<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Sat, Nov 23, 2013 at 2:04 PM, Geoffrey Irving <span dir="ltr"><<a href="mailto:irving@naml.us" target="_blank">irving@naml.us</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5">On Sat, Nov 23, 2013 at 10:11 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>> wrote:<br>
> On Sat, Nov 23, 2013 at 12:07 PM, Geoffrey Irving <<a href="mailto:irving@naml.us">irving@naml.us</a>> wrote:<br>
>><br>
>> On Sat, Nov 23, 2013 at 4:43 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>><br>
>> wrote:<br>
>> > On Fri, Nov 22, 2013 at 6:42 PM, Geoffrey Irving <<a href="mailto:irving@naml.us">irving@naml.us</a>> wrote:<br>
>> >><br>
>> >> On Fri, Nov 22, 2013 at 4:25 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>><br>
>> >> wrote:<br>
>> >> > On Fri, Nov 22, 2013 at 6:09 PM, Geoffrey Irving <<a href="mailto:irving@naml.us">irving@naml.us</a>><br>
>> >> > wrote:<br>
>> >> >><br>
>> >> >> On Fri, Nov 22, 2013 at 3:41 PM, Matthew Knepley <<a href="mailto:knepley@gmail.com">knepley@gmail.com</a>><br>
>> >> >> wrote:<br>
>> >> >> > On Fri, Nov 22, 2013 at 5:36 PM, Geoffrey Irving <<a href="mailto:irving@naml.us">irving@naml.us</a>><br>
>> >> >> > wrote:<br>
>> >> >> >><br>
>> >> >> >> I have a duplicate of snes ex12 (FEM Poisson) which works with<br>
>> >> >> >> Dirichlet boundary conditions, but it's breaking for me with<br>
>> >> >> >> Neumann<br>
>> >> >> >> conditions. In particular, with Neumann conditions I get results<br>
>> >> >> >> which explode even though I believe I am setting a constant<br>
>> >> >> >> nullspace.<br>
>> >> >> >><br>
>> >> >> >> For example, if I use two first order elements (the unit square<br>
>> >> >> >> divided into two triangles), the resulting solution has<br>
>> >> >> >><br>
>> >> >> >> L2 error = 1.75514e+08<br>
>> >> >> >> u = [-175513825.75680602, -175513825.66302037,<br>
>> >> >> >> -175513825.48390722, -175513824.84436429]<br>
>> >> >> >><br>
>> >> >> >> This looks rather a lot like the null space isn't getting<br>
>> >> >> >> through.<br>
>> >> >> >> I<br>
>> >> >> >> am creating the constant nullspace with<br>
>> >> >> >><br>
>> >> >> >> MatNullSpace null;<br>
>> >> >> >> CHECK(MatNullSpaceCreate(comm(),PETSC_TRUE,0,0,&null));<br>
>> >> >> >> CHECK(MatSetNullSpace(m,null));<br>
>> >> >> >> CHECK(MatNullSpaceDestroy(&null));<br>
>> >> >> >><br>
>> >> >> >> If I pass "-ksp_view -mat_view", I get the following. The matrix<br>
>> >> >> >> entries seem right (they do indeed have the constant nullspace),<br>
>> >> >> >> and<br>
>> >> >> >> ksp_view shows that a nullspace is attached. Is attaching the<br>
>> >> >> >> nullspace to the matrix with MatSetNullSpace enough, or do I need<br>
>> >> >> >> to<br>
>> >> >> >> additionally attach it to the KSP object?<br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > 1) I always run with -ksp_monitor_true_residual now when<br>
>> >> >> > debugging.<br>
>> >> >> > This<br>
>> >> >> > can<br>
>> >> >> > give<br>
>> >> >> > you an idea whether you have a singular PC, which I suspect<br>
>> >> >> > here.<br>
>> >> >> ><br>
>> >> >> > 2) Can you try using -pc_type jacobi? I think ILU might go crazy<br>
>> >> >> > on a<br>
>> >> >> > deficient matrix.<br>
>> >> >><br>
>> >> >> Here are results with -ksp_monitor_true_residual -pc_type none:<br>
>> >> >><br>
>> >> >> <a href="http://naml.us/random/laplace-rtol.txt" target="_blank">http://naml.us/random/laplace-rtol.txt</a> # with -ksp_rtol 1e-5<br>
