[MOAB-dev] vertex to cell adjacencies in parallel
Hong-Jun Kim
hongjun at mcs.anl.gov
Tue Oct 11 14:15:55 CDT 2011
Sorry, it should be as follows.
rval = pcomm.get_shared_entities(-1, shared_owned_vols, 3, false, true);
-----------------------------
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: "Tim Tautges" <tautges at mcs.anl.gov>
To: "Hong-Jun Kim" <hongjun at mcs.anl.gov>
Cc: "Lorenzo Alessio Botti" <ihabiamx at yahoo.it>, moab-dev at mcs.anl.gov
Sent: Tuesday, October 11, 2011 1:55:33 PM
Subject: Re: [MOAB-dev] vertex to cell adjacencies in parallel
I don't think that will return any region entities, as those aren't marked as interface. You'll only get vertices,
faces, and edges from that.
- tim
On 10/11/2011 01:31 PM, Hong-Jun Kim wrote:
> As Tim mentioned, you can reduce your code with the following 1 function to get shared and owned elements.
>
> Range shared_owned_vols;
> rval = pcomm.get_shared_entities(-1, shared_owned_vols, 3, true, true);
>
> 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: "Tim Tautges"<tautges at mcs.anl.gov>
> To: "Hong-Jun Kim"<hongjun at mcs.anl.gov>
> Cc: "Lorenzo Alessio Botti"<ihabiamx at yahoo.it>, moab-dev at mcs.anl.gov
> Sent: Tuesday, October 11, 2011 12:58:21 PM
> Subject: Re: [MOAB-dev] vertex to cell adjacencies in parallel
>
> You should also be able to get the same thing with get_shared_entities, passing true for interface and owned.
>
> - tim
>
> On 10/11/2011 11:01 AM, Hong-Jun Kim wrote:
>> Hi, Lorenzo
>>
>> By detouring wrong way, I think I finally found a bug in your code.
>> I thought the bug came from MOAB then, I have digged the wrong place.
>>
>> To get owned elements, the line 226 in your code should be changed as follows (not pstatus[0] != PSTATUS_SHARED).
>>
>> if (pstatus[0] == PSTATUS_SHARED&& pstatus[0] != PSTATUS_NOT_OWNED&& pstatus[0] != PSTATUS_GHOST)
>>
>> Moreover, I think you'd better use bitwise operator to get it as follows.
>> if (pstatus[0]& PSTATUS_SHARED&& !(pstatus[0]& PSTATUS_NOT_OWNED)&& !(pstatus[0]& PSTATUS_GHOST))
>>
>> 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: "Hong-Jun Kim"<hongjun at mcs.anl.gov>
>> Sent: Friday, October 7, 2011 10:52:49 AM
>> Subject: Re: [MOAB-dev] vertex to cell adjacencies in parallel
>>
>> Hi Hong-Jun,
>> I attach the code you can run it as
>> mpiexec -n 2 [exe_name] -P -R [path_to_one_of_the_mesh_files_here_attached]
>>
>> Let me explain it a bit.
>> I start from a 5x5x5 hex cube with 2 partitions.
>>
>> The cells on the interface form more or less a 5x5x1 25 hexes row.
>> (They do in the hex 27 mesh while in the hex 8 an hex is misplaced for some reason)
>>
>> 25 elements have a face on the interface, 25 elements share a face with owned cells,
>> 20 elements have a face on boundary. You can take a look to the .vtk output.
>>
>> Let me comment the output
>> iface faces size 25 ok
>> ghost cells size 50 shared = 25 ok, every face on iface has two neighbors one owned one not owned
>>
>> Now the code searches the vertex adjacencies for the 25 owned cells, this is the output
>> owned entities = 25 adjacent entities not found = 45 this in wrong, the number of adjacencies not found should be 25 smaller, that is equal to number of faces on the boundary.
>>
>> Thanks a lot.
>> Lorenzo
>>
>>
>>
>>
>>
>> On Oct 7, 2011, at 4:53 PM, Hong-Jun Kim wrote:
>>
>>> 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
>>>>>
>>
>>
>
--
================================================================
"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
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