[petsc-users] Creating a DMNetwork from a DMPlex

Mon May 20 22:34:12 CDT 2019

Hi Matt,

I am trying to code my interpolation in parallel using
DMInterpolationEvaluate. Do you have an example which I could refer to?

Thanks,
Swarnava

On Mon, May 20, 2019 at 2:00 PM Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, May 20, 2019 at 12:51 PM Swarnava Ghosh <swarnava89 at gmail.com>
> wrote:
>
>> Hi Barry and Matt,
>>
>> Maybe try building by hand in a DMNetwork using a handrawn mesh with just
>> a few vertices and endless and see if what you want to do makes sense
>> > Okay, will try to do that. Do you have any DMNetwork example which I
>> could follow.
>>
>> I think DMNetwork is not buying you anything here. It seems to make more
>> sense to do it directly in Plex.
>> You can easily lay down a P1 element for each field so that you can
>> interpolate wherever you want.
>> > Okay, then will it be possible to do vertex partitioning with plex?
>> Essentially two processes can share an element but not vertex.
>>
>
> We can worry about that when everything works. Some things are easy but
> that breaks a lot of the model, so it
> unclear what all would have to change in order to do what you want. The
> partitioning of vertices, however, is trivial.
>
>
>> I would start from a clean example, such as SNES ex17. That solves
>> elasticity, so it has multiple fields and FEM.
>> The change is that you don't want to use any of the assembly functions,
>> so you keep the code that does data layout
>> and FEM discretization, but it ignore the residual/Jacobian stuff. Feel
>> free to ask about using the lower-level
>> interpolation stuff which is not as documented.
>> >Thanks for pointing out the reference. Could you please share the
>> functions for interpolation?
>>
>
> There are at least two ways to do it:
>
>   1) Locally: DMPlexEvaluateFieldJets_Internal() or DMFieldEvaluate()
> which is newer
>
>   2) Globally:
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/DMInterpolationEvaluate.html
>
>   Thanks,
>
>     Matt
>
>
>> Sincerely,
>> SG
>>
>>
>> On Mon, May 20, 2019 at 4:02 AM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Mon, May 20, 2019 at 3:05 AM Swarnava Ghosh via petsc-users <
>>> petsc-users at mcs.anl.gov> wrote:
>>>
>>>> Hi Barry,
>>>>
>>>> Thank you for your email. My planned discretization is based on the
>>>> fact that I need a distributed unstructured mesh, where at each vertex
>>>> point I perform local calculations. For these calculations, I do NOT need
>>>> need to assemble any global matrix. I will have fields defined at the
>>>> vertices, and using linear interpolation, I am planing to find the values
>>>> of these fields at some spatial points with are within a ball around each
>>>> vertex. Once the values of these fields are known within the compact
>>>> support around each vertex, I do local computations to calculate my unknown
>>>> field. My reason for having the a mesh is essentially to 1) define fields
>>>> at the vertices and 2) perform linear interpolation (using finite elements)
>>>> at some spatial points. Also the local computations around at each vertex
>>>> is computationally the most expensive step. In that case, having a cell
>>>> partitioning will result in vertices being shared among processes, which
>>>> will result in redundant computations.
>>>>
>>>> My idea is therefore to have DMNetwork to distribute vertices across
>>>> processes and use finite elements for the linear interpolation part.
>>>>
>>>
>>> I think DMNetwork is not buying you anything here. It seems to make more
>>> sense to do it directly in Plex.
>>> You can easily lay down a P1 element for each field so that you can
>>> interpolate wherever you want.
>>>
>>> I would start from a clean example, such as SNES ex17. That solves
>>> elasticity, so it has multiple fields and FEM.
>>> The change is that you don't want to use any of the assembly functions,
>>> so you keep the code that does data layout
>>> and FEM discretization, but it ignore the residual/Jacobian stuff. Feel
>>> free to ask about using the lower-level
>>> interpolation stuff which is not as documented.
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>> Thanks,
>>>> SG
>>>>
>>>>
>>>>
>>>> On Sun, May 19, 2019 at 6:54 PM Smith, Barry F. <bsmith at mcs.anl.gov>
>>>> wrote:
>>>>
>>>>>
>>>>>   I am not sure you want DMNetwork, DMNetwork has no geometry; it only
>>>>> has vertices and edges. Vertices are connected to other vertices through
>>>>> the edges. For example I can't see how one would do vertex centered finite
>>>>> volume methods with DMNetwork. Maybe if you said something more about your
>>>>> planned discretization we could figure something out.
>>>>>
>>>>> > On May 19, 2019, at 8:32 PM, Swarnava Ghosh <swarnava89 at gmail.com>
>>>>> wrote:
>>>>> >
>>>>> > Hi Barry,
>>>>> >
>>>>> > No, the gmesh file contains a mesh and not a graph/network.
>>>>> > In that case, is it possible to create a DMNetwork first from the
>>>>> DMPlex and then distribute the DMNetwork.
>>>>> >
>>>>> > I have this case, because I want a vertex partitioning of my mesh.
>>>>> Domain decomposition of DMPlex gives me cell partitioning. Essentially what
>>>>> I want is that no two processes can share a vertex BUT that can share an
>>>>> edge. Similar to how a DMDA is distributed.
>>>>> >
>>>>> > Thanks,
>>>>> > Swarnava
>>>>> >
>>>>> > On Sun, May 19, 2019 at 4:50 PM Smith, Barry F. <bsmith at mcs.anl.gov>
>>>>> wrote:
>>>>> >
>>>>> >    This use case never occurred to us. Is the gmesh file containing
>>>>> a graph/network (as opposed to a mesh)? There seem two choices
>>>>> >
>>>>> > 1) if the gmesh file contains a graph/network one could write a
>>>>> gmesh reader for that case that reads directly for and constructs a
>>>>> DMNetwork or
>>>>> >
>>>>> > 2) write a converter for a DMPlex to DMNetwork.
>>>>> >
>>>>> >    I lean toward the first
>>>>> >
>>>>> >    Either way you need to understand the documentation for DMNetwork
>>>>> and how to build one up.
>>>>> >
>>>>> >
>>>>> >    Barry
>>>>> >
>>>>> >
>>>>> > > On May 19, 2019, at 6:34 PM, Swarnava Ghosh via petsc-users <
>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>> > >
>>>>> > > Hi Petsc users and developers,
>>>>> > >
>>>>> > > I am trying to find a way of creating a DMNetwork from a DMPlex. I
>>>>> have read the DMPlex from a gmesh file and have it distributed.
>>>>> > >
>>>>> > > Thanks,
>>>>> > > SG
>>>>> >
>>>>>
>>>>>
>>>
>>> --
>>> 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
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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