>> >> >> <a href="http://naml.us/random/laplace-atol.txt" target="_blank">http://naml.us/random/laplace-atol.txt</a> # with -ksp_atol 1e-5<br>
>> >> ><br>
>> >> ><br>
>> >> > Okay, if you have an inconsistent RHS I do not think that<br>
>> >> > true_residual<br>
>> >> > will work<br>
>> >> > since it uses the unprojected b, but the solve should be fine.<br>
>> >><br>
>> >> I still don't understand why the atol version is able to drift so far<br>
>> >> away from zero mean, even after tens of thousands of iterations. If<br>
>> >> KSP sees a null space on the matrix, shouldn't it project that null<br>
>> >> space out of the *linear system* residual and also out of solution on<br>
>> >> each iteration? Even if it is only projecting out of the solution<br>
>> >> delta, how can null space errors be accumulating?<br>
>> ><br>
>> ><br>
>> > Both the KSP and Mat show that the null space is set, so everything<br>
>> > should<br>
>> > work fine,<br>
>> > and at this point its no longer DMPlex that is in control, its standard<br>
>> > PETSc.<br>
>> ><br>
>> > We have reached the limit of usefu talking. Something is obviously wrong<br>
>> > with the code,<br>
>> > but since this routinely works in PETSc examples. In situations like<br>
>> > these I think we need<br>
>> > to follow the execution in the debugger to see what is wrong..You can<br>
>> > look at Vec values<br>
>> > in the debugger using<br>
>> ><br>
>> > (gdb) p ((Vec_Seq*) b-.data)->array[0]@v->map.n<br>
>> ><br>
>> > and I look at DMPlex things with<br>
>> ><br>
>> > (gdb) p ((DM_Plex*) dm->data)->coneSection<br>
>> ><br>
>> > etc.<br>
>><br>
>> Thanks, I appreciate the help. It looks like there were at least two<br>
>> different problems:<br>
>><br>
>> 1. The boundary FE I was creating had the same dimension as the<br>
>> interior FE (instead of codimension 1), due to misreading ex12 even<br>
>> though I had correctly refactored it. I added a dimension consistency<br>
>> check to my code, but I can do this in DMPlexComputeResidualFEM as<br>
>> well to catch future user errors.<br>
>><br>
>> 2. Even after fixing the dimensions, my boundary functions in PetscFEM<br>
>> are getting x values both inside and completely outside the domain.<br>
>> Almost certainly more user error, but hopefully also something I can<br>
>> add a check for in petsc once I localize it.<br>
><br>
> This could be my bug. The test I have for ex12 is the variable coefficient problem<br>
> with div (x + y) grad u = f. This seems to check between the analytic and field<br>
> versions, meaning that the x coming into f1() matches the x I used to make the<br>
> field, and my exact solution.<br>
<br>
</div></div>It does seem to happen with stock snes ex12:<br>
<br>
branch: irving/assert-ex12-in-box1<br>
<br>
% mpiexec -host localhost -n 1<br>
/home/irving/petsc/debug/lib/ex12-obj/ex12 -run_type test<br>
-refinement_limit 0.0 -bc_type neumann -interpolate 1<br>
-petscspace_order 1 -bd_petscspace_order 1 -show_initial<br>
-dm_plex_print_fem 1 -dm_view ::ascii_info_detail<br>
...<br>
[0]PETSC ERROR: evaluation at point outside unit box: 0 1.25<br>
<br>
I'll trace down why this is happening.</blockquote><div><br></div><div>My first guess is a triangle with backwards edge. This could cause the</div><div>geometry routines to barf.</div><div><br></div><div> Matt</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="HOEnZb"><font color="#888888"><br>
Geoffrey<br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>