[petsc-dev] Fwd: Re: MatDestroySubMatrices_SeqAIJ and reference counting

Hong hzhang at mcs.anl.gov
Sun Jan 14 21:09:31 CST 2018 

Stefano:
Sequential version works because it does not use common data structure.
The old version of MatCreateSubMatrices() does not reuse internal data
structures, thus inefficient.
During its optimization, the internal data structures are introduced.

I'll check it and see if I can provide these type of usage.

Hong

>
> On Jan 14, 2018, at 7:16 AM, Hong <hzhang at mcs.anl.gov> wrote:
>
> Stefano,
> MatCreateSubMatrices() must be destroyed by MatDestroySubMatrices()
> because all submatrices in the array share common internal data structure
> for reuse.
>
> +  ierr = PetscObjectReference((PetscObject)submat);CHKERRQ(ierr);
>
> Only submat = submatrices[0] adds reference count.
>
>    ierr = MatDestroySubMatrices(1,&submatrices);CHKERRQ(ierr);
> Now, the internal common data structure is destroyed.
>
> +  ierr = MatDestroy(&submat);CHKERRQ(ierr);
> I guess submat becomes an orphan, it cannot be destroyed using previous
> ops->destroy routine.
>
> Shall we allow user to pick a single matrix out of submatrices array, and
> use/destroy it as a regular single matrix?
>
>
> I accept the fact that the array of submatrices obtained by
> MatCreateSubMatrices shall be destroyed by MatDestroySubMatrices.
> However, not being able to take reference on one of the submats is not
> properly PETSc philosophy :-), as the Mats returned do not behave like
> proper Mat objects
> How difficult is to allow this? and what is the common data structure the
> submats share?
>
> Hong
>
> On Sat, Jan 13, 2018 at 1:09 PM, Stefano Zampini <
> stefano.zampini at gmail.com> wrote:
>
>> Cc'ing petsc-dev
>> ---------- Messaggio inoltrato ----------
>> Da: "Stefano Zampini" <stefano.zampini at gmail.com>
>> Data: 12 Gen 2018 9:32 PM
>> Oggetto: Re: MatDestroySubMatrices_SeqAIJ and reference counting
>> A: "Hong" <hzhang at mcs.anl.gov>
>> Cc:
>>
>>
>> Sorry, I do not understand your question. Where comes matrix B?
>>
>>
>> It’s not important where matrix B comes from. The error is reproducible
>> by just increasing the reference count of any of the submats. See below the
>> patch for ex4.c
>>
>> Can you give me an example of this error?
>>
>>
>> here you have
>>
>> *diff --git a/src/mat/examples/tests/ex4.c b/src/mat/examples/tests/ex4.c*
>> *index 0555a54d9d..1d1961e4fa 100644*
>> *--- a/src/mat/examples/tests/ex4.c*
>> *+++ b/src/mat/examples/tests/ex4.c*
>> @@ -68,7 +68,9 @@ int main(int argc,char **argv)
>>    ierr = MatView(submat,sviewer);CHKERRQ(ierr);
>>    ierr = PetscViewerRestoreSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_
>> COMM_SELF,&sviewer);CHKERRQ(ierr);
>>    ierr = PetscViewerFlush(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
>> +  ierr = PetscObjectReference((PetscObject)submat);CHKERRQ(ierr);
>>    ierr = MatDestroySubMatrices(1,&submatrices);CHKERRQ(ierr);
>> +  ierr = MatDestroy(&submat);CHKERRQ(ierr);
>>
>>    /* Form submatrix with rows 2-4 and all columns */
>>    ierr   = ISDestroy(&icol);CHKERRQ(ierr);
>>
>> Hong
>>
>> Hong,
>>>
>>> can you explain what’s the rationale behind calling explicitly the
>>> Layout and header destroy for the submit case in the loop here
>>> https://bitbucket.org/petsc/petsc/src/ac3af1b492556bac9
>>> 856a6aee1c73992bd0b1779/src/mat/impls/aij/seq/aij.c?at=maste
>>> r&fileviewer=file-view-default#aij.c-2531
>>>
