[petsc-users] DMNetworkGetEdgeRange() in parallel

Matthew Knepley knepley at gmail.com
Mon Feb 23 14:05:49 CST 2015 

On Mon, Feb 23, 2015 at 1:40 PM, Miguel Angel Salazar de Troya <
salazardetroya at gmail.com> wrote:

> Wouldn't including the edge variables in the global vector make the code
> slower? I'm using the global vector in a TS, using one of the explicit RK
> schemes. The edge variables would not be updated in the RHSFunction
> evaluation. I only change the edge variables in the TSUpdate. If the global
> vector had the edge variables, it would be a much larger vector, and all
> the vector operations performed by the TS would be slower. Although the
> vector F returned by the RHSFunction would be zero in the edge variable
> components. I guess that being the vector sparse that would not be a
> problem.
>
> I think I'm more interested in the PetscSection approach because it might
> require less modifications in my code. However, I don't know how I could do
> this. Maybe something like this?
>
> PetscSectionCreate(PETSC_COMM_WORLD, &s);
> PetscSectionSetNumFields(s, 1);
> PetscSectionSetFieldComponents(s, 0, 1);
>
> // Now to set the chart, I pick the edge range
>
> DMNetworkGetEdgeRange(dm, & eStart, & eEnd
>
> PetscSectionSetChart(s, eStart, eEnd);
>
> for(PetscInt e = eStart; c < eEnd; ++e) {
>      PetscSectionSetDof(s, e, 1);
>      PetscSectionSetFieldDof(s, e, 1, 1);
>

It should be PetscSectionSetFieldDof(s, e, 0, 1);


> }
> PetscSectionSetUp(s);
>
> Now in the manual I see this:
>

First you want to do:

  DMClone(dm, &dmEdge);

and then use dmEdge below.


> DMSetDefaultSection(dm, s);
> DMGetLocalVector(dm, &localVec);
> DMGetGlobalVector(dm, &globalVec);
>
> Setting up the default section in the DM would interfere with the section
> already set up with the variables in the vertices?
>

Yep, thats why you would use a clone.

