.
>>> Barry
>>>
>>>> Thanks.
>>>>
>>>> Best,
>>>> Xiangdong
>>>
>>>
>>
