libmesh-users

[Libmesh-users] repartitioning

[Griffith, B. E. <bo...@em...>]

Folks --

I want to play around with an application-specific mesh partitioning that will change during the course of a time-dependent simulation.  (Basically, I want to experiment with using the partitioning of a different parallel data structure to drive the mesh partitioning.)

I think that the main thing that I need to do is to implement _do_partition().  (I will also implement _do_repartition() once the basic _do_partition() is working.)  I was wondering what else needs to be done so that distributed System data are redistributed.  Does this happen automatically when calling Partitioner::repartition(), or is there more to it than that?

Thanks!

-- Boyce

Re: [Libmesh-users] repartitioning

[John P. <jwp...@gm...>]

On Mon, Jun 11, 2018 at 10:16 AM, Griffith, Boyce Eugene <
bo...@em...> wrote:

> Folks --
>
> I want to play around with an application-specific mesh partitioning that
> will change during the course of a time-dependent simulation.  (Basically,
> I want to experiment with using the partitioning of a different parallel
> data structure to drive the mesh partitioning.)
>
> I think that the main thing that I need to do is to implement
> _do_partition().  (I will also implement _do_repartition() once the basic
> _do_partition() is working.)  I was wondering what else needs to be done so
> that distributed System data are redistributed.  Does this happen
> automatically when calling Partitioner::repartition(), or is there more to
> it than that?
>

I think the System data should be handled by System::reinit() which is be
called by EquationSystems::reinit().

-- 
John

Re: [Libmesh-users] repartitioning

[Griffith, B. E. <bo...@em...>]

On Jun 11, 2018, at 9:23 PM, John Peterson <jwp...@gm...<mailto:jwp...@gm...>> wrote:



On Mon, Jun 11, 2018 at 10:16 AM, Griffith, Boyce Eugene <bo...@em...<mailto:bo...@em...>> wrote:
Folks --

I want to play around with an application-specific mesh partitioning that will change during the course of a time-dependent simulation.  (Basically, I want to experiment with using the partitioning of a different parallel data structure to drive the mesh partitioning.)

I think that the main thing that I need to do is to implement _do_partition().  (I will also implement _do_repartition() once the basic _do_partition() is working.)  I was wondering what else needs to be done so that distributed System data are redistributed.  Does this happen automatically when calling Partitioner::repartition(), or is there more to it than that?

I think the System data should be handled by System::reinit() which is be called by EquationSystems::reinit().

OK, so something like:

partiontiner->repartition();
equation_systems->reinit();

and then continue?


--
John

Re: [Libmesh-users] repartitioning

[Roy S. <roy...@ic...>]

On Tue, 12 Jun 2018, Griffith, Boyce Eugene wrote:

> OK, so something like:
>
> partiontiner->repartition();
> equation_systems->reinit();
>
> and then continue?

Did this work for you?

The code above is what I'd have written as v0.1 too, but I added a
quick unit test to make sure and (at least with DistributedMesh) no
luck.  I'll see what I can figure out; surely you can do this without
a whole prepare_for_use()...
---
Roy

Re: [Libmesh-users] repartitioning

[Griffith, B. E. <bo...@em...>]

> On Jun 19, 2018, at 11:58 PM, Roy Stogner <roy...@ic...> wrote:
> 
> 
> On Tue, 12 Jun 2018, Griffith, Boyce Eugene wrote:
> 
>> OK, so something like:
>> 
>> partiontiner->repartition();
>> equation_systems->reinit();
>> 
>> and then continue?
> 
> Did this work for you?
> 
> The code above is what I'd have written as v0.1 too, but I added a
> quick unit test to make sure and (at least with DistributedMesh) no
> luck.  I'll see what I can figure out; surely you can do this without
> a whole prepare_for_use()…

I haven’t gotten a chance to implement the new partitioner yet. We will be using ReplicatedMesh for the foreseeable future.

— Boyce

Re: [Libmesh-users] repartitioning

[Griffith, B. E. <bo...@em...>]

> On Jun 20, 2018, at 9:48 AM, Griffith, Boyce Eugene <bo...@em...> wrote:
> 
> 
> 
>> On Jun 19, 2018, at 11:58 PM, Roy Stogner <roy...@ic...> wrote:
>> 
>> 
>> On Tue, 12 Jun 2018, Griffith, Boyce Eugene wrote:
>> 
>>> OK, so something like:
>>> 
>>> partiontiner->repartition();
>>> equation_systems->reinit();
>>> 
>>> and then continue?
>> 
>> Did this work for you?
>> 
>> The code above is what I'd have written as v0.1 too, but I added a
>> quick unit test to make sure and (at least with DistributedMesh) no
>> luck.  I'll see what I can figure out; surely you can do this without
>> a whole prepare_for_use()…
> 
> I haven’t gotten a chance to implement the new partitioner yet. We will be using ReplicatedMesh for the foreseeable future.

Did you get a chance to figure out the correct sequence of calls to make something like this work? I am happy to run some tests with your unit test if it would be helpful.

Thanks!

-- Boyce

Re: [Libmesh-users] repartitioning

[Roy S. <roy...@ic...>]

On Fri, 29 Jun 2018, Griffith, Boyce Eugene wrote:

> On Jun 20, 2018, at 9:48 AM, Griffith, Boyce Eugene <bo...@em...> wrote:
>
>> On Jun 19, 2018, at 11:58 PM, Roy Stogner <roy...@ic...> wrote:
>>
>>> On Tue, 12 Jun 2018, Griffith, Boyce Eugene wrote:
>>>
>>>> OK, so something like:
>>>>
>>>> partiontiner->repartition();
>>>> equation_systems->reinit();
>>>>
>>>> and then continue?
>>>
>>> Did this work for you?
>>>
>>> The code above is what I'd have written as v0.1 too, but I added a
>>> quick unit test to make sure and (at least with DistributedMesh) no
>>> luck.  I'll see what I can figure out; surely you can do this without
>>> a whole prepare_for_use()…
>>
>> I haven’t gotten a chance to implement the new partitioner yet. We will be using ReplicatedMesh for the foreseeable future.
>
> Did you get a chance to figure out the correct sequence of calls to
> make something like this work? I am happy to run some tests with
> your unit test if it would be helpful.

It looks like my unit test inadvertently triggered a *different*
failure, simply because my set up (moving a mesh back on to processor
0 even if it was already distributed) was a corner case we'd never
supported.

https://github.com/libMesh/libmesh/pull/1773 should fix that corner
case and add the unit test, and in theory your above code should
already have worked fine on more realistic cases.
---
Roy