On Sun, Oct 27, 2013 at 2:53 PM, Matthew Knepley <[email protected]> wrote:
> On Sat, Oct 26, 2013 at 8:27 AM, Bishesh Khanal <[email protected]>wrote: > >> >> >> >> 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 >> > > 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 [email protected] ******************************************************************** 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 >>>> [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 >>> >> >> > > > -- > 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 >
