[MOAB-dev] Fwd: Interface: Partitioner

[Tim Tautges]

On 09/08/2013 10:55 AM, Alexander Nikolas Breuer wrote:
> Hey Timothy Tautges,
>
> I got your e-mail address from a colleague of mine. Maybe you are able to give me some hints on partitioning based on
> MOAB. My original e-mail is attached to this one.
>

Aha.  I'll cc moab-dev, feel free to email that list with these types of questions too.
> Best regards,
>
> Alexander Breuer
>

 > From: Alexander Nikolas Breuer <breuera at in.tum.de>
 > Subject: Interface: Partitioner
 > Date: September 2, 2013 8:30:09 PM GMT+02:00
 > To: moab at software.sandia.gov
 >
 > Hey MOAB-developers,
 >
 > first of all: Thank's for developing this nice piece of software.
 >
 > I started using MOAB in the pre-processing phase of a finite element-code to cluster time step widths. We plan to go 
above 10^9 elements soon, so this might be an interesting benchmark. I think I figured out how to use the basics of 
MOAB, like getting enities or using mesh sets. My next step is the partitioning:

Great, let us know if you encounter problems.

 >
 > I will have the mesh in MOAB including information for computational and communication costs in the FEM setting. Each 
of my tetrahedrons is part of a local time stepping cluster, which has a weight for computation - the lower the time 
step width, the higher the amount of computation in this element, because it has to be updated more often in the LTS 
scheme. Each face has a weight for communication: Two elements with large time step widths have to communicate much less 
than neighboured elements with low time step widths.
 >
 > To my question: I need to get that information into a partitioner like ParMetis without writing to disk in between. 
MOAB seems to have some functionality for that, i.e.: 
http://www.mcs.anl.gov/~fathom/moab-docs/html/mbpart_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97 Do you have some 
documentation on the interfaces? Or more examples?

Depends on what you're looking for.  mbpart is our tool to generate partitions, but it works for static partitioning; we 
don't really do dynamic partitioning at the moment.  mbpart can establish the graph, which it passes to Zoltan to do the 
actual partitioning.  Zoltan in theory can use metis to generate the partition, though I haven't had much luck with it 
that way (though maybe Zoltan2, which we haven't updated to, works better) (though now that I say that, it could just as 
easily be a bug in moab which we haven't found).

So, you could take the code from mbpart that generates the graph and passes to parmetis, and that would give you back a 
partition.  You'd just need to make sure to establish shared mesh between processors correctly before doing that (and 
possibly exchanging a row of ghost elements), to make sure that both processors sharing vertices would see the same 
connected elements.  The HelloParMOAB example 
(http://www.mcs.anl.gov/~fathom/moab-docs/html/HelloParMOAB_8cpp-example.html) shows how to request ghosting, after 
you've established shared entities.

- tim

 >
 > ***
 >
 > I hope this is right way to ask questions. If not: I would be happy, if you could point me to the right place.
 >
 > Thanks in advance and regards,
 >
 > Alex
 >
 > --
 > Dipl.-Math. Alexander Breuer
 > Technische Universität München
 > Department of Informatics
 > Chair of Scientific Computing
 > Boltzmannstrasse 3, 85748 Garching, Germany
 > Tel: +49 89 358 31 7811, Fax: +49 89 289 18 607
 > http://www5.in.tum.de
 >
 >
 >




-- 
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   steadfast, because he trusts in you."               Isaiah 26:3

              Tim Tautges            Argonne National Laboratory
          (tautges at mcs.anl.gov)      (telecommuting from UW-Madison)
  phone (gvoice): (608) 354-1459      1500 Engineering Dr.
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