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

[Geoffrey Irving]

On Sat, Nov 23, 2013 at 10:11 AM, Matthew Knepley <knepley at gmail.com> wrote:
> 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.

It does seem to happen with stock snes ex12:

    branch: irving/assert-ex12-in-box1

    % mpiexec -host localhost -n 1
/home/irving/petsc/debug/lib/ex12-obj/ex12 -run_type test
-refinement_limit 0.0    -bc_type neumann   -interpolate 1
-petscspace_order 1 -bd_petscspace_order 1 -show_initial
-dm_plex_print_fem 1 -dm_view ::ascii_info_detail
    ...
    [0]PETSC ERROR: evaluation at point outside unit box: 0 1.25

I'll trace down why this is happening.

Geoffrey