[petsc-users] Jacobian test by finite difference

[Matthew Knepley]

On Tue, May 19, 2020 at 1:57 AM zakaryah . <zakaryah at gmail.com> wrote:

> Hi all,
>
> I'm debugging some convergence issues and I came across something strange.
> I am using a nonlinear solver on a structured grid. The DMDA is 3
> dimensional, with 3 dof, and a box stencil of width 1. There are some small
> errors in the hand-coded Jacobian, which I am trying to sort out, but at
> least the fill pattern of the matrix is correct.
>
> However, when I run with -snes_test_jacobian -snes_test_jacobian_display
> -snes_compare_explicit, I see something very strange. The finite difference
> Jacobian has large terms outside the stencil. For example, for x,y,z,c =
> 0,0,0,0 (row 0), the columns 6, 7, 8, 12, 13, and 14 (column 6 =>
> x=2,y=0,z=0,c=0, etc.) have large values, while columns 9 through 20 are
> calculated but equal to zero. The "correct" values, i.e., in the stencil,
> are calculated as well, and nearly agree with my hand-coded Jacobian. This
> issue does NOT occur in serial, but occurs for any number of processors
> greater than 1.
>
> I have checked the indexing by hand, carefully, and the memory access with
> valgrind, and the results were clean. Does anyone have an idea why the
> finite difference calculation of the Jacobian would produce large values
> outside the stencil? I am using PETSc 3.12.2 and openMPI 3.1.0. Thanks for
> your help.
>

Since it only appears in parallel, I am guessing that your calculation of
global ordering does not take into account that we locally
reorder, rather than using lexicographic ordering, and you might have
periodic boundary conditions.

  Thanks,

     Matt

-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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