On Sat, Nov 23, 2013 at 2:04 PM, Geoffrey Irving <[email protected]> wrote:
> On Sat, Nov 23, 2013 at 10:11 AM, Matthew Knepley <[email protected]> > wrote: > > On Sat, Nov 23, 2013 at 12:07 PM, Geoffrey Irving <[email protected]> > wrote: > >> > >> On Sat, Nov 23, 2013 at 4:43 AM, Matthew Knepley <[email protected]> > >> wrote: > >> > On Fri, Nov 22, 2013 at 6:42 PM, Geoffrey Irving <[email protected]> > wrote: > >> >> > >> >> On Fri, Nov 22, 2013 at 4:25 PM, Matthew Knepley <[email protected]> > >> >> wrote: > >> >> > On Fri, Nov 22, 2013 at 6:09 PM, Geoffrey Irving <[email protected]> > >> >> > wrote: > >> >> >> > >> >> >> On Fri, Nov 22, 2013 at 3:41 PM, Matthew Knepley < > [email protected]> > >> >> >> wrote: > >> >> >> > On Fri, Nov 22, 2013 at 5:36 PM, Geoffrey Irving < > [email protected]> > >> >> >> > 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
