[petsc-dev] Fwd: Re: MatDestroySubMatrices_SeqAIJ and reference counting
Stefano Zampini
stefano.zampini at gmail.com
Tue Jan 16 01:45:02 CST 2018
Hong,
It works nicely. thanks. If you are fine, I can push it to maint and add a
test case in ex4.c
Stefano
2018-01-15 22:10 GMT+03:00 Hong <hzhang at mcs.anl.gov>:
> Stefano:
> This patch
> diff --git a/src/mat/impls/aij/seq/aij.c b/src/mat/impls/aij/seq/aij.c
> index df16825..5c40de6 100644
> --- a/src/mat/impls/aij/seq/aij.c
> +++ b/src/mat/impls/aij/seq/aij.c
> @@ -2542,11 +2542,14 @@ PetscErrorCode MatDestroySubMatrices_SeqAIJ(PetscInt
> n,Mat *mat[])
> c = (Mat_SeqAIJ*)C->data;
> submatj = c->submatis1;
> if (submatj) {
> - ierr = submatj->destroy(C);CHKERRQ(ierr);
> - ierr = MatDestroySubMatrix_Private(submatj);CHKERRQ(ierr);
> - ierr = PetscLayoutDestroy(&C->rmap);CHKERRQ(ierr);
> - ierr = PetscLayoutDestroy(&C->cmap);CHKERRQ(ierr);
> - ierr = PetscHeaderDestroy(&C);CHKERRQ(ierr);
> + if (--((PetscObject)C)->refct > 0) {
> + } else {
> + ierr = submatj->destroy(C);CHKERRQ(ierr);
> + ierr = MatDestroySubMatrix_Private(submatj);CHKERRQ(ierr);
> + ierr = PetscLayoutDestroy(&C->rmap);CHKERRQ(ierr);
> + ierr = PetscLayoutDestroy(&C->cmap);CHKERRQ(ierr);
> + ierr = PetscHeaderDestroy(&C);CHKERRQ(ierr);
> + }
> } else {
>
> should fix the problem. Let me know your thought.
> Hong
>
> On Sun, Jan 14, 2018 at 9:09 PM, Hong <hzhang at mcs.anl.gov> wrote:
>
>> 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/petsc/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)
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>
--
Stefano
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