On Dec 6, 2011, at 11:39 PM, Xiangdong Liang wrote:
> 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.
You will see the same message. You are not setting any zero entries so the
option doesn't matter in your case.
> How can I see the differences in the spare matrix
> generated With/Without this option?
You will not see a difference in the output.
Don't worry about it. The option does prevent zero entries from being
inserted and thus slowing down the matrix operations.
Barry
> 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
>>>>>
>>>>>
>>>>
>>
