[petsc-dev] Segmentation fault GAMG + MatView
Hong
hzhang at mcs.anl.gov
Thu Feb 9 17:20:59 CST 2017
Change below fixed the problem. I'll turn off additional ops later.
Hong
diff --git a/src/mat/impls/aij/seq/aij.c b/src/mat/impls/aij/seq/aij.c
index 1e0b0b8..5cee782 100644
--- a/src/mat/impls/aij/seq/aij.c
+++ b/src/mat/impls/aij/seq/aij.c
@@ -4169,6 +4169,11 @@ PetscErrorCode MatCreateSeqAIJWithArrays(MPI_Comm
comm,PetscInt m,PetscInt n,Pe
}
#endif
+ if (!a) {
+ (*mat)->ops->view = 0;
+ }
+
ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
Hong
On Thu, Feb 9, 2017 at 4:53 PM, Hong <hzhang at mcs.anl.gov> wrote:
> I'll check it tomorrow and fix it.
> Hong
>
> On Thu, Feb 9, 2017 at 4:27 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> When called with a NULL set of numerical values
>> MatCreateSeqAIJWithArrays() should turn off the function pointers for
>> things that don't make sense for matrices without numerical values, for
>> example MatMult() and MatView(), in fact most function pointers don't make
>> sense and should be turned off.
>> This could be done with a
>> if (!a) {
>> ...
>> }
>> after the call to MatSetType().
>>
>> Barry
>>
>> > On Feb 9, 2017, at 4:08 PM, Matthew Knepley <knepley at gmail.com> wrote:
>> >
>> > On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet <
>> pierre.jolivet at enseeiht.fr> wrote:
>> > Oh my, this example also segfaults (at least on my Mac) when running:
>> > mpirun -np 1 ./ex1 -pc_type gamg -mat_view
>> >
>> > Hong, in
>> >
>> > MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ() on line 1015
>> >
>> > you create a matrix without values, not surprising since this is the
>> symbolic phase. However,
>> > it calls MatAssemblyEnd(), which calls ViewFromOptions(), which gets an
>> SEGV because
>> > it does not think to check if a->a is NULL.
>> >
>> > a) Should we make View robust to missing matrix values?
>> >
>> > b) I don't think this internal matrix should really be viewed like
>> this, so maybe change its prefix?
>> >
>> > Thanks,
>> >
>> > Matt
>> >
>> > [0]PETSC ERROR: [0] MatView_SeqAIJ_ASCII line 560
>> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c
>> > [0]PETSC ERROR: [0] MatView_SeqAIJ line 915
>> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c
>> > [0]PETSC ERROR: [0] MatView line 920 /Volumes/Data/Repositories/pet
>> sc/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: [0] PetscObjectView line 92
>> /Volumes/Data/Repositories/petsc/src/sys/objects/destroy.c
>> > [0]PETSC ERROR: [0] PetscObjectViewFromOptions line 2702
>> /Volumes/Data/Repositories/petsc/src/sys/objects/options.c
>> > [0]PETSC ERROR: [0] MatAssemblyEnd line 5151
>> /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: [0] MatCreateSeqAIJWithArrays line 4137
>> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/aij.c
>> > [0]PETSC ERROR: [0] MatTransposeMatMultSymbolic_SeqAIJ_SeqAIJ line
>> 1012 /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c
>> > [0]PETSC ERROR: [0] MatTransposeMatMult_SeqAIJ_SeqAIJ line 994
>> /Volumes/Data/Repositories/petsc/src/mat/impls/aij/seq/matmatmult.c
>> > [0]PETSC ERROR: [0] MatTransposeMatMult line 9607
>> /Volumes/Data/Repositories/petsc/src/mat/interface/matrix.c
>> > [0]PETSC ERROR: [0] PCGAMGCoarsen_AGG line 914
>> /Volumes/Data/Repositories/petsc/src/ksp/pc/impls/gamg/agg.c
>> > [0]PETSC ERROR: [0] PCSetUp_GAMG line 425 /Volumes/Data/Repositories/pet
>> sc/src/ksp/pc/impls/gamg/gamg.c
>> > [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/pet
>> sc/src/ksp/pc/interface/precon.c
>> > [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/pet
>> sc/src/ksp/ksp/interface/itfunc.c
>> >
>> > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3046-gde967d2
>> GIT Date: 2017-02-09 18:59:37 +0000
>> > [0]PETSC ERROR: Configure options --LDFLAGS=-L/opt/intel/lib
>> --download-hypre --download-metis --download-mumps --download-parmetis
>> --download-pastix --download-ptscotch --with-blacs-include=/opt/intel/mkl/include
>> --with-blacs-lib=/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so
>> --with-blaslapack-dir=/opt/intel/mkl --with-chtml=0
>> --with-mkl_pardiso-include=/opt/intel/mkl/include --with-mkl_pardiso=1
>> --with-scalapack-include=/opt/intel/mkl/include
>> --with-scalapack-lib="[/opt/intel/mkl/lib/libmkl_scalapack_
>> lp64.so,/opt/intel/mkl/lib/libmkl_blacs_mpich_lp64.so]"
>> --with-shared-libraries=1 --with-x=1 PETSC_ARCH=arch-darwin-c-debug
>> >
>> >> On Feb 9, 2017, at 10:52 PM, Pierre Jolivet <
>> pierre.jolivet at enseeiht.fr> wrote:
>> >>
>> >> There, attached.
