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

Sat Oct 26 07:57:44 CDT 2013

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.

  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
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