[petsc-users] Suggestions for code with dof >> 1 ?

Christophe Ortiz christophe.ortiz at ciemat.es
Thu Oct 24 05:09:37 CDT 2013 

On Wed, Oct 23, 2013 at 7:14 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> Christophe Ortiz <christophe.ortiz at ciemat.es> writes:
>
> >> That does not sound right.  Can you send a reproducible test case (best
> >> as a patch to PETSc)?
> >>
> >
> > What do you mean by patch to PETSc ? How do I do that ?
>
> See "contributing a small patch" (or any of the other workflows).
>
> https://bitbucket.org/petsc/petsc/wiki/Home


Ok, I will read the instructions and try.


>
>
> > Sorry about that. Here is the entire error message:
> >
> > [0]PETSC ERROR: No support for this operation for this object type!
> > [0]PETSC ERROR: Mat type mffd!
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Release Version 3.4.1, Jun, 10, 2013
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: ./diffusion_c on a ifort-icc-nompi-double-debug named
> > mazinger.ciemat.es by u5751 Wed Oct 23 12:46:04 2013
> > [0]PETSC ERROR: Libraries linked from
> > /home/u5751/petsc-3.4.1/ifort-icc-nompi-double-debug/lib
> > [0]PETSC ERROR: Configure run at Mon Oct 14 05:43:50 2013
> > [0]PETSC ERROR: Configure options --with-mpi=0 --with-fc=ifort
> > --with-cc=icc --with-debugging=1 --with-scalar-type=real
> > --with-precision=double --with-blas-lapack-dir=/opt/intel/mkl
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: MatZeroEntries() line 5189 in src/mat/interface/matrix.c
> > [0]PETSC ERROR: FormIJacobian() line 689 in
> > src/ts/examples/tutorials/diffusion.c
>
> This is your code calling MatZeroEntries on the Amat (first Mat
> argument).  The convention is to assemble into Pmat (the preconditioning
> matrix; second Mat argument).
>

I assemble first Pmat but in my code MatZeroEntries was used with Amat,
which PETSc did not appreciate...
I changed that and here is the output. While without these options it
converges--though giving solution with oscillations--now with
-ts_arkimex_fully_implicit -snes_mf_operator it does not converge at all.
No step is accepted, not even the first one:

      TSAdapt 'basic': step   0 stage rejected t=0          + 1.000e-12
retrying with dt=2.500e-13
      TSAdapt 'basic': step   0 stage rejected t=0          + 2.500e-13
retrying with dt=6.250e-14
      TSAdapt 'basic': step   0 stage rejected t=0          + 6.250e-14
retrying with dt=1.562e-14
      TSAdapt 'basic': step   0 stage rejected t=0          + 1.562e-14
retrying with dt=3.906e-15

...  ....
      TSAdapt 'basic': step   0 stage rejected t=0          +2.888e-287
retrying with dt=7.221e-288
      TSAdapt 'basic': step   0 stage rejected t=0          +7.221e-288
retrying with dt=1.805e-288
      TSAdapt 'basic': step   0 stage rejected t=0          +1.805e-288
retrying with dt=4.513e-289
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Floating point exception!
[0]PETSC ERROR: Vec entry at local location 1103 is not-a-number or
infinite at end of function: Parameter number 3!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.4.1, Jun, 10, 2013
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./diffusion_c on a ifort-icc-nompi-double-debug named
mazinger.ciemat.es by u5751 Thu Oct 24 03:37:56 2013
[0]PETSC ERROR: Libraries linked from
/home/u5751/petsc-3.4.1/ifort-icc-nompi-double-debug/lib
[0]PETSC ERROR: Configure run at Mon Oct 14 05:43:50 2013
[0]PETSC ERROR: Configure options --with-mpi=0 --with-fc=ifort
--with-cc=icc --with-debugging=1 --with-scalar-type=real
--with-precision=double --with-blas-lapack-dir=/opt/intel/mkl
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: VecValidValues() line 30 in src/vec/vec/interface/rvector.c
[0]PETSC ERROR: SNESComputeFunction() line 1998 in src/snes/interface/snes.c
[0]PETSC ERROR: SNESSolve_NEWTONLS() line 162 in src/snes/impls/ls/ls.c
[0]PETSC ERROR: SNESSolve() line 3636 in src/snes/interface/snes.c
[0]PETSC ERROR: TSStep_ARKIMEX() line 765 in src/ts/impls/arkimex/arkimex.c
[0]PETSC ERROR: TSStep() line 2458 in src/ts/interface/ts.c
[0]PETSC ERROR: TSSolve() line 2583 in src/ts/interface/ts.c
[0]PETSC ERROR: main() line 457 in src/ts/examples/tutorials/diffusion.c
./compile_diffusion: line 17: 23584 Aborted                 ./diffusion_c
-ts_adapt_monitor -ts_adapt_basic_clip 0.1,1.1 -draw_pause -2
-ts_arkimex_type 1bee -ts_max_snes_failures -1 -snes_type newtonls
-snes_linesearch_type bt -ts_arkimex_fully_implicit -snes_mf_operator

Using -snes_converged_reason and -ksp_converged_reason gives:

    Linear solve did not converge due to DIVERGED_DTOL iterations 30
  Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 0
      TSAdapt 'basic': step   0 stage rejected t=0          + 1.000e-12
retrying with dt=2.500e-13

Thus, I increased the maximum number of iterations of the KSP with
  ierr = SNESSetMaxLinearSolveFailures(snes,100);
and
  ierr =
KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1000);

Then it converges, steps are accepted. However, the solution obtained is
weird, as if there was no diffusion. Moreover, values are incorrect. I
start with a gaussian peak at 1e19 and end up with a gaussian with a peak
at 1e25.

BTW, why using -ts_arkimex_fully_implicit if all the terms are in the F
(LHS) ? You said that by definition there is no explicit stage in that case.

However, I could obtain a good solution by adding mesh points (without
fully implicit and mf_operator). Maybe it was due to large gradients and
not enough points.

Christophe
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