[petsc-users] Field split questions

Matthew Knepley knepley at gmail.com
Mon Aug 20 07:19:37 CDT 2012 

On Mon, Aug 20, 2012 at 7:17 AM, Colin McAuliffe <cjm2176 at columbia.edu>wrote:

> 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
>>
>
> It would be really great to define the initial data layout using IS to
> define the equation numbers of the splits, while letting the new DM stuff
> handle creating all the nested splits given command line options. Is
> something like this possible?
>

This is just what I say above. Is something not working?

   Matt


> Colin
>
> Quoting Matthew Knepley <knepley at gmail.com>:
>
>  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/>
>>>>>>>>> >
>>>>>>>>> >
>>>>>>>>> <http://www.ce.**berkeley.edu/****projects/feap/<http://berkeley.edu/**projects/feap/>
>>>>>>>>> <http://**berkeley.edu/projects/feap/<http://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://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<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
>>
>>
>
>
> --
> 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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