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.
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
>>
>>
>
