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! Geoffrey
