[petsc-users] Why use MATMPIBAIJ?
Matthew Knepley
knepley at gmail.com
Fri Jan 22 12:07:04 CST 2016
On Fri, Jan 22, 2016 at 11:47 AM, Hom Nath Gharti <hng.email at gmail.com>
wrote:
> Thanks a lot.
>
> With AMG it did not converge within the iteration limit of 3000.
>
> In solid: elastic wave equation with added gravity term \rho \nabla\phi
> In fluid: acoustic wave equation with added gravity term \rho \nabla\phi
> Both solid and fluid: Poisson's equation for gravity
> Outer space: Laplace's equation for gravity
>
> We combine so called mapped infinite element with spectral-element
> method (higher order FEM that uses nodal quadrature) and solve in
> frequency domain.
>
1) The Poisson and Laplace equation should be using MG, however you are
using SEM, so
you would need to use a low order PC for the high order problem, also
called p-MG (Paul Fischer), see
http://epubs.siam.org/doi/abs/10.1137/110834512
2) The acoustic wave equation is Helmholtz to us, and that needs special MG
tweaks that
are still research material so I can understand using ASM.
3) Same thing for the elastic wave equations. Some people say they have
this solved using
hierarchical matrix methods, something like
http://portal.nersc.gov/project/sparse/strumpack/
However, I think the jury is still out.
If you can do 100 iterations of plain vanilla solvers, that seems like a
win right now. You might improve
the time using FS, but I am not sure about the iterations on the smaller
problem.
Thanks,
Matt
> Hom Nath
>
> On Fri, Jan 22, 2016 at 12:16 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Fri, Jan 22, 2016 at 11:10 AM, Hom Nath Gharti <hng.email at gmail.com>
> > wrote:
> >>
> >> Thanks Matt.
> >>
> >> Attached detailed info on ksp of a much smaller test. This is a
> >> multiphysics problem.
> >
> >
> > You are using FGMRES/ASM(ILU0). From your description below, this sounds
> > like
> > an elliptic system. I would at least try AMG (-pc_type gamg) to see how
> it
> > does. Any
> > other advice would have to be based on seeing the equations.
> >
> > Thanks,
> >
> > Matt
> >
> >>
> >> Hom Nath
> >>
> >> On Fri, Jan 22, 2016 at 12:01 PM, Matthew Knepley <knepley at gmail.com>
> >> wrote:
> >> > On Fri, Jan 22, 2016 at 10:52 AM, Hom Nath Gharti <
> hng.email at gmail.com>
> >> > wrote:
> >> >>
> >> >> Dear all,
> >> >>
> >> >> I take this opportunity to ask for your important suggestion.
> >> >>
> >> >> I am solving an elastic-acoustic-gravity equation on the planet. I
> >> >> have displacement vector (ux,uy,uz) in solid region, displacement
> >> >> potential (\xi) and pressure (p) in fluid region, and gravitational
> >> >> potential (\phi) in all of space. All these variables are coupled.
> >> >>
> >> >> Currently, I am using MATMPIAIJ and form a single global matrix. Does
> >> >> using a MATMPIBIJ or MATNEST improve the convergence/efficiency in
> >> >> this case? For your information, total degrees of freedoms are about
> a
> >> >> billion.
> >> >
> >> >
> >> > 1) For any solver question, we need to see the output of -ksp_view,
> and
> >> > we
> >> > would also like
> >> >
> >> > -ksp_monitor_true_residual -ksp_converged_reason
> >> >
> >> > 2) MATNEST does not affect convergence, and MATMPIBAIJ only in the
> >> > blocksize
> >> > which you
> >> > could set without that format
> >> >
> >> > 3) However, you might see benefit from using something like
> PCFIELDSPLIT
> >> > if
> >> > you have multiphysics here
> >> >
> >> > Matt
> >> >
> >> >>
> >> >> Any suggestion would be greatly appreciated.
> >> >>
> >> >> Thanks,
> >> >> Hom Nath
> >> >>
> >> >> On Fri, Jan 22, 2016 at 10:32 AM, Matthew Knepley <knepley at gmail.com
> >
> >> >> wrote:
> >> >> > On Fri, Jan 22, 2016 at 9:27 AM, Mark Adams <mfadams at lbl.gov>
> wrote:
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>> I said the Hypre setup cost is not scalable,
> >> >> >>
> >> >> >>
> >> >> >> I'd be a little careful here. Scaling for the matrix triple
> product
> >> >> >> is
> >> >> >> hard and hypre does put effort into scaling. I don't have any data
> >> >> >> however.
> >> >> >> Do you?
> >> >> >
> >> >> >
> >> >> > I used it for PyLith and saw this. I did not think any AMG had
> >> >> > scalable
> >> >> > setup time.
> >> >> >
> >> >> > Matt
> >> >> >
> >> >> >>>
> >> >> >>> but it can be amortized over the iterations. You can quantify
> this
> >> >> >>> just by looking at the PCSetUp time as your increase the number
> of
> >> >> >>> processes. I don't think they have a good
> >> >> >>> model for the memory usage, and if they do, I do not know what it
> >> >> >>> is.
> >> >> >>> However, generally Hypre takes more
> >> >> >>> memory than the agglomeration MG like ML or GAMG.
> >> >> >>>
> >> >> >>
> >> >> >> agglomerations methods tend to have lower "grid complexity", that
> is
> >> >> >> smaller coarse grids, than classic AMG like in hypre. THis is more
> >> >> >> of a
> >> >> >> constant complexity and not a scaling issue though. You can
> address
> >> >> >> this
> >> >> >> with parameters to some extent. But for elasticity, you want to at
> >> >> >> least
> >> >> >> try, if not start with, GAMG or ML.
> >> >> >>
> >> >> >>>
> >> >> >>> Thanks,
> >> >> >>>
> >> >> >>> Matt
> >> >> >>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> Giang
> >> >> >>>>
> >> >> >>>> On Mon, Jan 18, 2016 at 5:25 PM, Jed Brown <jed at jedbrown.org>
> >> >> >>>> wrote:
> >> >> >>>>>
> >> >> >>>>> Hoang Giang Bui <hgbk2008 at gmail.com> writes:
> >> >> >>>>>
> >> >> >>>>> > Why P2/P2 is not for co-located discretization?
> >> >> >>>>>
> >> >> >>>>> Matt typed "P2/P2" when me meant "P2/P1".
> >> >> >>>>
> >> >> >>>>
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>> --
> >> >> >>> 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
> >> >> >>
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > 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
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > 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
> >
> >
> >
> >
> > --
> > 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
>
--
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
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