[petsc-users] using petsc tools to solve isolated irregular domains with finite difference

Matthew Knepley knepley at gmail.com
Sun Oct 27 08:53:22 CDT 2013 

On Sat, Oct 26, 2013 at 8:27 AM, Bishesh Khanal <bisheshkh at gmail.com> wrote:

>
>
>
> On Sat, Oct 26, 2013 at 2:57 PM, Matthew Knepley <knepley at gmail.com>wrote:
>
>> On Sat, Oct 26, 2013 at 3:12 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>
>>>
>>>
>>>
>>> On Fri, Oct 25, 2013 at 10:21 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>
>>>> On Fri, Oct 25, 2013 at 2:55 PM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>>
>>>>> On Fri, Oct 25, 2013 at 8:18 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>
>>>>>> On Fri, Oct 25, 2013 at 12:09 PM, Bishesh Khanal <bisheshkh at gmail.com
>>>>>> > wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>> I would like to know if some of the petsc objects that I have not
>>>>>>> used so far (IS, DMPlex, PetscSection) could be useful in the following
>>>>>>> case (of irregular domains):
>>>>>>>
>>>>>>> Let's say that I have a 3D binary image (a cube).
>>>>>>> The binary information of the image partitions the cube into a
>>>>>>> computational domain and non-computational domain.
>>>>>>> I must solve a pde (say a Poisson equation) only on the
>>>>>>> computational domains (e.g: two isolated spheres within the cube). I'm
>>>>>>> using finite difference and say a dirichlet boundary condition
>>>>>>>
>>>>>>> I know that I can create a dmda that will let me access the
>>>>>>> information from this 3D binary image, get all the coefficients, rhs values
>>>>>>> etc using the natural indexing (i,j,k).
>>>>>>>
>>>>>>> Now, I would like to create a matrix corresponding to the laplace
>>>>>>> operator (e.g. with standard 7 pt. stencil), and the corresponding RHS that
>>>>>>> takes care of the dirchlet values too.
>>>>>>> But in this matrix it should have the rows corresponding to the
>>>>>>> nodes only on the computational domain. It would be nice if I can easily
>>>>>>> (using (i,j,k) indexing) put on the rhs dirichlet values corresponding to
>>>>>>> the boundary points.
>>>>>>> Then, once the system is solved, put the values of the solution back
>>>>>>> to the corresponding positions in the binary image.
>>>>>>> Later, I might have to extend this for the staggered grid case too.
>>>>>>> So is petscsection or dmplex suitable for this so that I can set up
>>>>>>> the matrix with something like DMCreateMatrix ? Or what would you suggest
>>>>>>> as a suitable approach to this problem ?
>>>>>>>
>>>>>>> I have looked at the manual and that led me to search for a simpler
>>>>>>> examples in petsc src directories. But most of the ones I encountered are
>>>>>>> with FEM (and I'm not familiar at all with FEM, so these examples serve
>>>>>>> more as a distraction with FEM jargon!)
>>>>>>>
>>>>>>
>>>>>> It sounds like the right solution for this is to use PetscSection on
>>>>>> top of DMDA. I am working on this, but it is really
>>>>>> alpha code. If you feel comfortable with that level of development,
>>>>>> we can help you.
>>>>>>
>>>>>
>>>>> Thanks, with the (short) experience of using Petsc so far and being
>>>>> familiar with the awesomeness (quick and helpful replies) of this mailing
>>>>> list, I would like to give it a try. Please give me some pointers to get
>>>>> going for the example case I mentioned above. A simple example of using
>>>>> PetscSection along with DMDA for finite volume (No FEM) would be great I
>>>>> think.
>>>>> Just a note: I'm currently using the petsc3.4.3 and have not used the
>>>>> development version before.
>>>>>
>>>>
>>>> Okay,
>>>>
>>>> 1)  clone the repository using Git and build the 'next' branch.
>>>>
>>>
>>> I encountered errors when doing make on the 'next' branch. The errors
>>> are as follows (I tried attached the configure.log file but the email
>>> bounced back saying it awaits moderator approval for having too big an
>>> attachment, so I'm sending this one with only make.log attached. ) :
>>>
>>
>> They are fixed. Pull again and rebuild.
>>
>
> doing git pull in the next branch says "Already up-to-date.", I'm not sure
> if it should have said that then. Still tried ./configure and make again
> but returns the same error. Does it take sometime to get updated in the
> servers or do I need to do anything special again other than the following
> ? :
> git checkout next
> git pull
>

