On Tue, Aug 6, 2013 at 4:40 PM, Matthew Knepley <[email protected]> wrote:
> On Tue, Aug 6, 2013 at 8:06 AM, Bishesh Khanal <[email protected]>wrote: > >> >> >> >> On Mon, Aug 5, 2013 at 4:14 PM, Matthew Knepley <[email protected]>wrote: >> >>> On Mon, Aug 5, 2013 at 8:48 AM, Bishesh Khanal <[email protected]>wrote: >>> >>>> >>>> >>>> >>>> On Mon, Aug 5, 2013 at 3:17 PM, Matthew Knepley <[email protected]>wrote: >>>> >>>>> On Mon, Aug 5, 2013 at 7:54 AM, Bishesh Khanal <[email protected]>wrote: >>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Jul 17, 2013 at 9:48 PM, Jed Brown <[email protected]>wrote: >>>>>> >>>>>>> Bishesh Khanal <[email protected]> writes: >>>>>>> >>>>>>> > Now, I implemented two different approaches, each for both 2D and >>>>>>> 3D, in >>>>>>> > MATLAB. It works for the smaller sizes but I have problems solving >>>>>>> it for >>>>>>> > the problem size I need (250^3 grid size). >>>>>>> > I use staggered grid with p on cell centers, and components of v >>>>>>> on cell >>>>>>> > faces. Similar split up of K to cell center and faces to account >>>>>>> for the >>>>>>> > variable viscosity case) >>>>>>> >>>>>>> Okay, you're using a staggered-grid finite difference discretization >>>>>>> of >>>>>>> variable-viscosity Stokes. This is a common problem and I recommend >>>>>>> starting with PCFieldSplit with Schur complement reduction (make that >>>>>>> work first, then switch to block preconditioner). You can use PCLSC >>>>>>> or >>>>>>> (probably better for you), assemble a preconditioning matrix >>>>>>> containing >>>>>>> the inverse viscosity in the pressure-pressure block. This diagonal >>>>>>> matrix is a spectrally equivalent (or nearly so, depending on >>>>>>> discretization) approximation of the Schur complement. The velocity >>>>>>> block can be solved with algebraic multigrid. Read the PCFieldSplit >>>>>>> docs (follow papers as appropriate) and let us know if you get stuck. >>>>>>> >>>>>> >>>>>> I was trying to assemble the inverse viscosity diagonal matrix to use >>>>>> as the preconditioner for the Schur complement solve step as you >>>>>> suggested. >>>>>> I've few questions about the ways to implement this in Petsc: >>>>>> A naive approach that I can think of would be to create a vector with >>>>>> its components as reciprocal viscosities of the cell centers >>>>>> corresponding >>>>>> to the pressure variables, and then create a diagonal matrix from this >>>>>> vector. However I'm not sure about: >>>>>> How can I make this matrix, (say S_p) compatible to the Petsc >>>>>> distribution of the different rows of the main system matrix over >>>>>> different >>>>>> processors ? The main matrix was created using the DMDA structure with 4 >>>>>> dof as explained before. >>>>>> The main matrix correspond to the DMDA with 4 dofs but for the S_p >>>>>> matrix would correspond to only pressure space. Should the distribution >>>>>> of >>>>>> the rows of S_p among different processor not correspond to the >>>>>> distribution of the rhs vector, say h' if it is solving for p with Sp = >>>>>> h' >>>>>> where S = A11 inv(A00) A01 ? >>>>>> >>>>> >>>>> PETSc distributed vertices, not dofs, so it never breaks blocks. The P >>>>> distribution is the same as the entire problem divided by 4. >>>>> >>>> >>>> Thanks Matt. So if I create a new DMDA with same grid size but with >>>> dof=1 instead of 4, the vertices for this new DMDA will be identically >>>> distributed as for the original DMDA ? Or should I inform PETSc by calling >>>> a particular function to make these two DMDA have identical distribution of >>>> the vertices ? >>>> >>> >>> Yes. >>> >>> >>>> Even then I think there might be a problem due to the presence of >>>> "fictitious pressure vertices". The system matrix (A) contains an identity >>>> corresponding to these fictitious pressure nodes, thus when using a >>>> -pc_fieldsplit_detect_saddle_point, will detect a A11 zero block of size >>>> that correspond to only non-fictitious P-nodes. So the preconditioner S_p >>>> for the Schur complement outer solve with Sp = h' will also need to >>>> correspond to only the non-fictitious P-nodes. This means its size does not >>>> directly correspond to the DMDA grid defined for the original problem. >>>> Could you please suggest an efficient way of assembling this S_p matrix ? >>>> >>> >>> Don't use detect_saddle, but split it by fields -pc_fieldsplit_0_fields >>> 0,1,2 -pc_fieldsplit_1_fields 4 >>> >> >> How can I set this split in the code itself without giving it as a >> command line option when the system matrix is assembled from the DMDA for >> the whole system with 4 dofs. (i.e. *without* using the DMComposite or * >> without* using the nested block matrices to assemble different blocks >> separately and then combine them together). >> I need the split to get access to the fieldsplit_1_ksp in my code, >> because not using detect_saddle_point means I cannot use >> -fieldsplit_1_ksp_constant_null_space due to the presence of identity for >> the fictitious pressure