dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Thursday 05 March 2009 09:40:03 Garth N. Wells wrote:
> Johan Hake wrote:
> > On Thursday 05 March 2009 08:43:44 Garth N. Wells wrote:
> >> Johan Hake wrote:
> >>> Hello Marc!
> >>>
> >>>>     here's a little patch I did to handle the change in MatInfo from
> >>>> Petsc-3.0.0 (which no longer includes global sizes...this is handled
> >>>> by MatGetSize)
> >>>
> >>> Ok.
> >>>
> >>>> I believe this bit of code has the same  functionality as your
> >>>> original code (whether that test is appropriate for determining the
> >>>> same NonZeroStructure, I'm not sure)
> >>>
> >>> Thanks!
> >>>
> >>>>   // mspieg: matinfo no longer includes sizes in petsc-dev
> >>>>    MatInfo this_info, other_info;
> >>>>    MatGetInfo(*(this->A), MAT_GLOBAL_SUM, &this_info);
> >>>>    MatGetInfo(*A.mat(),   MAT_GLOBAL_SUM, &other_info);
> >>>>    PetscInt this_m, this_n, other_m, other_n;
> >>>>    MatGetSize(*(this->A),&this_m,&this_n);
> >>>>    MatGetSize(*(this->A),&other_m,&other_n);
> >>>>
> >>>>    return this_info.nz_allocated   == other_info.nz_allocated   && \
> >>>>           this_n == other_n && \
> >>>>           this_m  == other_m;
> >>>
> >>> However as you say I am not sure this is enough to determine the same
> >>> nonzero patter. As a side note we also store the size of the global
> >>> matrix so we probably do not have to call PETSc for this.
> >>>
> >>> Should we include more comparisions from the MatInfo, memory,
> >>> blocksize?
> >>
> >> This should be left to the user,
> >>
> >>     void PETScMatrix::axpy(double a, const GenericMatrix& A, bool
> >> same_nonzero_pattern = false);
> >
> > Sounds reasonable.
> >
> > Should this signature be added in GenericMatrix.h? It is only
> > EpetraMatrix and PETScMatrix that need to relate to this information.
> >
> >> The test for the non-zero pattern doesn't look robust to me. I would
> >> expect that if there was an efficient, robust test to compare sparsity
> >> patterns that PETSc would perform this.
> >
> > Ok.
> >
> >> Also, there is a problem with the code in PETScMatrix::axpy(..). Instead
> >> of
> >>
> >>    dolfin_assert(sameNonzeroPattern(*AA));
> >>    MatAXPY(*(this->A), a, *AA->mat(), SAME_NONZERO_PATTERN);
> >>
> >> it should be
> >>
> >>    if (sameNonzeroPattern(*AA))
> >>      MatAXPY(*(this->A), a, *AA->mat(), SAME_NONZERO_PATTERN);
> >>    else
> >>      MatAXPY(*(this->A), a, *AA->mat(), DIFFERENT_NONZERO_PATTERN);
> >
> > Yes, you are right. I think did it by prupose though, i.e., only letting
> > matrices with the same nonzero pattern be addable. :P
>
> That would work with enableDebug=yes, but comes unstuck if debugging is
> disabled.

Yepp! 