Okay, it should be this

git checkout next
git pull
make allfortranstubs
make

  Thanks,

     Matt


>
>>   Matt
>>
>>
>>>           CXX arch-linux2-cxx-debug/obj/src/
>>> mat/order/ftn-auto/spectralf.o
>>>          CXX
>>> arch-linux2-cxx-debug/obj/src/mat/order/ftn-custom/zsorderf.o
>>> src/mat/order/wbm.c: In function ‘PetscErrorCode MatGetOrdering_WBM(Mat,
>>> MatOrderingType, _p_IS**, _p_IS**)’:
>>> src/mat/order/wbm.c:12:24: warning: variable ‘cntl’ set but not used
>>> [-Wunused-but-set-variable]
>>> src/mat/order/wbm.c:15:36: warning: unused variable ‘num’
>>> [-Wunused-variable]
>>> src/mat/order/wbm.c:15:56: warning: variable ‘icntl’ set but not used
>>> [-Wunused-but-set-variable]
>>> src/mat/order/wbm.c:15:66: warning: unused variable ‘info’
>>> [-Wunused-variable]
>>>          CXX arch-linux2-cxx-debug/obj/src/mat/matfd/fdmatrix.o
>>> src/mat/order/ftn-auto/spectralf.c: In function ‘void
>>> matcreatelaplacian_(Mat, PetscReal*, PetscBool*, _p_Mat**, int*)’:
>>> src/mat/order/ftn-auto/spectralf.c:44:40: error: ‘MatCreateLaplacian’
>>> was not declared in this scope
>>> gmake[2]: ***
>>> [arch-linux2-cxx-debug/obj/src/mat/order/ftn-auto/spectralf.o] Error 1
>>> gmake[2]: *** Waiting for unfinished jobs....
>>> src/mat/order/hslmc64.c: In function ‘PetscErrorCode HSLmc64AD(const
>>> PetscInt*, PetscInt*, PetscInt*, PetscInt*, const PetscInt*, const
>>> PetscInt*, PetscScalar*, PetscInt*, PetscInt*, PetscInt*, PetscInt*,
>>> PetscInt*, PetscScalar*, PetscInt*, PetscScalar*, PetscInt*)’:
>>> src/mat/order/hslmc64.c:332:21: warning: variable ‘warn1’ set but not
>>> used [-Wunused-but-set-variable]
>>> src/mat/order/hslmc64.c:332:28: warning: variable ‘warn2’ set but not
>>> used [-Wunused-but-set-variable]
>>> src/mat/order/hslmc64.c:332:35: warning: variable ‘warn4’ set but not
>>> used [-Wunused-but-set-variable]
>>> gmake[2]: Leaving directory `/home/bkhanal/Documents/softwares/petsc'
>>> gmake[1]: *** [gnumake] Error 2
>>> gmake[1]: Leaving directory `/home/bkhanal/Documents/softwares/petsc'
>>> **************************ERROR*************************************
>>>   Error during compile, check arch-linux2-cxx-debug/conf/make.log
>>>   Send it and arch-linux2-cxx-debug/conf/configure.log to
>>> petsc-maint at mcs.anl.gov
>>> ********************************************************************
>>> make: *** [all] Error 1
>>>
>>>
>>>
>>>>
>>>> 2) then we will need to create a PetscSection that puts unknowns where
>>>> you want them
>>>>
>>>> 3) Setup the solver as usual
>>>>
>>>> You can do 1) an 3) before we do 2).
>>>>
>>>>
>>>>  If not, just put the identity into
>>>>>> the rows you do not use on the full cube. It will not hurt
>>>>>> scalability or convergence.
>>>>>>
>>>>>
>>>>> In the case of Poisson with Dirichlet condition this might be the
>>>>> case. But is it always true that having identity rows in the system matrix
>>>>> will not hurt convergence ? I thought otherwise for the following reasons:
>>>>> 1)  Having read Jed's answer here :
>>>>> http://scicomp.stackexchange.com/questions/3426/why-is-pinning-a-point-to-remove-a-null-space-bad/3427#3427
>>>>>
>>>>
>>>> Jed is talking about a constraint on a the pressure at a point. This is
>>>> just decoupling these unknowns from the rest
>>>> of the problem.
>>>>
>>>>
>>>>> 2) Some observation I am getting (but I am still doing more
>>>>> experiments to confirm) while solving my staggered-grid 3D stokes flow with
>>>>> schur complement and using -pc_type gamg for A00 matrix. Putting the
>>>>> identity rows for dirichlet boundaries and for ghost cells seemed to have
>>>>> effects on its convergence. I'm hoping once I know how to use PetscSection,
>>>>> I can get rid of using ghost cells method for the staggered grid and get
>>>>> rid of the identity rows too.
>>>>>
>>>>
>>>> It can change the exact iteration, but it does not make the matrix
>>>> conditioning worse.
>>>>
>>>>    Matt
>>>>
>>>>
>>>>>  Anyway please provide me with some pointers so that I can start
>>>>> trying with petscsection on top of a dmda, in the beginning for
>>>>> non-staggered case.
>>>>>
>>>>> Thanks,
>>>>> Bishesh
>>>>>
>>>>>>
>>>>>>   Matt
>>>>>>
>>>>>>
>>>>>>> Thanks,
>>>>>>> Bishesh
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> 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
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