On Wed, Dec 7, 2011 at 12:11 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> 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.
I am sorry I am still not clear. Do "extra" nonzeros refer to
?nonzeros=20? or "allocated nonzeros=40"? With or without
MatSetOption(A,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE), I see the same
mat_view_info. How can I see the differences in the spare matrix
generated With/Without this option? Thanks.
Xiangdong
>
> ?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
>>>>
>>>>
>>>
>
