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

[Christophe Ortiz]

On Wed, Oct 23, 2013 at 5:39 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> Christophe Ortiz <christophe.ortiz at ciemat.es> writes:
>
> >> Does a shorter time step fix the oscillations?
> >
> >
> > Hi Jed,
> >
> > Thanks for the prompt reply.
> >
> > No, it did not in this case. However, I noticed for "smoother" cases that
> > max timestep matters. I try to fix it to finaltime/100 to avoid too large
> > timesteps. I also use -ts_adapt_basic_clip 0.1,1.1 to avoid large
> timesteps.
>
> This just slows the rate of increasing time step.
>
> >>  Is this with
> >> -ts_arkimex_type 1bee or something else?
> >>
> >
> > It occurs with 1bee, a2 or arkimex 3.
>
> Stick with 1bee until we understand better.
>

Ok.


>
> >> Can you try -ts_arkimex_fully_implicit and add -snes_mf_operator if
> >> necessary to get SNES to converge?
> >
> >
> >
> > I tried -ts_arkimex_fully_implicit and it gave a wrong result. As if
> there
> > was no diffusion. Seems there is an artefact with fullyimplicit option.
>
> 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 ?


>
> > With -snes_mf_operator I got an error message:
> > [0]PETSC ERROR: No support for this operation for this object type!
> > [0]PETSC ERROR: Mat type mffd!
>
> ALWAYS, ALWAYS, ALWAYS send the ENTIRE error message!
>
> (Sorry about shouting, but I have to type this many times per day.
> Truncating error messages kills kittens!)
>


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
[0]PETSC ERROR: TSComputeIJacobian() line 718 in src/ts/interface/ts.c
[0]PETSC ERROR: SNESTSFormJacobian_ARKIMEX() line 995 in
src/ts/impls/arkimex/arkimex.c
[0]PETSC ERROR: SNESTSFormJacobian() line 3397 in src/ts/interface/ts.c
[0]PETSC ERROR: SNESComputeJacobian() line 2152 in src/snes/interface/snes.c
[0]PETSC ERROR: SNESSolve_NEWTONLS() line 218 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: 20506 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 -snes_mf_operator



>
> >>  (I'm assuming you have used an IMEX
> >> formulation here, but perhaps you already use fully implicit?)
> >>
> >
> > I put everything under IFunction and IJacobian. This part is not clear to
> > me actually. I understand that in IMEX methods, the LHS is solved
> > implicitely and the RHS explicitely. What happens when I use an IMEX
> method
> > with no RHS, everything in the LHS ? Is there any explicit stage ?
>
> No, if the RHS is empty, it should reduce to an implicit method.
>
> > Actually, I could solve the problem by adding mesh points. Since I start
> > from steep gaussian distributions with large peak values, maybe there
> was a
> > problem with large gradients.
> >
> > BTW, is it possible to have adaptive mesh in 1D with PETSc ? I am
> thinking
> > of steep profiles that evolve and that require a fine mesh at the
> beginning.
>
> You can do moving meshes (r-adaptivity) by writing coordinates as a
> coupled system.  Or you can create a new grid and interpolate.  You can
> use DMRefine and DMCoarsen.
>

Great. I will check this out.

Christophe
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