>>> A code like this fails since you don’t take into account reference
>>> counting on the submatrices.
>>>
>>> MatCreateSubMatrices(A,….&submats)
>>> PetscObjectCompose(B,”_XXXX”,submats[0);
>>> …..
>>> MatDestroySubMatrices(..,submats);
>>> MatDestroy(B); //Error, corrupt argument when trying to destroy composed
>>> objects
>>>
>>> Here is a representative valgrind stack trace
>>>
>>> ==90133== Invalid read of size 4
>>> ==90133==    at 0x100368F63: PetscCheckPointer
>>> (/Users/szampini/software/petsc/src/sys/error/checkptr.c:108)
>>> ==90133==    by 0x1001ACA9F: PetscObjectDereference
>>> (/Users/szampini/software/petsc/src/sys/objects/inherit.c:564)
>>> ==90133==    by 0x10019AC07: PetscObjectListDestroy
>>> (/Users/szampini/software/petsc/src/sys/objects/olist.c:154)
>>> ==90133==    by 0x1001A8176: PetscHeaderDestroy_Private
>>> (/Users/szampini/software/petsc/src/sys/objects/inherit.c:115)
>>> ==90133==    by 0x100626CAD: MatDestroy (/Users/szampini/software/pets
>>> c/src/mat/interface/matrix.c:1237)
>>> ==90133==  Address 0x106c4c320 is 1,632 bytes inside a block of size
>>> 4,420 free'd
>>> ==90133==    at 0x10014C9F3: free (in /usr/local/Cellar/valgrind/3.1
>>> 3.0/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
>>> ==90133==    by 0x100229B7A: PetscFreeAlign
>>> (/Users/szampini/software/petsc/src/sys/memory/mal.c:88)
>>> ==90133==    by 0x10022D771: PetscTrFreeDefault
>>> (/Users/szampini/software/petsc/src/sys/memory/mtr.c:309)
>>> ==90133==    by 0x100A7034D: MatDestroySubMatrices_SeqAIJ
>>> (/Users/szampini/software/petsc/src/mat/impls/aij/seq/aij.c:2549)
>>> ==90133==    by 0x1006260BD: MatDestroySubMatrices
>>> (/Users/szampini/software/petsc/src/mat/interface/matrix.c:6957)
>>> ==90133==    by 0x1006D82EC: _DestroyContainer
>>> ==90133==    by 0x1001AFA31: PetscContainerDestroy
>>> (/Users/szampini/software/petsc/src/sys/objects/inherit.c:899)
>>> ==90133==    by 0x1001ACBE5: PetscObjectDereference
>>> (/Users/szampini/software/petsc/src/sys/objects/inherit.c:566)
>>> ==90133==    by 0x10019AC07: PetscObjectListDestroy
>>> (/Users/szampini/software/petsc/src/sys/objects/olist.c:154)
>>> ==90133==    by 0x1001A8176: PetscHeaderDestroy_Private
>>> (/Users/szampini/software/petsc/src/sys/objects/inherit.c:115)
>>> ==90133==    by 0x100626CAD: MatDestroy (/Users/szampini/software/pets
>>> c/src/mat/interface/matrix.c:1237)
>>> ==90133==  Block was alloc'd at
>>> ==90133==    at 0x10014C616: malloc (in /usr/local/Cellar/valgrind/3.1
>>> 3.0/lib/valgrind/vgpreload_memcheck-amd64-darwin.so)
>>> ==90133==    by 0x1002299AC: PetscMallocAlign
>>> (/Users/szampini/software/petsc/src/sys/memory/mal.c:48)
>>> ==90133==    by 0x10022CA73: PetscTrMallocDefault
>>> (/Users/szampini/software/petsc/src/sys/memory/mtr.c:183)
>>> ==90133==    by 0x10022B328: PetscMallocA (/Users/szampini/software/pets
>>> c/src/sys/memory/mal.c:396)
>>> ==90133==    by 0x100C12E05: MatCreate (/Users/szampini/software/pets
>>> c/src/mat/utils/gcreate.c:89)
>>> ==90133==    by 0x100B839F6: MatCreateSubMatrices_MPIAIJ_Local
>>> (/Users/szampini/software/petsc/src/mat/impls/aij/mpi/mpiov.c:2554)
>>> ==90133==    by 0x100B7DEE7: MatCreateSubMatrices_MPIAIJ
>>> (/Users/szampini/software/petsc/src/mat/impls/aij/mpi/mpiov.c:2038)
>>> ==90133==    by 0x10066703A: MatCreateSubMatrices
>>> (/Users/szampini/software/petsc/src/mat/interface/matrix.c:6806)
>>>
>>>
>>
>>
>>
>
>
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