[petsc-users] Suggestions for code with dof >> 1 ?
Christophe Ortiz
christophe.ortiz at ciemat.es
Tue Oct 22 08:29:43 CDT 2013
Hi Barry,
Thanks for suggestions. Here is the output.
Before using the options you suggest I get:
TSAdapt 'basic': step 182 accepted t=0.341561 + 3.416e-02 wlte=1.1e-09
family='arkimex' scheme=0:'3' dt=3.757e-02
TSAdapt 'basic': step 183 accepted t=0.375717 + 3.757e-02
wlte=9.05e-14 family='arkimex' scheme=0:'3' dt=4.133e-02
TSAdapt 'basic': step 184 stage rejected t=0.413289 + 4.133e-02
retrying with dt=1.033e-02
TSAdapt 'basic': step 184 stage rejected t=0.413289 + 1.033e-02
retrying with dt=2.583e-03
...
TSAdapt 'basic': step 184 stage rejected t=0.413289 +2.212e-198
retrying with dt=5.529e-199
TSAdapt 'basic': step 184 stage rejected t=0.413289 +5.529e-199
retrying with dt=1.382e-199
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Floating point exception!
[0]PETSC ERROR: Vec entry at local location 12 is not-a-number or infinite
at end of function: Parameter number 3!
I re-checked my Jacobian several times, and I found few errors. But now I
think it is ok.
Then, with the options you suggest, it stops immediatly. Not even one
timestep:
0 SNES Function norm 5.929210530071e+26
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Detected zero pivot in LU factorization:
see http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot!
[0]PETSC ERROR: Zero pivot row 17 value 1.35114e-16 tolerance 2.22045e-14!
...
[0]PETSC ERROR: MatPivotCheck_none() line 589 in
src/mat/impls/aij/seq//home/u5751/petsc-3.4.1/include/petsc-private/matimpl.h
[0]PETSC ERROR: MatPivotCheck() line 608 in
src/mat/impls/aij/seq//home/u5751/petsc-3.4.1/include/petsc-private/matimpl.h
[0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ_Inode() line 1626 in
src/mat/impls/aij/seq/inode.c
[0]PETSC ERROR: MatLUFactorNumeric() line 2889 in src/mat/interface/matrix.c
[0]PETSC ERROR: PCSetUp_LU() line 152 in src/ksp/pc/impls/factor/lu/lu.c
[0]PETSC ERROR: PCSetUp() line 890 in src/ksp/pc/interface/precon.c
[0]PETSC ERROR: KSPSetUp() line 278 in src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: KSPSolve() line 399 in src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: SNESSolve_NEWTONLS() line 220 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 455 in src/ts/examples/tutorials/diffusion.c
Does this give you a hint ?
Christophe
CIEMAT
Laboratorio Nacional de Fusión por Confinamiento Magnético
Unidad de Materiales
Edificio 2 - Planta 0 - Despacho 28m
Avenida Complutense 40,
28040 Madrid, Spain
Tel: +34 91496 2582
Fax: +34 91346 6442
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On Tue, Oct 22, 2013 at 1:58 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> Add -snes_monitor -snes_converged_reason -ksp_monitor
> -ksp_converged_reason -pc_type lu (send the output)
>
> Does it now get stuck at the same time step or does it get past it?
> The most common cause of this problem is an incorrect Jacobian
> http://www.mcs.anl.gov/petsc/documentation/faq.html#newton
>
> Barry
>
>
> On Oct 22, 2013, at 4:16 AM, Christophe Ortiz <christophe.ortiz at ciemat.es>
> wrote:
>
> > Hi Jed,
> >
> > I added a third specie to my problem (step by step :-)).
> >
> > Now my system is the following:
> >
> > u_t - alpha u_xx +(k.u.v - q.w) = 0
> > v_t - beta v_xx +(k.u.v - q.w) = 0
> > w_t -(k.u.v - q.w) = 0
> >
> >
> > So I have 2 PDEs and 1 ODE. I put everything under IFunction and
> IJacobian.
> > For the PDEs I defined Dirichlet boundary conditions.
