[petsc-users] neumann failure in my version of snes ex12

[Matthew Knepley]

On Sat, Nov 23, 2013 at 12:07 PM, Geoffrey Irving <irving at naml.us> wrote:

> On Sat, Nov 23, 2013 at 4:43 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Fri, Nov 22, 2013 at 6:42 PM, Geoffrey Irving <irving at naml.us> wrote:
> >>
> >> On Fri, Nov 22, 2013 at 4:25 PM, Matthew Knepley <knepley at gmail.com>
> >> wrote:
> >> > On Fri, Nov 22, 2013 at 6:09 PM, Geoffrey Irving <irving at naml.us>
> wrote:
> >> >>
> >> >> On Fri, Nov 22, 2013 at 3:41 PM, Matthew Knepley <knepley at gmail.com>
> >> >> wrote:
> >> >> > On Fri, Nov 22, 2013 at 5:36 PM, Geoffrey Irving <irving at naml.us>
> >> >> > wrote:
> >> >> >>
> >> >> >> I have a duplicate of snes ex12 (FEM Poisson) which works with
> >> >> >> Dirichlet boundary conditions, but it's breaking for me with
> Neumann
> >> >> >> conditions.  In particular, with Neumann conditions I get results
> >> >> >> which explode even though I believe I am setting a constant
> >> >> >> nullspace.
> >> >> >>
> >> >> >> For example, if I use two first order elements (the unit square
> >> >> >> divided into two triangles), the resulting solution has
> >> >> >>
> >> >> >>     L2 error = 1.75514e+08
> >> >> >>     u = [-175513825.75680602, -175513825.66302037,
> >> >> >> -175513825.48390722, -175513824.84436429]
> >> >> >>
> >> >> >> This looks rather a lot like the null space isn't getting through.
> >> >> >> I
> >> >> >> am creating the constant nullspace with
> >> >> >>
> >> >> >>       MatNullSpace null;
> >> >> >>       CHECK(MatNullSpaceCreate(comm(),PETSC_TRUE,0,0,&null));
> >> >> >>       CHECK(MatSetNullSpace(m,null));
> >> >> >>       CHECK(MatNullSpaceDestroy(&null));
> >> >> >>
> >> >> >> If I pass "-ksp_view -mat_view", I get the following.  The matrix
> >> >> >> entries seem right (they do indeed have the constant nullspace),
> and
> >> >> >> ksp_view shows that a nullspace is attached.  Is attaching the
> >> >> >> nullspace to the matrix with MatSetNullSpace enough, or do I need
> to
> >> >> >> additionally attach it to the KSP object?
> >> >> >
> >> >> >
> >> >> > 1) I always run with -ksp_monitor_true_residual now when debugging.
> >> >> > This
> >> >> > can
> >> >> > give
> >> >> >     you an idea whether you have a singular PC, which I suspect
> here.
> >> >> >
> >> >> > 2) Can you try using -pc_type jacobi? I think ILU might go crazy
> on a
> >> >> > deficient matrix.
> >> >>
> >> >> Here are results with -ksp_monitor_true_residual -pc_type none:
> >> >>
> >> >>     http://naml.us/random/laplace-rtol.txt # with -ksp_rtol 1e-5
> >> >>     http://naml.us/random/laplace-atol.txt # with -ksp_atol 1e-5
> >> >
> >> >
> >> > Okay, if you have an inconsistent RHS I do not think that
> true_residual
> >> > will work
> >> > since it uses the unprojected b, but the solve should be fine.
> >>
> >> I still don't understand why the atol version is able to drift so far
> >> away from zero mean, even after tens of thousands of iterations.  If
> >> KSP sees a null space on the matrix, shouldn't it project that null
> >> space out of the *linear system* residual and also out of solution on
> >> each iteration?  Even if it is only projecting out of the solution
> >> delta, how can null space errors be accumulating?
> >
> >
> > Both the KSP and Mat show that the null space is set, so everything
> should
> > work fine,
> > and at this point its no longer DMPlex that is in control, its standard
> > PETSc.
> >
> > We have reached the limit of usefu talking. Something is obviously wrong
> with the code,
> > but since this routinely works in PETSc examples. In situations like
> these I think we need
> > to follow the execution in the debugger to see what is wrong..You can
> look at Vec values
> > in the debugger using
> >
> >   (gdb) p ((Vec_Seq*) b-.data)->array[0]@v->map.n
> >
> > and I look at DMPlex things with
> >
> >   (gdb) p ((DM_Plex*) dm->data)->coneSection
> >
> > etc.
>
> Thanks, I appreciate the help.  It looks like there were at least two
> different problems:
>
> 1. The boundary FE I was creating had the same dimension as the
> interior FE (instead of codimension 1), due to misreading ex12 even
> though I had correctly refactored it.  I added a dimension consistency
> check to my code, but I can do this in DMPlexComputeResidualFEM as
> well to catch future user errors.
>
> 2. Even after fixing the dimensions, my boundary functions in PetscFEM
> are getting x values both inside and completely outside the domain.
> Almost certainly more user error, but hopefully also something I can
> add a check for in petsc once I localize it.


This could be my bug. The test I have for ex12 is the variable coefficient
problem
with div (x + y) grad u = f. This seems to check between the analytic and
field
versions, meaning that the x coming into f1() matches the x I used to make
the
field, and my exact solution.

   Matt


>
> Geoffrey
>



-- 
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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