[petsc-users] Field split questions

Matthew Knepley knepley at gmail.com
Tue Aug 14 00:38:58 CDT 2012 

On Mon, Aug 13, 2012 at 4:06 PM, Colin McAuliffe <cjm2176 at columbia.edu>wrote:

> No, No, No. You do not have to write a DM implementation.
>>
>> You just have to define the data layout in a PetscSection and attach it to
>> the DM with DMSetDefaultSection.
>>
>>     Matt
>>
>
> Does use of the PetscSection mean that it is neccesary to define a DMMesh?
> In other
> words is there a way to create the data layout for the physics without
> having to specify
> any information about the mesh?
>

Yes, just call DMSetDefaultSection(). However, note that you will have
everything sized
correctly, but handling topology and iteration for the residual calculation
would be completely
up to you.

   Matt


> Thanks
> Colin
>
>
>
> Quoting Matthew Knepley <knepley at gmail.com>:
>
>  On Thu, Aug 9, 2012 at 10:22 AM, Dmitry Karpeev <karpeev at mcs.anl.gov>
>> wrote:
>>
>>
>>>
>>> On Thu, Aug 9, 2012 at 10:02 AM, Colin McAuliffe  <cjm2176 at columbia.edu
>>> >wrote:
>>>
>>>  Sanjay, thanks for the reply but I am avoiding using blocked format
>>>> since
>>>> my problem has 10 dofs per node but only has either dofs 1-3 or 4-10
>>>> active
>>>> on a particular node. If I use block the equations I run out of memory
>>>> pretty quickly on my machine but can get to reasonable sized problems
>>>> with
>>>> the unblocked format.
>>>>
>>>> Matt, sorry I am not getting this, but I am still not sure how the DM
>>>> interface works. I can see in the function PCFieldSplitSetDefaults that
>>>> there is an initial call to DMCreateFieldDecomposition and subsequent
>>>> calls
>>>> to DMCreateSubDM based on the command line options. What I am missing is
>>>> how the first call to DMCreateFieldDecomposition is able to figure out
>>>> which equations belong to which field just from command line info such
>>>> as
>>>> -pc_fieldsplit_0_fields 2,0. Where/how are the fields 2 and 0 defined?
>>>>
>>>>  This might change slightly in the near future in petsc-dev to allow
>>> one to
>>> define splits using named fields.
>>> In any event, there has to be DM support to implement the decompositions
>>> over a particular mesh/problem over that mesh.
>>> With DMDA you can essentially get combinations of strided fields in each
>>> split. DMCOMPOSITE allows you
>>> to pull out combinations of the subproblems that were put in there to
>>> begin with. If you have your own mesh, you have to write
>>> a DM implementation around it to expose the available fields.
>>>
>>>
>> No, No, No. You do not have to write a DM implementation.
>>
>> You just have to define the data layout in a PetscSection and attach it to
>> the DM with DMSetDefaultSection.
>>
>>     Matt
>>
>>
>>  Dmitry.
>>>
>>>
>>>> Thanks
>>>>
>>>> Colin
>>>>
>>>>
>>>> Quoting Matthew Knepley <knepley at gmail.com>:
>>>>
>>>>  On Thu, Aug 9, 2012 at 9:21 AM, Sanjay Govindjee <s_g at berkeley.edu>
>>>>
>>>>> wrote:
>>>>>
>>>>>  Colin,
>>>>>
>>>>>>   I you block the equations in FEAP, then the restrained BCs are
>>>>>> 'included' in assembled PETSc matrix (these dofs have rows that are
>>>>>> zero
>>>>>> modulo a value of unity on the diagonal and the restrained value on
>>>>>> the
>>>>>> right-hand side).
>>>>>>
>>>>>>
>>>>>>  However, this is not necessary with the DM interface.
>>>>>
>>>>>    Matt
>>>>>
>>>>>
>>>>>  -sg
>>>>>
>>>>>>
>>>>>> On 8/9/12 8:41 AM, Colin McAuliffe wrote:
>>>>>>
>>>>>>  From what I can gather from the petsc-dev source it looks like the
>>>>>>
>>>>>>> commands in 4) will then generate the splits using strided blocks.
>>>>>>> The
>>>>>>> problem with that is the fortran code I am using (FEAP) uses petsc to
>>>>>>> assemble and solve the linear problem within its own nonlinear and
>>>>>>> time
>>>>>>> stepping schemes. The linear problem that petsc solves already has
>>>>>>> boundary
>>>>>>> conditions applied to it so petsc only sees the active (unrestrained)
>>>>>>> equations. So then in general fields can't be extracted from the
