[MOAB-dev] vertex to cell adjacencies in parallel

[Hong-Jun Kim]

Could you please send me the code to replicate?
Thanks.

-----------------------------
Hong-Jun Kim
Post-doc researcher
MCS, Argonne National Laboratory
9700 S. Cass Ave. B240/R2147
Argonne, IL 60439
630-252-4791
hongjun at mcs.anl.gov
-----------------------------

----- Original Message -----
> From: "Lorenzo Alessio Botti" <ihabiamx at yahoo.it>
> To: "Tim Tautges" <tautges at mcs.anl.gov>, MOAB-dev at mcs.anl.gov
> Sent: Friday, October 7, 2011 9:47:52 AM
> Subject: Re: [MOAB-dev] vertex to cell adjacencies in parallel
> Thanks a lot for the reply.
> Let me know if you need the code to replicate this issue...
> 
> >> For my application it would be very interesting to be able to
> >> partition based on entity sets.
> >>
> >
> > If those entity sets form a covering for the entities (each of the
> > entities included in exactly one of those sets), and those sets can
> > be identified by a tag and optionally tag value, then you should be
> > able to already read in parallel based on that partition (which has
> > to already be in the file). See section 5 of the user's guide (in
> > the doc subdir) and the description of how to read according to a
> > material_set partition.
> 
> My request was a bit too cryptic...
> I'm now reading parallel meshes generated with mbzoltan with the
> partition tag set to PARALLEL_PARTITION.
> It would be useful (for geometric h-multigrid, adaptivity based on
> element agglomeration ecc...)
> to repartition based on tagged entity sets that form a covering for
> the entities
> (such sets might be generated requiring a lot of partitions to the
> partitioner)
> instead of mesh elements.
> A simpler trick would be to create a lot of tagged entity sets and run
> in parallel
> with n_processes = n_entity_set/n_entity_sets_per_process, using once
> again the
> entity sets as mesh elements.
> In this context the entity set can be viewed as very general elements
> (eg polygons).
> In both cases the ability to get the adjacencies of entity set would
> be also required.
> 
> By the way I've seen that you already have a polygonal element
> implementation
> but I don't know if it has been introduced with the same goal.
> 
> Now I'm still working on the standard element dG finite element
> library
> but later on it would be interesting to explore more general
> implementations.
> 
> Lorenzo
> 
> On Oct 7, 2011, at 3:54 PM, Tim Tautges wrote:
> 
> >
> >
> > On 10/07/2011 04:05 AM, Lorenzo Alessio Botti wrote:
> >> Hi all,
> >> I have a question about getting adjacencies in parallel.
> >>
> >> After having partitioned a mesh, resolved shared entities and
> >> exchanged ghost cells I fail to
> >> update the mesh cell adjacencies so to include ghost cells.
> >>
> >> The face to elements adjacencies are correctly updated, that is the
> >> faces obtained with
> >> pcomm.get_iface_entities(1,2,faces); (I'm running on 2 processors)
> >> have two neighbors one owned and one non owned.
> >>
> >> However the vertex to cell adjacencies do not seem to be updated to
> >> include ghost cells
> >> and even after
> >>   mb.get_entities_by_dimension(0,3,entities);
> >>   mb.get_adjacencies(entities, 0, true, vertexEntities,
> >>   Interface::UNION);
> >>   entities.clear();
> >>   mb.get_adjacencies(vertexEntities, 3, true, entities,
> >>   Interface::UNION);
> >> I'm not able to find vertex to not owned cells adjacencies.
> >>
> >> Is get_adjacencies(...,create if missing=true,...) supposed to work
> >> also for non owned cells?
> >> It seems that the vertex to non owned cell adjacencies are detected
> >> but not created.
> >>
> >
> > That sounds like a bug; Hong-Jun, could you look at that?
> >
> > MOAB's parallel model is that all locally-represented entities,
> > which includes ghost and shared interface entities, should appear
> > locally as a serial mesh, with all adjacencies and other API calls
> > available.
> >
> >> Overall MOAB works fine in parallel and
> >> pcomm.assign_global_ids(...) is useful.
> >> Are you also planning to introduce some repartitioning
> >> capabilities?
> >
> > Yes, this year's work plan includes migrating entities for
> > repartitioning. In theory, the partitioning class in tools/mbzoltan
> > should work to compute the new partition in parallel, though I think
> > it's currently hardwired to run on one processor (on my list to get
> > rid of that restriction).
> >
> >> For my application it would be very interesting to be able to
> >> partition based on entity sets.
> >>
> >
> > If those entity sets form a covering for the entities (each of the
> > entities included in exactly one of those sets), and those sets can
> > be identified by a tag and optionally tag value, then you should be
> > able to already read in parallel based on that partition (which has
> > to already be in the file). See section 5 of the user's guide (in
> > the doc subdir) and the description of how to read according to a
> > material_set partition.
> >
> > - tim
> >
> >> Thanks for help.
> >> Lorenzo
> >
> > --
> > ================================================================
> > "You will keep in perfect peace him whose mind is
> >  steadfast, because he trusts in you." Isaiah 26:3
> >
> >             Tim Tautges Argonne National Laboratory
> >         (tautges at mcs.anl.gov) (telecommuting from UW-Madison)
> >         phone: (608) 263-8485 1500 Engineering Dr.
> >           fax: (608) 263-4499 Madison, WI 53706
> >