nodes present in the fieldsplit_1_ block. I need to >> use PCFieldSplitGetSubKsp() so that I can set proper null-space basis. >> > > This is currently a real problem with the DMDA. In the unstructured case, > where we always need specialized spaces, you can > use something like > > PetscObject pressure; > MatNullSpace nullSpacePres; > > ierr = DMGetField(dm, 1, &pressure);CHKERRQ(ierr); > ierr = MatNullSpaceCreate(PetscObjectComm(pressure), PETSC_TRUE, 0, > NULL, &nullSpacePres);CHKERRQ(ierr); > ierr = PetscObjectCompose(pressure, "nullspace", (PetscObject) > nullSpacePres);CHKERRQ(ierr); > ierr = MatNullSpaceDestroy(&nullSpacePres);CHKERRQ(ierr); > > and then DMGetSubDM() uses this information to attach the null space to > the IS that is created using the information in the PetscSection. > If you use a PetscSection to set the data layout over the DMDA, I think > this works correctly, but this has not been tested at all and is very > new code. Eventually, I think we want all DMs to use this mechanism, but > we are still working it out. > Currently I do not use PetscSection. If this makes a cleaner approach, I'd try it too but may a bit later (right now I'd like test my model with a quickfix even if it means a little dirty code!) > > Bottom line: For custom null spaces using the default layout in DMDA, you > need to take apart the PCFIELDSPLIT after it has been setup, > which is somewhat subtle. You need to call KSPSetUp() and then reach in > and get the PC, and the subKSPs. I don't like this at all, but we > have not reorganized that code (which could be very simple and inflexible > since its very structured). > So I tried to get this approach working but I could not succeed and encountered some errors. Here is a code snippet: //mDa is the DMDA that describes the whole grid with all 4 dofs (3 velocity components and 1 pressure comp.) ierr = DMKSPSetComputeRHS(mDa,computeRHSTaras3D,this);CHKERRQ(ierr); ierr = DMKSPSetComputeOperators(mDa,computeMatrixTaras3D,this);CHKERRQ(ierr); ierr = KSPSetDM(mKsp,mDa);CHKERRQ(ierr); ierr = KSPSetNullSpace(mKsp,mNullSpaceSystem);CHKERRQ(ierr); //I've the mNullSpaceSystem based on mDa, that contains a null space basis for the complete system. ierr = KSPSetFromOptions(mKsp);CHKERRQ(ierr); //This I expect would register these options I give:-pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_0_fields 0,1,2 //-pc_fieldsplit_1_fields 3 ierr = KSPSetUp(mKsp);CHKERRQ(ierr); ierr = KSPGetPC(mKsp,&mPcOuter); //Now get the PC that was obtained from the options (fieldsplit) ierr = PCFieldSplitSchurPrecondition(mPcOuter,PC_FIELDSPLIT_SCHUR_PRE_USER,mPcForSc);CHKERRQ(ierr); //I have created the matrix mPcForSc using a DMDA with identical //size to mDa but with dof=1 corresponding to the pressure nodes (say mDaPressure). ierr = PCSetUp(mPcOuter);CHKERRQ(ierr); KSP *kspSchur; PetscInt kspSchurPos = 1; ierr = PCFieldSplitGetSubKSP(mPcOuter,&kspSchurPos,&kspSchur);CHKERRQ(ierr); ierr = KSPSetNullSpace(kspSchur[1],mNullSpacePressure);CHKERRQ(ierr); //The null space is the one that correspond to only pressure nodes, created using the mDaPressure. ierr = PetscFree(kspSchur);CHKERRQ(ierr); ierr = KSPSolve(mKsp,NULL,NULL);CHKERRQ(ierr); The errors I get when running with options: -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: No support for this operation for this object type! [0]PETSC ERROR: Support only implemented for 2d! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: src/AdLemMain on a arch-linux2-cxx-debug named edwards by bkhanal Tue Aug 6 17:35:30 2013 [0]PETSC ERROR: Libraries linked from /home/bkhanal/Documents/softwares/petsc-3.4.2/arch-linux2-cxx-debug/lib [0]PETSC ERROR: Configure run at Fri Jul 19 14:25:01 2013 [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=g77 --with-cxx=g++ --download-f-blas-lapack=1 --download-mpich=1 -with-clanguage=cxx --download-hypre=1 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: DMCreateSubDM_DA() line 188 in /home/bkhanal/Documents/softwares/petsc-3.4.2/src/dm/impls/da/dacreate.c [0]PETSC ERROR: DMCreateSubDM() line 1267 in /home/bkhanal/Documents/softwares/petsc-3.4.2/src/dm/interface/dm.c [0]PETSC ERROR: PCFieldSplitSetDefaults() line 337 in /home/bkhanal/Documents/softwares/petsc-3.4.2/src/ksp/pc/impls/fieldsplit/fieldsplit.c [0]PETSC ERROR: PCSetUp_FieldSplit() line 458 in /home/bkhanal/Documents/softwares/petsc-3.4.2/src/ksp/pc/impls/fieldsplit/fieldsplit.c [0]PETSC ERROR: PCSetUp() line 890 in /home/bkhanal/Documents/softwares/petsc-3.4.2/src/ksp/pc/interface/precon.c [0]PETSC ERROR: KSPSetUp() line 278 in /home/bkhanal/Documents/softwares/petsc-3.4.2/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: solveModel() line 181 in "unknowndirectory/"/user/bkhanal/home/works/AdLemModel/src/PetscAdLemTaras3D.cxx WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! Option left: name:-pc_fieldsplit_1_fields value: 3 > > Matt > > >> >>> Matt >>> >>> >>>> >>>>> Matt >>>>> >>>>> -- >>>>> 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 >
