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

[Hong]

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?

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/pets
>> c/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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