  Thanks,

     Matt


> Thanks a lot for your responses.
>
>
>
> On Mon, Feb 23, 2015 at 11:37 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Mon, Feb 23, 2015 at 9:27 AM, Miguel Angel Salazar de Troya <
>> salazardetroya at gmail.com> wrote:
>>
>>> I'm iterating through local edges given in DMNetworkGetEdgeRange(). For
>>> each edge, I extract or modify its corresponding value in a global petsc
>>> vector. Therefore that vector must have as many components as edges there
>>> are in the network. To extract the value in the vector, I use VecGetArray()
>>> and a variable counter that is incremented in each iteration. The array
>>> that I obtain in VecGetArray() has to be the same size than the edge
>>> range. That variable counter starts as 0, so if the array that I obtained
>>> in VecGetArray() is x_array, x_array[0] must be the component in the
>>> global vector that corresponds with the start edge given in
>>> DMNetworkGetEdgeRange()
>>>
>>> I need that global petsc vector because I will use it in other
>>> operations, it's not just data. Sorry for the confusion. Thanks in advance.
>>>
>>
>> This sounds like an assembly operation. The usual paradigm is to compute
>> in the local space, and then communicate to get to the global space. So you
>> would make a PetscSection that had 1 (or some) unknowns on each cell (edge)
>> and then you can use DMCreateGlobal/LocalVector() and DMLocalToGlobal() to
>> do this.
>>
>> Does that make sense?
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Miguel
>>>
>>>
>>> On Mon, Feb 23, 2015 at 9:09 AM, Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Mon, Feb 23, 2015 at 8:42 AM, Miguel Angel Salazar de Troya <
>>>> salazardetroya at gmail.com> wrote:
>>>>
>>>>> Thanks, that will help me. Now what I would like to have is the
>>>>> following: if I have two processors and ten edges, the partitioning results
>>>>> in the first processor having the edges 0-4 and the second processor, the
>>>>> edges 5-9. I also have a global vector with as many components as edges,
>>>>> 10. How can I partition it so the first processor also has the 0-4
>>>>> components and the second, the 5-9 components of the vector?
>>>>>
>>>> I think it would help to know what you want to accomplish. This is how
>>>> you are proposing to do it.'
>>>>
>>>> If you just want to put data on edges, DMNetwork has a facility for
>>>> that already.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> Miguel
>>>>> On Feb 23, 2015 8:08 AM, "Abhyankar, Shrirang G." <abhyshr at mcs.anl.gov>
>>>>> wrote:
>>>>>
>>>>>>  Miguel,
>>>>>>    One possible way is to store the global numbering of any
>>>>>> edge/vertex in the "component" attached to it. Once the mesh gets
>>>>>> partitioned, the components are also distributed so you can easily retrieve
>>>>>> the global number of any edge/vertex by accessing its component. This is
>>>>>> what is done in the DMNetwork example pf.c although the global numbering is
>>>>>> not used for anything.
>>>>>>
>>>>>>  Shri
>>>>>>  From: Matthew Knepley <knepley at gmail.com>
>>>>>> Date: Mon, 23 Feb 2015 07:54:34 -0600
>>>>>> To: Miguel Angel Salazar de Troya <salazardetroya at gmail.com>
>>>>>> Cc: "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
>>>>>> Subject: Re: [petsc-users] DMNetworkGetEdgeRange() in parallel
>>>>>>
>>>>>>   On Sun, Feb 22, 2015 at 3:59 PM, Miguel Angel Salazar de Troya <
>>>>>> salazardetroya at gmail.com> wrote:
>>>>>>
>>>>>>> Thanks. Once I obtain that Index Set with the routine DMPlexCreateCellNumbering()
>>>>>>> (I assume that the edges in DMNetwork correspond to cells in DMPlex) can I
>>>>>>> use it to partition a vector with as many components as edges I have in my
>>>>>>> network?
>>>>>>>
>>>>>>
>>>>>>  I do not completely understand the question.
>>>>>>
>>>>>>  If you want a partition of the edges, you can use
>>>>>> DMPlexCreatePartition() and its friend DMPlexDistribute(). What
>>>>>> are you trying to do?
>>>>>>
>>>>>>     Matt
>>>>>>
>>>>>>
>>>>>>>  Thanks
>>>>>>> Miguel
>>>>>>>
>>>>>>> On Sun, Feb 22, 2015 at 12:15 PM, Matthew Knepley <knepley at gmail.com
>>>>>>> > wrote:
>>>>>>>
>>>>>>>>  On Sun, Feb 22, 2015 at 11:01 AM, Miguel Angel Salazar de Troya <
>>>>>>>> salazardetroya at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi
>>>>>>>>>
>>>>>>>>>  I noticed that the routine DMNetworkGetEdgeRange() returns the
>>>>>>>>> local indices for the edge range. Is there any way to obtain the global
>>>>>>>>> indices? So if my network has 10 edges, the processor 1 has the 0-4 edges
>>>>>>>>> and the processor 2, the 5-9 edges, how can I obtain this information?
>>>>>>>>>
>>>>>>>>
>>>>>>>>  One of the points of DMPlex is we do not require a global
>>>>>>>> numbering. Everything is numbered
>>>>>>>> locally, and the PetscSF maps local numbers to local numbers in
>>>>>>>> order to determine ownership.
>>>>>>>>
>>>>>>>>  If you want to create a global numbering for some reason, you can
>>>>>>>> using DMPlexCreatePointNumbering().
>>>>>>>> There are also cell and vertex versions that we use for output, so
>>>>>>>> you could do it just for edges as well.
>>>>>>>>
>>>>>>>>    Thanks,
>>>>>>>>
>>>>>>>>       Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>>  Thanks
>>>>>>>>>  Miguel
>>>>>>>>>
>>>>>>>>>  --
>>>>>>>>>  *Miguel Angel Salazar de Troya*
>>>>>>>>> Graduate Research Assistant
>>>>>>>>> Department of Mechanical Science and Engineering
>>>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>>>> (217) 550-2360
>>>>>>>>> salaza11 at illinois.edu
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>  --
>>>>>>>> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>  --
>>>>>>>  *Miguel Angel Salazar de Troya*
>>>>>>> Graduate Research Assistant
>>>>>>> Department of Mechanical Science and Engineering
>>>>>>> University of Illinois at Urbana-Champaign
>>>>>>> (217) 550-2360
>>>>>>> salaza11 at illinois.edu
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>  --
>>>>>> 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
>>>>>>
>>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>>>
>>> --
>>> *Miguel Angel Salazar de Troya*
>>> Graduate Research Assistant
>>> Department of Mechanical Science and Engineering
>>> University of Illinois at Urbana-Champaign
>>> (217) 550-2360
>>> salaza11 at illinois.edu
>>>
>>>
>>
>>
>> --
>> 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
>>
>
>
>
> --
> *Miguel Angel Salazar de Troya*
> Graduate Research Assistant
> Department of Mechanical Science and Engineering
> University of Illinois at Urbana-Champaign
> (217) 550-2360
> salaza11 at illinois.edu
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20150223/3f94d49e/attachment-0001.html>

More information about the petsc-users mailing list