# [petsc-users] degub of computating Jacobian for SNES

Hong hzhang at mcs.anl.gov
Tue Jul 3 11:30:29 CDT 2018

```LEI :
>
> One strange thing is that the Jacobian stiffness matrix include ‘nan’. I
> output the element stiffness matrix and the element degree of freedom
> before assembly. There is nothing abnormal.
>
How do you check the element? Some elements might divide zero.

> But after assembly by
>
> ierr1 = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr1);
>
> ierr1 = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr1);
>
> I got some ‘nan’ in the stiffness matrix A. Any idea on this?
>

For sequential run, MatAssemly() does do much. Check every element of your
matrix.
With 1 MPI process and LU precondition, the code should work with correctly
assembled matrix.
Hong

>
>
> Nonlinear solve did not converge due to DIVERGED_FNORM_NAN iterations 0
>
> SNES Object: 1 MPI processes
>
>   type: newtonls
>
>   maximum iterations=40, maximum function evaluations=40
>
>   tolerances: relative=0.0001, absolute=0.0001, solution=1e-08
>
>   total number of linear solver iterations=0
>
>   total number of function evaluations=1
>
>   norm schedule ALWAYS
>
>   SNESLineSearch Object:   1 MPI processes
>
>     type: basic
>
>     maxstep=1.000000e+08, minlambda=1.000000e-12
>
>     tolerances: relative=1.000000e-08, absolute=1.000000e-15,
> lambda=1.000000e-08
>
>     maximum iterations=40
>
>   KSP Object:   1 MPI processes
>
>     type: gmres
>
>       GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
> Orthogonalization with no iterative refinement
>
>       GMRES: happy breakdown tolerance 1e-30
>
>     maximum iterations=100, initial guess is zero
>
>     tolerances:  relative=1e-10, absolute=1e-10, divergence=10000.
>
>     left preconditioning
>
>     using DEFAULT norm type for convergence test
>
>   PC Object:   1 MPI processes
>
>     type: lu
>
>     PC has not been set up so information may be incomplete
>
>       LU: out-of-place factorization
>
>       tolerance for zero pivot 2.22045e-14
>
>       matrix ordering: nd
>
>     linear system matrix = precond matrix:
>
>     Mat Object:     1 MPI processes
>
>       type: seqaij
>
>       rows=78, cols=78
>
>       total: nonzeros=3204, allocated nonzeros=46800
>
>       total number of mallocs used during MatSetValues calls =0
>
>         using I-node routines: found 25 nodes, limit used is 5
>
> No. of Iterations: 0
>
> Convergence reason: -4: SNES_DIVERGED_FNORM_NAN
>
>
>
>
>
>
>
>
>
> *From:* Hong [mailto:hzhang at mcs.anl.gov]
> *Sent:* 03 July 2018 15:31
> *To:* WANG, LEI
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] degub of computating Jacobian for SNES
>
>
>
> LEI:
>
> Run your code with option '-snes_converged_reason -ksp_converged_reason
> -ksp_monitor -snes_monitor' to check which solver leads to divergence. Then
> use option '-snes_view' to check what solver is used.
>
> Hong
>
> Dear all
>
>
>
> I am using SNES for solving a large nonlinear system for Material Point
> Method. But it always diverged after server steps, I think there are some
> bug in the computation of Jacobian matrix. Do anyone have practical
> approach for identified these bugs in a large matrix? Currently, I saved
> the matrix to a txt file and load it to Matlab for checking. Is there
> function for checking Petsc Mat in Petsc itself?
>
>
>
> Cheers
>
> Lei
>
>
>
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