[petsc-users] ParMETIS question

[Thomas Witkowski]

So, I found the problem related to empty partitions. It is not possible 
to weight vertices (i.e. elements of a mesh) in such a way that one 
weight is much higher than the other ones. For more details see

http://glaros.dtc.umn.edu/flyspray/task/11

Its a pity that ParMetis makes is very hard to find this kind of errors.

The open question for me is about the non continuous partitions. Is it a 
normal behavior of ParMetis to create partitions that are not continous?

Thomas

Thomas Witkowski wrote:
> Okay, in my computations, I have empty partitions on some ranks and 
> definitely not
> minimal boundary sizes. So may be I generate a wrong input. But if 
> this is the case, I
> wonder why the resulting mesh partitioning is quite good. If I neglect 
> the problem of
> empty partitions, the redistributed mesh leads to a very good load 
> balancing. Is there
> any meaningful way to debug the problem? Is there something link a 
> "verbose mode" in
> ParMetis that says me whats happen on the input data? Otherwise I have 
> to print all the
> input data to the screen and check it by hand. Although I have a quite 
> small example with
> 128 overall coarse mesh elements on 8 ranks, this is not big fun :)
>
> Thomas
>
> @Matthew: By mistake I've answered your mail directly to you and not 
> to the mailing list, therefore I sent it now here again
>
> Matthew Knepley wrote:
>> On Tue, Dec 21, 2010 at 5:49 AM, Thomas Witkowski 
>> <thomas.witkowski at tu-dresden.de 
>> <mailto:thomas.witkowski at tu-dresden.de>> wrote:
>>
>>     Hi,
>>
>>     I have a not directly PETSc related question, but I hope to get
>>     some answer from the community here. In my FEM code, I make use of
>>     ParMETIS to partition the mesh. I make direct use of this library
>>     and not of PETSc's ParMETIS integration. The initial partition is
>>     always fine, but I use the ParMETIS_V3_AdaptiveRepart function for
>>     repartition the mesh due to local mesh adaption. In most cases,
>>     the result is fine, but there are two points, where I have trouble
>>     with:
>>
>>     1) Sometimes ParMETIS generates empty partitions, i.e., a
>>     processor has zero mesh elements. This is something my code cannot
>>     handle. Is this a bug or a feature? If it is a feature, is there
>>     any possiblity to disable it?
>>
>>
>> ParMetis has a balance constraint if you weight vertices. This will 
>> enforce equal size partitions.
>>  
>>
>>     2) In most cases the specific partitions are not connected. If I
>>     put all data to ParMETIS in a correct way, is this okay? My code
>>     can handle it, but is slows down the computation due to larger
>>     interior boundaries and therefore to more communications.
>>
>>
>> ParMetis minimizes the overall boundary size, so I do not understand 
>> how you could see this slowdown.
>>
>>    Matt
>>  
>>
>>     Does anyone of you know an answer to these question? Is there a
>>     debug mode in ParMETIS, where I can see which data is set to its
>>     function calls?
>>
>>     Regards,
>>
>>     Thomas
>>
>>
>>
>>
>> -- 
>> 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
>
>
>