On Sun, Nov 24, 2013 at 6:18 PM, Geoffrey Irving <[email protected]> wrote:
> On Sun, Nov 24, 2013 at 4:10 PM, Matthew Knepley <[email protected]> > wrote: > > On Sun, Nov 24, 2013 at 6:06 PM, Geoffrey Irving <[email protected]> wrote: > >> > >> On Sun, Nov 24, 2013 at 5:41 AM, Matthew Knepley <[email protected]> > >> wrote: > >> > On Sat, Nov 23, 2013 at 5:44 PM, Geoffrey Irving <[email protected]> > wrote: > >> >> > >> >> On Sat, Nov 23, 2013 at 12:20 PM, Matthew Knepley <[email protected] > > > >> >> wrote: > >> >> > 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. > >> >> > >> >> 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
