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

Bishesh Khanal bisheshkh at gmail.com
Sun Oct 27 10:04:44 CDT 2013 

On Sun, Oct 27, 2013 at 2:53 PM, Matthew Knepley <knepley at gmail.com> wrote:

> 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, but now it reports another error:

         CXX arch-linux2-cxx-debug/obj/src/dm/impls/redundant/dmredundant.o
         CXX
arch-linux2-cxx-debug/obj/src/dm/impls/redundant/ftn-auto/dmredundantf.o
         CXX arch-linux2-cxx-debug/obj/src/dm/impls/plex/plexcreate.o
src/dm/impls/da/hypre/mhyp.c: In function ‘PetscErrorCode
MatSetupDM_HYPREStruct(Mat, DM)’:
src/dm/impls/da/hypre/mhyp.c:485:58: error: invalid conversion from
‘PetscInt** {aka int**}’ to ‘const PetscInt** {aka const int**}’
[-fpermissive]
/home/bkhanal/Documents/softwares/petsc/include/petscdmda.h:68:27: error:
initializing argument 3 of ‘PetscErrorCode DMDAGetGlobalIndices(DM,
PetscInt*, const PetscInt**)’ [-fpermissive]
src/dm/impls/da/hypre/mhyp.c: In function ‘PetscErrorCode
MatSetupDM_HYPRESStruct(Mat, DM)’:
src/dm/impls/da/hypre/mhyp.c:963:58: error: invalid conversion from
‘PetscInt** {aka int**}’ to ‘const PetscInt** {aka const int**}’
[-fpermissive]
/home/bkhanal/Documents/softwares/petsc/include/petscdmda.h:68:27: error:
initializing argument 3 of ‘PetscErrorCode DMDAGetGlobalIndices(DM,
PetscInt*, const PetscInt**)’ [-fpermissive]
gmake[2]: *** [arch-linux2-cxx-debug/obj/src/dm/impls/da/hypre/mhyp.o]
Error 1
gmake[2]: *** Waiting for unfinished jobs....
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


>
>   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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