[petsc-dev] proposed minor PetscPartitioner changes

Matthew Knepley knepley at gmail.com
Sat Nov 11 11:34:59 CST 2017

On Fri, Nov 10, 2017 at 8:56 AM, Jed Brown <jed at jedbrown.org> wrote:

> Vaclav Hapla <vaclav.hapla at erdw.ethz.ch> writes:
> >> 10. 11. 2017 v 5:09, Smith, Barry F. <bsmith at mcs.anl.gov>:
> >>
> >>
> >>
> >>> On Nov 8, 2017, at 3:52 AM, Vaclav Hapla <vaclav.hapla at erdw.ethz.ch>
> wrote:
> >>>
> >>>
> >>>> 8. 11. 2017 v 9:06, Lisandro Dalcin <dalcinl at gmail.com>:
> >>>>
> >>>> On 8 November 2017 at 05:51, Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
> >>>>>
> >>>>>> On Nov 7, 2017, at 1:33 AM, Lisandro Dalcin <dalcinl at gmail.com>
> wrote:
> >>>>>>
> >>>>>> The only concern I have about PetscPartitioner is that the API
> depends
> >>>>>> on DM (PetscPartitionerPartition_<TYPE> routines). Maybe
> >>>>>> PetscPartitioner should eventually move to became more agnostic, and
> >>>>>> that way it can be used to partition matrices and meshes.
> >>>>>
> >>>>> This is certainly a serious flaw if PetscPartitioner is intended as
> THE API to use for partitioning. If it is not intended as THE API for
> partitioning then that is also a problem, because why have multiple APIs
> for what is essentially one set of abstractions.
> >>>>>
> >>>>
> >>>> Note however that things looks easy to refactor. I'll try to team up
> >>>> with Matt to improve things.
> >>>
> >>> Wait, now we are at the beginning again. I actually wanted to do some
> refactoring of PetscPartitioner, starting with few cosmetic changes to make
> it better settable from options. But Barry kept me back of any edits since
> he think it's anti-systematic to keep two independent classes doing
> essentially the same. And I agree with that to be honest. It's strange to
> have two ParMetis, two Scotch and two whatever interfaces.
> >>
> >>  Strange is not the word, f***up is the word
> >>
> >>> The only thing I don't like on MatPartitioning is its name as it's not
> just for Mat Partitioning :-)
> >>>
> >>> There are from my point of view multiple issues with PetscPartitioner.
> Let's look e.g. at PetscPartitionerPartition. It takes as arguments both
> PetscPartitioner and DM. This DM must be in fact DMPlex which is not
> checked so it will probably crash somewhere deep in the stack once the
> first DMPlex specific line is reached. Then there are two output arguments
> PetscSection partSection and IS *partition. The first must be created
> beforehand while the second is created inside. And I guess they must keep
> the same basic information just in two different forms.
> >>>
> >>> Actually the original problem I wanted to solve is that
> src/dm/impls/plex/examples/tutorials/ex5.c fails with partitioner set to
> PETSCPARTITIONERPARMETIS for certain numbers of processes, see below. Let
> me start with pull request altering ex5.c so that partitioner type can be
> set from options properly and this bug can be reproduced easily.
> >>> [ 0] ***ASSERTION failed on line 176 of file
> /scratch/petsc-dev/arch-linux-gcc-salvus/externalpackages/
> git.parmetis/libparmetis/comm.c: j == nnbrs
> >>> [ 2] ***ASSERTION failed on line 176 of file
> /scratch/petsc-dev/arch-linux-gcc-salvus/externalpackages/
> git.parmetis/libparmetis/comm.c: j == nnbrs
> >>> ex5: /scratch/petsc-dev/arch-linux-gcc-salvus/externalpackages/
> git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j
> == nnbrs' failed.
> >>> ex5: /scratch/petsc-dev/arch-linux-gcc-salvus/externalpackages/
> git.parmetis/libparmetis/comm.c:176: libparmetis__CommSetup: Assertion `j
> == nnbrs' failed.
> >>>
> >>> I'm wondering whether the MatPartitioning interface has the same
> problem. But anyhow I mean it's maybe time to decide about the two
> interfaces before chasing all these PetscPartitioner issues.
> >>>
> >>> I propose
> >>> - to rename Mat Partitioning to just Partitioning/-er or take over the
> name PetscPartitioner,
> >>
> >>  Why? What is wrong with Mat? Mat can represent any graph and graphs
> are always what partitioning packages actually partition. I don't see a
> reason for a different name. MatPartitioner does not, nor should it,
> directly partition meshes etc, those can/should be done by; the proper
> massaging of data, the creation of a MatPartitioner object, calling the
> partitioner and then using the result of the partitioner to build whatever
> appropriate data structures are needed for the mesh partitioner.
> >
> > Yes. Mat can represent any graph in several different ways -
> > e.g. Laplacian, adjacency, incidence, oriented incidence matrix. The
> > graph could be also represented in other way like a list of vertices
> > and edges.
> Also known as COO format for a matrix.
> > MatPartitioning picks just one representation as an input - the
> > adjacency matrix. But I mean the picked representation does not
> > matter, and the result is not a partitioning of any matrix, but
> > partitioning of the graph. The graph is the underlying concept. This
> > is why I don't consider the Mat prefix optimal.
> Matrix and graph are equivalent concepts.

This is clearly wrong. A matrix is the coordinate representation of a
linear operator, and thus has a specific
behavior under coordinate transformations. A graph is just connectivity,
and really just a relation. I cannot
count the number of times Barry has ranted about this on petsc-maint
(usually about Vecs and arrays). The
mathematical object is not its data structure.


> Mat is already extensible in
> the sense that it can have many representations.
> > (*) It's a similar problem as MatCreateVecs means to me "create a matrix
> of Vecs type" according to usual convention.
> I think the key here is to look at the types.  VecCreateFromMat() might
> be more clear in this context, but isn't clearly better.  Alternatively,
> PetscCreateVec() and MatCreateVecs() would have this symmetry, but don't
> follow our usual prefix conventions.

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

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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