You're all too right :P

Johan


> Garth
>
> > Johan
> >
> >> Garth
> >>
> >>> Johan
> >>>
> >>>> cheers
> >>>> marc
> >>>>
> >>>> On Mar 4, 2009, at 2:50 PM, Johan Hake wrote:
> >>>>> On Wednesday 04 March 2009 20:16:56 Garth N. Wells wrote:
> >>>>>> Johan Hake wrote:
> >>>>>>> On Wednesday 04 March 2009 12:46:10 DOLFIN wrote:
> >>>>>>>> One or more new changesets pushed to the primary dolfin
> >>>>>>>> repository. A short summary of the last three changesets is
> >>>>>>>> included below.
> >>>>>>>>
> >>>>>>>> changeset:   5791:7b24d1479dff485f4db0ba38c2e28984a0a3cf46
> >>>>>>>> tag:         tip
> >>>>>>>> user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> >>>>>>>> date:        Wed Mar 04 11:33:23 2009 +0000
> >>>>>>>> files:       dolfin/la/PETScKrylovSolver.cpp
> >>>>>>>> dolfin/la/PETScKrylovSolver.h dolfin/la/PETScMatrix.cpp
> >>>>>>>> dolfin/la/PETScMatrix.h
> >>>>>>>> dolfin/la/PETScPreconditioner.cpp dolfin/la/PETScPreconditioner.h
> >>>>>>>> description:
> >>>>>>>> Fixes for PETSc 2.3.3 compatibility.
> >>>>>>>
> >>>>>>> This commit broke the linear algebra test for PETSc matrices. The
> >>>>>>> check
> >>>>>>> for the sparsity pattern is commented out, and en error is raised
> >>>>>>> instead. Is it not possible to check the non zero pattern for PETSc
> >>>>>>> matrices in 3.0?
> >>>>>>
> >>>>>> The same check doesn't work with PETSc 3.0 because of changes to
> >>>>>> MatInfo.
> >>>>>
> >>>>> Ok.
> >>>>>
> >>>>>> The check is not pretty so we should find a better solution if this
> >>>>>> function is required.
> >>>>>
> >>>>> I think it would be nice to have it, as PETSc can do some
> >>>>> optimalizations if
> >>>>> two matrices have the same pattern.
> >>>>>
> >>>>>> There is a PETSc function
> >>>>>> MatGetSeqNonzeroStructure which may help, but I haven't had time
> >>>>>> to look
> >>>>>> at it.
> >>>>>
> >>>>> Haven't looked to deep into MatGetSeqNonzeroStructure. But it
> >>>>> sounds like it
> >>>>> gives the nonzero sparsity pattern which we really are not
> >>>>> interested in.
> >>>>>
> >>>>>> Why is the function PETScMatrix::sameNonzeroPattern required? It's
> >>>>>> not
> >>>>>> implemented for all backends.
> >>>>>
> >>>>> When I implemented the axpy function I added this test. I do check
> >>>>> the nonzero
> >>>>> pattern for EpetraMatrices too, but there I only do it once, so no
> >>>>> extra
> >>>>> function.
> >>>>>
> >>>>> I think we should be able to still use the MatInfo structure, but
> >>>>> maybe some
> >>>>> guidence from the PETSc developers could help?
> >>>>>
> >>>>> Johan
> >>>>>
> >>>>>> Garth
> >>>>>>
> >>>>>>> Johan
> >>>>>>>
> >>>>>>>> changeset:   5790:05d6f03e87a8bb33cc5dc55add40e8de1c6ebfd0
> >>>>>>>> user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> >>>>>>>> date:        Wed Mar 04 11:21:41 2009 +0000
> >>>>>>>> files:       dolfin/la/PETScKrylovMatrix.cpp
> >>>>>>>> dolfin/la/PETScKrylovSolver.cpp dolfin/la/PETScKrylovSolver.h
> >>>>>>>> dolfin/la/PETScLUSolver.cpp dolfin/la/PETScMatrix.cpp
> >>>>>>>> dolfin/la/PETScMatrix.h dolfin/la/PETScPreconditioner.cpp
> >>>>>>>> dolfin/la/PETScPreconditioner.h description:
> >>>>>>>> PETSc 3 updates.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> changeset:   5789:3abcc647c6141cc4b2fd035cc417eedf80872ae7
> >>>>>>>> user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> >>>>>>>> date:        Wed Mar 04 10:45:44 2009 +0000
> >>>>>>>> files:       dolfin/la/PETScKrylovSolver.cpp
> >>>>>>>> description:
> >>>>>>>> Some updates for PETSc 3.
> >>>>>>>>
> >>>>>>>> ------------------------------------------------------------------
> >>>>>>>>- ---
> >>>>>>>> For more details, visit http://www.fenics.org/hg/dolfin
> >>>>>>>> _______________________________________________
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> >>>>>>>> DOLFIN-dev@xxxxxxxxxx
> >>>>>>>> http://www.fenics.org/mailman/listinfo/dolfin-dev
> >>>>>>>
> >>>>>>> _______________________________________________
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> >>>>>
> >>>>> _______________________________________________
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> >>>>
> >>>> ----------------------------------------------------
> >>>> Marc Spiegelman
> >>>> Lamont-Doherty Earth Observatory
> >>>> Dept. of Applied Physics/Applied Math
> >>>> Columbia University
> >>>> http://www.ldeo.columbia.edu/~mspieg
> >>>> tel: 845 704 2323 (SkypeIn)
> >>>> ----------------------------------------------------