[petsc-users] zeros in sparse aij

[Xiangdong Liang]

On Fri, Dec 9, 2011 at 7:23 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Dec 9, 2011 at 6:15 PM, Xiangdong Liang <xdliang at gmail.com> wrote:
>>
>> If I use MAT_IGNORE_ZERO_ENTRIES option, is it possible that I still
>> see some zeros in the sparse matrix? In my problem, when I use this
>
>
> Not if they are truly zero.
>
>>
>> ignore_zero options, the number of nonzeros is significantly reduced
>> (from mat_view_info) but still larger than the number of nonzeros
>> counting from matlab. When I use mat_view_draw, I see some light green
>> lines (corresponding to zeros). I am wondering where these zeros come
>> from? Thanks

I figured out where these extra zeros comes from. At these positions,
I first addvalues 1 then addvalues -1. Therefore, even thought the
value at this position is zero, it cannot be ignored by the
ignore_zero_options.

Another quick question, when I use mat_view_draw command line option,
how can I make the figure X window larger? I think petsc
PetscDrawOpenX can do this job, but just wondering whether any quick
command line options? Thanks.

Xiangdong


>
>
> Print it and see where they are.
>
>   Matt
>
>>
>> Xiangdong
>>
>> On Wed, Dec 7, 2011 at 12:15 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>> > On Wed, 7 Dec 2011, Satish Balay wrote:
>> >
>> >> As indicated call "MatSetOption(A,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE)
>> >> - before any calls to MatSetValue/s()
>> >>
>> >> And verify with MatView()
>> >
>> > Ok - here is what you can see with a slightly modified
>> > mat/examples/tests/ex38.c
>> >
>> > Notice "C[0,1] = 0.0" and thats not visible anymore with
>> > MatSetOption(MAT_IGNORE_ZERO_ENTRIES)
>> >
>> > Satish
>> >
>> > --------
>> > asterix:/home/balay/spetsc/src/mat/examples/tests>cat ex38.c
>> > static char help[] = "Tests MatSetValues().\n\n";
>> > #include <petscmat.h>
>> > #undef __FUNCT__
>> > #define __FUNCT__ "main"
>> > int main(int argc,char **args)
>> > {
>> >  Mat            C;
>> >  PetscInt       i,n = 5,midx[3],nidx[2];
>> >  PetscErrorCode ierr;
>> >  PetscBool      flg;
>> >  PetscScalar    v[6];
>> >
>> >  PetscInitialize(&argc,&args,(char *)0,help);
>> >  ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
>> >  ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
>> >  ierr = MatSetFromOptions(C);CHKERRQ(ierr);
>> >
>> >  ierr =
>> > PetscOptionsHasName(PETSC_NULL,"-ignore_zero_entries",&flg);CHKERRQ(ierr);
>> >  if (flg) {  ierr =
>> > MatSetOption(C,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);}
>> >
>> >  for (i=0; i<6; i++) v[i] = (PetscReal)i;
>> >  midx[0] = 0; midx[1] = 2; midx[2] = 3;
>> >  nidx[0] = 1; nidx[1] = 3;
>> >  ierr = MatSetValues(C,3,midx,2,nidx,v,ADD_VALUES);CHKERRQ(ierr);
>> >  ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>> >  ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>> >  ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
>> >  ierr = MatDestroy(&C);CHKERRQ(ierr);
>> >  ierr = PetscFinalize();
>> >  return 0;
>> > }
>> >
>> > asterix:/home/balay/spetsc/src/mat/examples/tests>./ex38 -mat_view_info
>> > Matrix Object: 1 MPI processes
>> >  type: seqaij
>> >  rows=5, cols=5
>> >  total: nonzeros=6, allocated nonzeros=25
>> >  total number of mallocs used during MatSetValues calls =0
>> >    using I-node routines: found 4 nodes, limit used is 5
>> > Matrix Object: 1 MPI processes
>> >  type: seqaij
>> > row 0: (1, 0)  (3, 1)
>> > row 1:
>> > row 2: (1, 2)  (3, 3)
>> > row 3: (1, 4)  (3, 5)
>> > row 4:
>> > asterix:/home/balay/spetsc/src/mat/examples/tests>./ex38 -mat_view_info
>> > -ignore_zero_entries
>> > Matrix Object: 1 MPI processes
>> >  type: seqaij
>> >  rows=5, cols=5
>> >  total: nonzeros=5, allocated nonzeros=25
>> >  total number of mallocs used during MatSetValues calls =0
>> >    using I-node routines: found 4 nodes, limit used is 5
>> > Matrix Object: 1 MPI processes
>> >  type: seqaij
>> > row 0: (3, 1)
>> > row 1:
>> > row 2: (1, 2)  (3, 3)
>> > row 3: (1, 4)  (3, 5)
>> > row 4:
>> > asterix:/home/balay/spetsc/src/mat/examples/tests>
>
>
>
>
> --
> 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