Re: [petsc-dev] Segmentation fault GAMG + MatView

2017-02-14 Thread Hong 
Pierre :
The bug is fixed and pushed to petsc-maint
https://bitbucket.org/petsc/petsc/branch/maint
Thanks for reporting it.

Hong

Oh my, this example also segfaults (at least on my Mac) when running:
> mpirun -np 1 ./ex1 -pc_type gamg -mat_view
>
> [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/
> petsc/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/
> petsc/src/ksp/pc/impls/gamg/gamg.c
> [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/
> petsc/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/
> petsc/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 +
> [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 
> 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;
>
> 
>
> On Feb 9, 2017, at 2:56 PM, Matthew Knepley  wrote:
>
> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet  > wrote:
>
>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley  wrote:
>>
>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet > ht.fr> wrote:
>>
>>>
>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley  wrote:
>>>
>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet >> ht.fr> wrote:
>>>

 On Feb 9, 2017, at 1:37 PM, Matthew Knepley  wrote:

 On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet >>> ht.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 likel

Re: [petsc-dev] Segmentation fault GAMG + MatView

2017-02-09 Thread Hong 
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  wrote:

> I'll check it tomorrow and fix it.
> Hong
>
> On Thu, Feb 9, 2017 at 4:27 PM, Barry Smith  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  wrote:
>> >
>> > On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet <
>> pierre.joli...@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 +
>> > [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.joli...@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[] =

Re: [petsc-dev] Segmentation fault GAMG + MatView

2017-02-09 Thread Hong 
I'll check it tomorrow and fix it.
Hong

On Thu, Feb 9, 2017 at 4:27 PM, Barry Smith  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  wrote:
> >
> > On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet <
> pierre.joli...@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/
> petsc/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/
> petsc/src/ksp/pc/impls/gamg/gamg.c
> > [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/
> petsc/src/ksp/pc/interface/precon.c
> > [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/
> petsc/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 +
> > [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 
> 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;
> >>
> >> 
> >>
> >>> On Feb 9, 2017, at 2:56 PM, Matthew Knepley  wrote:
> >>>
> >>> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet <
> pierre.joli...@enseeiht.fr> wrote:
>  On Feb 9, 2017, at 2:31 PM, Matthew Knepley 
> wrote:
> 
>  On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet <
> pierre.joli...@enseeiht.fr> wrote:
> 
> > On Feb 9, 2017, at 2:17 PM, Matthew Knepley 
>

Re: [petsc-dev] Segmentation fault GAMG + MatView

2017-02-09 Thread Barry Smith 

   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  wrote:
> 
> On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet  
> 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/petsc/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/petsc/src/ksp/pc/impls/gamg/gamg.c
> [0]PETSC ERROR: [0] PCSetUp line 886 
> /Volumes/Data/Repositories/petsc/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: [0] KSPSetUp line 291 
> /Volumes/Data/Repositories/petsc/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 +
> [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  
>> 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;
>> 
>> 
>> 
>>> On Feb 9, 2017, at 2:56 PM, Matthew Knepley  wrote:
>>> 
>>> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet  
>>> wrote:
 On Feb 9, 2017, at 2:31 PM, Matthew Knepley  wrote:
 
 On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet 
  wrote:
 
> On Feb 9, 2017, at 2:17 PM, Matthew Knepley  wrote:
> 
> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet 
>  wrote:
> 
>> On Feb 9, 2017, at 1:37 PM, Matthew Knepley  wrote:
>> 
>> On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet 
>>  wrote:
>> Hello,
>> I _might_ be doing something wrong when calling 
>> KS

Re: [petsc-dev] Segmentation fault GAMG + MatView

2017-02-09 Thread Matthew Knepley 
On Thu, Feb 9, 2017 at 4:00 PM, Pierre Jolivet 
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/
> petsc/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/
> petsc/src/ksp/pc/impls/gamg/gamg.c
> [0]PETSC ERROR: [0] PCSetUp line 886 /Volumes/Data/Repositories/
> petsc/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: [0] KSPSetUp line 291 /Volumes/Data/Repositories/
> petsc/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 +
> [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 
> 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;
>
> 
>
> On Feb 9, 2017, at 2:56 PM, Matthew Knepley  wrote:
>
> On Thu, Feb 9, 2017 at 7:48 AM, Pierre Jolivet  > wrote:
>
>> On Feb 9, 2017, at 2:31 PM, Matthew Knepley  wrote:
>>
>> On Thu, Feb 9, 2017 at 7:29 AM, Pierre Jolivet > ht.fr> wrote:
>>
>>>
>>> On Feb 9, 2017, at 2:17 PM, Matthew Knepley  wrote:
>>>
>>> On Thu, Feb 9, 2017 at 7:06 AM, Pierre Jolivet >> ht.fr> wrote:
>>>

 On Feb 9, 2017, at 1:37 PM, Matthew Knepley  wrote:

 On Thu, Feb 9, 2017 at 4:56 AM, Pierre Jolivet >>> ht.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_vi