On Sat, Oct 26, 2013 at 2:57 PM, Matthew Knepley <[email protected]> wrote:
> On Sat, Oct 26, 2013 at 3:12 AM, Bishesh Khanal <[email protected]>wrote: > >> >> >> >> On Fri, Oct 25, 2013 at 10:21 PM, Matthew Knepley <[email protected]>wrote: >> >>> On Fri, Oct 25, 2013 at 2:55 PM, Bishesh Khanal <[email protected]>wrote: >>> >>>> On Fri, Oct 25, 2013 at 8:18 PM, Matthew Knepley <[email protected]>wrote: >>>> >>>>> On Fri, Oct 25, 2013 at 12:09 PM, Bishesh Khanal >>>>> <[email protected]>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 > 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 >> [email protected] >> ******************************************************************** >> 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 >
