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

Sun Nov 24 18:21:29 CST 2013

On Sun, Nov 24, 2013 at 6:18 PM, Geoffrey Irving <irving at naml.us> wrote:

> On Sun, Nov 24, 2013 at 4:10 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Sun, Nov 24, 2013 at 6:06 PM, Geoffrey Irving <irving at naml.us> wrote:
> >>
> >> On Sun, Nov 24, 2013 at 5:41 AM, Matthew Knepley <knepley at gmail.com>
> >> wrote:
> >> > On Sat, Nov 23, 2013 at 5:44 PM, Geoffrey Irving <irving at naml.us>
> wrote:
> >> >>
> >> >> On Sat, Nov 23, 2013 at 12:20 PM, Matthew Knepley <knepley at gmail.com
> >
> >> >> wrote:
> >> >> > 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.
> >> >>
> >> >> I don't think it's edge orientation: it breaks (though at different
> >> >> points) regardless of whether I orient all the edges clockwise or
> >> >> counterclockwise.  Also, I would expect bad edge orientation to
> result
> >> >> in bad normals but not to produce bad quadrature locations (nor bad
> >> >> residuals as long as the user routines don't depend on normal).
> >> >>
> >> >> Specifically, I think the problem is a sign error in
> >> >> DMPlexComputeProjection2Dto1D_Internal.  The following patch seems to
> >> >> fix the out of bounds evaluation problem.
> >> >> DMPlexComputeProjection2Dto1D is computing a matrix which maps from
> >> >> the given segment to the canonical segment, and
> >> >> DMPlexComputeLineGeometry_Internal expects a map from the canonical
> >> >> segment to the given segment.
> >> >>
> >> >> snes ex12 passes with and without this change, presumably because the
> >> >> only Neumann test has constants along each box side, and is therefore
> >> >> invariant to this error.
> >> >
> >> >
> >> > When I replaced my kludge with code using the normal explicitly, I get
> >> > the
> >> > same
> >> > error as you do. You fix is correct, and I checked it into
> >> > knepley/fix-fem-bd-integrate
> >> >
> >> >
> https://bitbucket.org/petsc/petsc/branch/knepley/fix-fem-bd-integrate
> >> >
> >> > along with other fixes that I think get Neumann all the way correct in
> >> > ex12.
> >> >
> >> >>
> >> >> Unfortunately, my Laplace test is also invariant to this error, so
> >> >> this bug is unrelated to the earlier problem.
> >> >
> >> > It could be one of the other fixes I made. Could you run again?
> >>
> >> Much better.  All the points and (inward) normals are right, and now
> >> my residuals have zero sum as expected.  There's still something
> >> wrong, since I don't get the exact solution with second order
> >> elements, but that's probably an independent problem.  I will trace it
> >> down.  Thanks for the help and fixes!
> >>
> >> Why did you choose inward pointing normals, by the way?  I would have
> >> though outward pointing normals are the nearly universal convention.
> >
> > That is a bug fixed in that branch. Did you try next?
>
> Oops, I had misread that commit message as "Use inward pointing
> normal" rather than "Used inward pointing normal".  I get outward
> normals if I reorient the outer boundary edges in my DMPlex to be
> clockwise, which I guess is what you intended.
>
> Closer and closer!

Hmm, no. I use counter-clockwise ordering too. Now I do not understand what
is going on. Something is wrong.

   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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