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

[Matthew Knepley]

On Sat, Nov 23, 2013 at 2:04 PM, Geoffrey Irving <irving at naml.us> wrote:

> 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.


My first guess is a triangle with backwards edge. This could cause the
geometry routines to barf.

  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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20131123/d52d602f/attachment-0001.html>