>> >>
>> >> Thanks.
>> >>
>> >> PS: here is the patch also, just in case
>> >> diff --git a/src/ksp/ksp/examples/tutorials/ex1.c
>> b/src/ksp/ksp/examples/tutorials/ex1.c
>> >> index 6382c09..d9dc69a 100644
>> >> --- a/src/ksp/ksp/examples/tutorials/ex1.c
>> >> +++ b/src/ksp/ksp/examples/tutorials/ex1.c
>> >> @@ -123,6 +123,11 @@ int main(int argc,char **args)
>> >> routines.
>> >> */
>> >> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
>> >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr);
>> >> + char right_options[] = "-ksp_norm_type unpreconditioned
>> -ksp_pc_side right";
>> >> + PetscOptionsInsertString(NULL,right_options);
>> >> + ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
>> >> + ierr = KSPSetUp(ksp);CHKERRQ(ierr);
>> >>
>> >> if (nonzeroguess) {
>> >> PetscScalar p = .5;
>> >>
>> >> <ex1.c>
>> >>
>> >>> On Feb 9, 2017, at 2:56 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >>>
>> >>> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet <
>> pierre.jolivet at enseeiht.fr> wrote:
>> >>>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >>>>
>> >>>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet <
>> pierre.jolivet at enseeiht.fr> wrote:
>> >>>>
>> >>>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >>>>>
>> >>>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet <
>> pierre.jolivet at enseeiht.fr> wrote:
>> >>>>>
>> >>>>>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >>>>>>
>> >>>>>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet <
>> pierre.jolivet at enseeiht.fr> wrote:
>> >>>>>> Hello,
>> >>>>>> I _might_ be doing something wrong when calling
>> KSPSetFromOptions/KSPSetUp, but still, am I supposed to get this kind of
>> error?
>> >>>>>> [0]PETSC ERROR: No support for this operation for this object type
>> >>>>>> [0]PETSC ERROR: KSP gmres does not support PRECONDITIONED with
>> RIGHT
>> >>>>>>
>> >>>>>> If not, I’ll try to send a MWE (it basically depends on where I
>> set the option -ksp_pc_side right).
>> >>>>>>
>> >>>>>> I believe its telling you that it cannot display the
>> preconditioned residual with right preconditioning, which is true.
>> >>>>>> Are you requesting both?
>> >>>>>
>> >>>>> No, I’m just using -ksp_view and -ksp_pc_side right. In the
>> “standard” case, it obviously work.
>> >>>>> However, the error is triggered if I set -ksp_pc_side right after a
>> first call to KSPSetOperators()/KSPSetUp() without destroying the KSP.
>> >>>>> Should I destroy my KSP before changing from left- (default) to
>> right-preconditioning if KSPSetOperators()/KSPSetUp has already been called?
>> >>>>>
>> >>>>> Its likely you have to use
>> >>>>>
>> >>>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages
>> /KSP/KSPSetNormType.html
>> >>>>>
>> >>>>> or
>> >>>>>
>> >>>>> -ksp_norm_type unpreconditioned
>> >>>>
>> >>>> If I use this after my first call to KSPSetUp, I now end up with:
>> >>>> [0]PETSC ERROR: KSP gmres does not support UNPRECONDITIONED with LEFT
>> >>>>
>> >>>> Yes, you would need to use it at the same time that you change the
>> preconditioning side.
>> >>>
>> >>> Yes, I’m using PetscOptionsInsert, and whether I let PETSc parse
>> "-ksp_pc_side right -ksp_norm_type unpreconditioned” or "-ksp_norm_type
>> unpreconditioned -ksp_pc_side right” I end up with the same error
>> afterwards.
>> >>>
>> >>> Can you make an example do it (SNES ex5)? Or can you send a small
>> example that does it?
>> >>>
>> >>> Thanks,
>> >>>
>> >>> Matt
>> >>>
>> >>> Thanks.
>> >>>
>> >>>> Thanks,
>> >>>>
>> >>>> Matt
>> >>>>> since we would not have a chance to change it since its been set
>> already.
>> >>>>>
>> >>>>> Thanks,
>> >>>>>
>> >>>>> Matt
>> >>>>>
>> >>>>> Thanks.
>> >>>>>
>> >>>>>> Thanks,
>> >>>>>>
>> >>>>>> Matt
>> >>>>>>
>> >>>>>> Thanks,
>> >>>>>> Pierre
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> --
>> >>>>>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> >>>>>> -- Norbert Wiener
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> >>>>> -- Norbert Wiener
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> >>>> -- Norbert Wiener
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> >>> -- Norbert Wiener
>> >>
>> >
>> >
>> >
>> >
>> > --
>> > What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> > -- Norbert Wiener
>>
>>
>
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