[MOAB-dev] ghost/halo elements

[Vijay S. Mahadevan]

It is your root set or fileset if you added entities to it. You can get the
root set handle from Core object.

Vijay

On Thu, Oct 25, 2018, 14:38 Ryan O'Kuinghttons <ryan.okuinghttons at noaa.gov>
wrote:

> Thanks again, Vijay. However, I still don't understand what this_set
> should be, is it an output maybe?
>
> Ryan
>
> On 10/25/18 12:27, Vijay S. Mahadevan wrote:
> > You can try either the first or the second variant instead [1] with
> > following arguments.
> >
> > ErrorCode moab::ParallelComm::resolve_shared_ents(EntityHandle this_set,
> > int resolve_dim = 2,
> > int shared_dim = -1,
> > const Tag * id_tag = 0
> > )
> >
> > That should resolve 2-dim entities with shared edges across
> > partitions. You can leave id_tag pointer as zero since the default is
> > GLOBAL_ID.
> >
> >> This brings up a more general question I've had about the moab
> > documentation for a while. In the doc for this routine, it only lists 2
> > parameters, proc_ents and shared_dim, even though in the function
> > signature above it clearly shows more. I've had trouble understanding
> > which parameters are relevant in the past, or what they do because I'm
> > not quite sure how to read the documentation.
> >
> > This is an oversight. We will go through and rectify some of the
> > inconsistencies in the documentation. We are preparing for an upcoming
> > release and I'll make sure that routines in Core/ParallelComm have
> > updated documentation that match the interfaces. Meanwhile, if you
> > have questions, feel free to shoot an email to the list.
> >
> > Hope that helps.
> >
> > Vijay
> >
> > [1]
> http://ftp.mcs.anl.gov/pub/fathom/moab-docs-develop/classmoab_1_1ParallelComm.html#a29a3b834b3fc3b4ddb3a5d8a78a37c8a
> > On Thu, Oct 25, 2018 at 1:58 PM Ryan O'Kuinghttons
> > <ryan.okuinghttons at noaa.gov> wrote:
> >> Hi Vijay,
> >>
> >> Thanks again for that explanation.
> >>
> >> ESMF does use unique global ids for the vertices and set them to the
> >> GLOBAL_ID in the moab mesh. So I think we are good there.
> >>
> >> I can't quite figure out how to use resolve_shared_entities though.
> >> There are three versions of the call in the documentation, and I assume
> >> that I should use the first and pass in a Range containing all entities
> >> for proc_ents:
> >>
> >>
> http://ftp.mcs.anl.gov/pub/fathom/moab-docs-develop/classmoab_1_1ParallelComm.html#a59e35d9906f2e33fe010138a144a5cb6
> >>
> >> However, I'm not sure what the this_set EntityHandle should be.
> >>
> >> This brings up a more general question I've had about the moab
> >> documentation for a while. In the doc for this routine, it only lists 2
> >> parameters, proc_ents and shared_dim, even though in the function
> >> signature above it clearly shows more. I've had trouble understanding
> >> which parameters are relevant in the past, or what they do because I'm
> >> not quite sure how to read the documentation.
> >>
> >> Any example or explanation you give me for resolve_shared_entities is
> >> much appreciated!
> >>
> >> Ryan
> >>
> >> On 10/25/18 09:40, Vijay S. Mahadevan wrote:
> >>> Hi Ryan,
> >>>
> >>> Glad the example helped.
> >>>
> >>>> The example shows the ghost exchange happening between shared owned
> >>> entities. In my experiments I've been unable to make the ghost exchange
> >>> work, and I think that might be because my entities are not shared.
> >>>
> >>> You need to call resolve_shared_entities on the entities prior to
> >>> doing ghost exchange. When we load the mesh from file, this happens
> >>> automatically based on the read options but if you are forming a mesh
> >>> in memory, you need to make sure that the shared vertices have the
> >>> same GLOBAL_ID numbering consistently across processes. That is shared
> >>> vertices are unique. Once that is set, shared entities resolution will
> >>> work correctly out of the box and you will have shared edges/entities
> >>> query working correctly. A call to get ghosted layers once this is
> >>> done would be the way to go.
> >>>
> >>> I assume ESMF has a unique global numbering for the vertices ? Use
> >>> that to set the GLOBAL_ID tag. Let us know if you are still having
> >>> issues.
> >>>
> >>> Vijay
> >>> On Thu, Oct 25, 2018 at 11:17 AM Ryan O'Kuinghttons
> >>> <ryan.okuinghttons at noaa.gov> wrote:
> >>>> Hi Vijay,
> >>>>
> >>>> I've had some time to play with this now, and I have another question.
> >>>> Thank you for sending along the example code, it has been extremely
> >>>> helpful.
> >>>>
> >>>> The example shows the ghost exchange happening between shared owned
> >>>> entities. In my experiments I've been unable to make the ghost
> exchange
> >>>> work, and I think that might be because my entities are not shared.
> The
> >>>> situation I have is entities that are owned wholly on a single
> >>>> processor, which need to be communicated to other processors which
> >>>> require them as part of a halo region for mesh based computation. In
> >>>> this situation would I need to "share" my entities across the whole
> >>>> processor space, before requesting a ghost exchange? I'm not even
> really
> >>>> sure what shared entities mean, is there a good place to look in the
> >>>> documentation to learn more about the terminology? Thanks,
> >>>>
> >>>> Ryan
> >>>>
> >>>> On 10/8/18 12:17, Vijay S. Mahadevan wrote:
> >>>>> Ryan,
> >>>>>
> >>>>> You need to use the ParallelComm object in MOAB to call
> >>>>> exchange_ghost_cells [1] with appropriate levels of ghost layers for
> >>>>> your mesh. This needs to be done after the mesh is loaded, or you can
> >>>>> pass this information also as part of the options when loading a file
> >>>>> and MOAB will internally load the file with ghosted layers. Here's an
> >>>>> example [2].
> >>>>>
> >>>>> Vijay
> >>>>>
> >>>>> [1]
> http://ftp.mcs.anl.gov/pub/fathom/moab-docs-develop/classmoab_1_1ParallelComm.html#a55dfa308f56fd368319bfb4244428878
> >>>>> [2]
> http://ftp.mcs.anl.gov/pub/fathom/moab-docs-develop/HelloParMOAB_8cpp-example.html
> >>>>> On Mon, Oct 8, 2018 at 1:23 PM Ryan O'Kuinghttons
> >>>>> <ryan.okuinghttons at noaa.gov> wrote:
> >>>>>> Hi, I am wondering if there is a way to create ghost elements in
> MOAB.
> >>>>>> By this I mean a list of copies of elements surrounding a specific
> MOAB
> >>>>>> element, ghost elements may exist on a different processor than the
> >>>>>> source element. I see a ghost_elems class in the appData namespace,
> but
> >>>>>> there is not much documentation on how to use it.. Thank you,
> >>>>>>
> >>>>>> --
> >>>>>> Ryan O'Kuinghttons
> >>>>>> Cherokee Nation Management and Consulting
> >>>>>> NESII/NOAA/Earth System Research Laboratory
> >>>>>> ryan.okuinghttons at noaa.gov
> >>>>>> https://www.esrl.noaa.gov/gsd/nesii/
> >>>>>>
>
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