[petsc-users] Moving from KSPSetNullSpace to MatSetNullSpace

Tue Sep 29 12:08:26 CDT 2015

PETSc is version 3.6.1 -- I just included a log from 3.5.4 to show that the
behavior seems to have changed between versions.  The only difference in
our code between 3.5.4 and 3.6.1 is the change from KSPSetNullSpace to
MatSetNullSpace.

On Tue, Sep 29, 2015 at 1:04 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   Update your PETSc
>
>
> > On Sep 29, 2015, at 12:00 PM, Gil Forsyth <gforsyth at gwu.edu> wrote:
> >
> > Hi Barry,
> >
> > We aren't explicitly setting GMRES anywhere in the code and I'm not sure
> why it's being used.  Running our 3.5.4 code using KSPSetNullSpace works
> with:
> >
> > $PETIBM_DIR/petibm3.5/bin/petibm2d -directory . -poisson_pc_type gamg
> -poisson_pc_gamg_type agg -poisson_pc_gamg_agg_nsmooths 1 -poisson_ksp_view
> -poisson_ksp_monitor_true_residual -poisson_ksp_converged_reason >
> kspview3.5.4
> >
> > and shows that the coarse grid solver is of type:preonly
> >
> > running the newer version that uses MatSetNullSpace in its stead and
> adding in -poisson_mg_coarse_ksp_type preonly
> >
> > $PETIBM_DIR/petibm3.6/bin/petibm2d -directory . -poisson_pc_type gamg
> -poisson_pc_gamg_type agg -poisson_pc_gamg_agg_nsmooths 1
> -poisson_mg_coarse_ksp_type preonly -poisson_ksp_view
> -poisson_ksp_monitor_true_residual -poisson_ksp_converged_reason >
> kspview3.6.1
> >
> > still shows
> >
> > KSP Object:(poisson_) 1 MPI processes
> >   type: cg
> >   maximum iterations=10000
> >   tolerances:  relative=1e-05, absolute=1e-50, divergence=10000
> >   left preconditioning
> >   using nonzero initial guess
> >   using PRECONDITIONED norm type for convergence test
> > PC Object:(poisson_) 1 MPI processes
> >   type: gamg
> >     MG: type is MULTIPLICATIVE, levels=3 cycles=v
> >       Cycles per PCApply=1
> >       Using Galerkin computed coarse grid matrices
> >       GAMG specific options
> >         Threshold for dropping small values from graph 0
> >         AGG specific options
> >           Symmetric graph false
> >   Coarse grid solver -- level -------------------------------
> >     KSP Object:    (poisson_mg_coarse_)     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=1, initial guess is zero
> >       tolerances:  relative=1e-05, absolute=1e-50, divergence=10000
> >       left preconditioning
> >       using NONE norm type for convergence test
> >
> >
> > both logs are attached.
> >
> >
> > On Tue, Sep 29, 2015 at 12:37 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> >
> >    This can't work. You can't use a GMRES inside a CG.   Try changing to
> -poisson_mg_coarse_ksp_type preonly
> >
> > KSP Object:(poisson_) 1 MPI processes
> >   type: cg
> >
> > KSP Object:    (poisson_mg_coarse_)     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=1, initial guess is zero
> >
> >
> > > On Sep 29, 2015, at 10:53 AM, Gil Forsyth <gforsyth at gwu.edu> wrote:
> > >
> > >
> > > On Tue, Sep 29, 2015 at 11:42 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > > On Tue, Sep 29, 2015 at 10:28 AM, Gil Forsyth <gforsyth at gwu.edu>
> wrote:
> > > Hi all,
> > >
> > > I've been having some trouble with what should be a relatively simple
> update to an immersed boundary CFD solver from PETSc 3.5.4 to 3.6.1
> > >
> > > I'm getting indefinite PC errors for a simple lid-driven cavity test
> problem, 32x32 at Re 100
> > >
> > > Under PETSc 3.5.4 using KSPSetNullSpace we used the following to set
> the null space.  This is for a 2D Poisson system with no immersed boundary
> and so the null space is the constant vector.
> > >
> > >   MatNullSpace nsp;
> > >   ierr = MatNullSpaceCreate(PETSC_COMM_WORLD, PETSC_TRUE, 0, NULL,
> &nsp); CHKERRQ(ierr);
> > >   ierr = KSPSetNullSpace(ksp2, nsp); CHKERRQ(ierr);
> > >   ierr = MatNullSpaceDestroy(&nsp); CHKERRQ(ierr);
> > >
> > > Clearly this has to happen in the reverse order, since ksp2 would not
> be created yet.
> > >
> > > For questions about solvers, we HAVE to see the complete output of
> -ksp_view so we
> > > know what we are dealing with. Its also nice to have
> -ksp_monitor_true_residual -ksp_converged_reason
> > >
> > >   Matt
> > >
> > > Yes -- sorry, those are both in inline files and are called in the
> reverse order that I wrote them out.
> > >
> > > I've attached the output of
> > >
> > > $PETIBM_DIR/petibm3.6/bin/petibm2d -directory . -poisson_pc_type gamg
> -poisson_pc_gamg_type agg -poisson_gamg_agg_nsmooths 1 -poisson_ksp_view
> -poisson_ksp_monitor_true_residual -poisson_ksp_converged_reason >
> kspview.log
> > >
> > >
> > >
> > > And then setup the KSP with
> > >   ierr = KSPCreate(PETSC_COMM_WORLD, &ksp2); CHKERRQ(ierr);
> > >   ierr = KSPSetOptionsPrefix(ksp2, "poisson_"); CHKERRQ(ierr);
> > >   ierr = KSPSetOperators(ksp2, QTBNQ, QTBNQ); CHKERRQ(ierr);
> > >   ierr = KSPSetInitialGuessNonzero(ksp2, PETSC_TRUE); CHKERRQ(ierr);
> > >   ierr = KSPSetType(ksp2, KSPCG); CHKERRQ(ierr);
> > >   ierr = KSPSetReusePreconditioner(ksp2, PETSC_TRUE); CHKERRQ(ierr);
> > >   ierr = KSPSetFromOptions(ksp2); CHKERRQ(ierr);
> > >
> > > The matrix QTBNQ does not change, only the rhs of the system is
> updated.
> > >
> > > We run this with `-pc_type gamg -pc_gamg_type agg
> -pc_gamg_agg_nsmooths 1` and everything seems to work as expected.
> > >
> > > Under PETSc 3.6.1, we change only the KSPSetNullSpace line, to
> > >
> > >   ierr = MatSetNullSpace(QTBNQ, nsp); CHKERRQ(ierr);
> > >
> > > and the same code diverges after 1 timestep and returns a -8
> KSP_DIVERGED_INDEFINITE_PC
> > >
> > > This is weird, especially because if we change nsmooths to 2, it runs
> for 264 timesteps and the returns the same error.  But we have explicitly
> set KSPSetReusePreconditioner so it should be using the same PC, right?
> > >
> > > Change nsmooths to 3 and it again diverges after 1 timestep.
> > >
> > > Change nsmooths to 4 and it runs to completion.
> > >
> > > It seems like either gamg's behavior has changed, or that
> KSPSetNullSpace was doing something implicitly that we now need to do
> explicitly in addition to MatSetNullSpace?
> > >
> > > Thanks,
> > > Gil Forsyth
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > > <kspview.log>
> >
> >
> > <kspview3.5.4><kspview3.6.1>
>
>
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