> >
> > For this simple system, I have lot of problems, it does not converge.
> >
> > I followed your suggestions and I removed any options from the code, and
> put TSSetFromOptions(); at the end.
> > The default options are thus SNESNEWTONLS, KSPGMRES, LineSearch bt,
> ARKIMEX 3.
> >
> > I obtain the following output:
> >
> > TSAdapt 'basic': step 101 accepted t=1.07438 + 3.223e-01 wlte=
> 0 family='arkimex' scheme=0:'3' dt=4.190e-01
> > TSAdapt 'basic': step 102 accepted t=1.39669 + 4.190e-01
> wlte=5.21e-13 family='arkimex' scheme=0:'3' dt=5.447e-01
> > TSAdapt 'basic': step 103 accepted t=1.8157 + 5.447e-01
> wlte=1.64e-13 family='arkimex' scheme=0:'3' dt=7.081e-01
> > TSAdapt 'basic': step 104 accepted t=2.36041 + 7.081e-01
> wlte=5.62e-14 family='arkimex' scheme=0:'3' dt=9.206e-01
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 9.206e-01,
> 1 failures exceeds current TS allowed
> > [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > [0]PETSC ERROR: !
> > [0]PETSC ERROR: TSStep has failed due to DIVERGED_NONLINEAR_SOLVE,
> increase -ts_max_snes_failures or make negative to attempt recovery!
> >
> >
> >
> > ThenI increase the max number of failures. When I do so, I get the
> following error message:
> >
> > TSAdapt 'basic': step 101 accepted t=1.07438 + 3.223e-01 wlte=
> 0 family='arkimex' scheme=0:'3' dt=4.190e-01
> > TSAdapt 'basic': step 102 accepted t=1.39669 + 4.190e-01
> wlte=5.21e-13 family='arkimex' scheme=0:'3' dt=5.447e-01
> > TSAdapt 'basic': step 103 accepted t=1.8157 + 5.447e-01
> wlte=1.64e-13 family='arkimex' scheme=0:'3' dt=7.081e-01
> > TSAdapt 'basic': step 104 accepted t=2.36041 + 7.081e-01
> wlte=5.62e-14 family='arkimex' scheme=0:'3' dt=9.206e-01
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 9.206e-01
> retrying with dt=2.301e-01
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 2.301e-01
> retrying with dt=5.753e-02
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 5.753e-02
> retrying with dt=1.438e-02
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 1.438e-02
> retrying with dt=3.596e-03
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 3.596e-03
> retrying with dt=8.990e-04
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 8.990e-04
> retrying with dt=2.247e-04
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 2.247e-04
> retrying with dt=5.619e-05
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 + 5.619e-05
> retrying with dt=1.405e-05
> >
> > ...
> > ...
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 +5.679e-179
> retrying with dt=1.420e-179
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 +1.420e-179
> retrying with dt=3.550e-180
> > TSAdapt 'basic': step 105 stage rejected t=3.06853 +3.550e-180
> retrying with dt=8.874e-181
> > [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> > [0]PETSC ERROR: Floating point exception!
> > [0]PETSC ERROR: Vec entry at local location 15 is not-a-number or
> infinite at end of function: Parameter number 3!
> >
> > It seems it is not able to recover, it decreases the timestep so much
> that at the end you are left with something that it not a number, or 0.
> >
> > Any idea how to solve that ?
> > Some time ago you told me it could be due to a problem associated with
> DAE formulation for boundary conditions and methods with explicit stages:
> >
> > Is your problem similar to ex25? (If I remember
> > correctly, that example uses a DAE formulation for boundary conditions
> > and thus has trouble with some methods with explicit stages. There may
> > be more going on.)
> >
> > How can I reformulate my problem so I do not use DAE formulation for
> boundary conditions ? For instance, if I want u=u* at i=0, or Neumann (or
> Robin) boundary conditions ?
> > If due to method with explicit stages, which method do you recommend ? I
> tried the FullyImplicit option for ARKIMEX, and it's even worse, it gets
> slower.
> >
> > Thanks a lot in advance for your help.
> > Christophe
> >
>
>
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