dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

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.

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
> > > > > > > > _______________________________________________
> > > > > > > > DOLFIN-dev mailing list
> > > > > > > > DOLFIN-dev@xxxxxxxxxx
> > > > > > > > http://www.fenics.org/mailman/listinfo/dolfin-dev
> > > > > > > _______________________________________________
> > > > > > > DOLFIN-dev mailing list
> > > > > > > DOLFIN-dev@xxxxxxxxxx
> > > > > > > http://www.fenics.org/mailman/listinfo/dolfin-dev
> > > > > _______________________________________________
> > > > > DOLFIN-dev mailing list
> > > > > DOLFIN-dev@xxxxxxxxxx
> > > > > http://www.fenics.org/mailman/listinfo/dolfin-dev
> > > > ----------------------------------------------------
> > > > 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)
> > > > ----------------------------------------------------