>>>>>>> active
>>>>>>> equations using strided blocks and I am stuck with generating the
>>>>>>> index
>>>>>>> sets defining the splits on my own. Will it still be possible to make
>>>>>>> use
>>>>>>> of the new DM functions in this case?
>>>>>>>
>>>>>>> FEAP website:
>>>>>>> http://www.ce.berkeley.edu/******projects/feap/<http://www.ce.berkeley.edu/****projects/feap/>
>>>>>>> <http://www.ce.**berkeley.edu/**projects/feap/<http://www.ce.berkeley.edu/**projects/feap/>
>>>>>>> >
>>>>>>> <http://www.ce.**berkeley.edu/**projects/feap/<http://berkeley.edu/projects/feap/>
>>>>>>> <http://www.ce.**berkeley.edu/projects/feap/<http://www.ce.berkeley.edu/projects/feap/>
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>> Colin
>>>>>>>
>>>>>>>
>>>>>>> Quoting Matthew Knepley <knepley at gmail.com>:
>>>>>>>
>>>>>>>  On Wed, Aug 8, 2012 at 10:51 PM, Matthew Knepley <knepley at gmail.com
>>>>>>> >
>>>>>>>
>>>>>>>  wrote:
>>>>>>>>
>>>>>>>>  On Wed, Aug 8, 2012 at 10:23 PM, Colin McAuliffe  <
>>>>>>>> cjm2176 at columbia.edu
>>>>>>>>
>>>>>>>>  >wrote:
>>>>>>>>>
>>>>>>>>>  Thanks all, regarding use of DM in 3.3, is the procedure now to
>>>>>>>>> create
>>>>>>>>>
>>>>>>>>>  the fields with PCFieldSplitSetIS and then use
>>>>>>>>>> DMCreateFieldDecompositionDM
>>>>>>>>>> to create a new DM based from the new fields and the DM for the
>>>>>>>>>> original
>>>>>>>>>> problem?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>  1) Use petsc-dev
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2) PCFieldSplitSetIS() is independent. This allows you to define
>>>>>>>>> splits
>>>>>>>>> however you want, but then recursive gets harder
>>>>>>>>>
>>>>>>>>> 3) In 3.3., it uses DMCreateFieldDecompositionDM() to split all
>>>>>>>>> fields
>>>>>>>>> apart at once
>>>>>>>>>
>>>>>>>>> 4) In petsc-dev, it uses DMCreateSubDM() which can split off any
>>>>>>>>> combination of fields, which from the command line is something
>>>>>>>>> like
>>>>>>>>>
>>>>>>>>>      -pc_fieldsplit_0_fields 2,0 -pc_fieldsplit_1_fields 1,3
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>  I should have shown recursive:
>>>>>>>>>
>>>>>>>>
>>>>>>>>   -fieldsplit_0_pc_type fieldsplit
>>>>>>>>
>>>>>>>> will split 2,0 into two blocks.
>>>>>>>>
>>>>>>>>    Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>       Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>>  Colin
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Colin McAuliffe
>>>>>>>>>> PhD Candidate
>>>>>>>>>> Columbia University
>>>>>>>>>> Department of Civil Engineering and Engineering Mechanics
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>  --
>>>>>>>
>>>>>> ------------------------------******-----------------
>>>>>>
>>>>>> Sanjay Govindjee, PhD, PE
>>>>>> Professor of Civil Engineering
>>>>>> Vice Chair for Academic Affairs
>>>>>>
>>>>>> 779 Davis Hall
>>>>>> Structural Engineering, Mechanics and Materials
>>>>>> Department of Civil Engineering
>>>>>> University of California
>>>>>> Berkeley, CA 94720-1710
>>>>>>
>>>>>> Voice:  +1 510 642 6060
>>>>>> FAX:    +1 510 643 5264
>>>>>> s_g at berkeley.edu
>>>>>> http://www.ce.berkeley.edu/~******sanjay<http://www.ce.berkeley.edu/~****sanjay>
>>>>>> <http://www.ce.**berkeley.edu/~**sanjay<http://www.ce.berkeley.edu/~**sanjay>
>>>>>> ><
>>>>>> http://www.ce.berkeley.edu/~****sanjay<http://www.ce.berkeley.edu/~**sanjay>
>>>>>> <http://www.ce.berkeley.**edu/~sanjay<http://www.ce.berkeley.edu/~sanjay>
>>>>>> >
>>>>>> >
>>>>>> ------------------------------******-----------------
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Colin McAuliffe
>>>> PhD Candidate
>>>> Columbia University
>>>> Department of Civil Engineering and Engineering Mechanics
>>>>
>>>>
>>>
>>>
>>
>> --
>> 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
>>
>>
>
>
> --
> Colin McAuliffe
> PhD Candidate
> Columbia University
> Department of Civil Engineering and Engineering Mechanics
>



-- 
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
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