[petsc-users] discontinuous viscosity stokes equation 3D staggered grid
Bishesh Khanal
bisheshkh at gmail.com
Fri Aug 23 07:46:24 CDT 2013
On Fri, Aug 23, 2013 at 2:33 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Aug 23, 2013 at 7:25 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>
>>
>>
>>
>> On Fri, Aug 23, 2013 at 2:09 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Fri, Aug 23, 2013 at 4:31 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>
>>>>
>>>> Thanks Matt and Mark for comments in using near null space [question I
>>>> asked in the thread with subject: *problem (Segmentation voilation)
>>>> using -pc_type hypre -pc_hypre_type -pilut with multiple nodes in a cluster
>>>> *].
>>>> So I understood that I have to set a nearNullSpace to A00 block where
>>>> the null space correspond to the rigid body motion. I tried it but still
>>>> the gamg just keeps on iterating and convergence is very very slow. I am
>>>> not sure what the problem is, right now gamg does not even work for the
>>>> constant viscosity case.
>>>> I have set up the following in my code:
>>>> 1. null space for the whole system A 2. null space for the Schur
>>>> complement S 3. Near null space for A00 4. a user preconditioner matrix of
>>>> inverse viscosity in the diagonal for S.
>>>>
>>>
>>> If you want to debug solvers, you HAVE to send -ksp_view.
>>>
>>
>> When I use gamg, the -fieldsplit_0_ksp was iterating on and on so didn't
>> get to the end to get -ksp_view results.
>> Instead here I have put the -ksp_view output when running the program
>> with following options: (In this case I get the results)
>> -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_dm_splits 0
>> -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3
>> -ksp_converged_reason -ksp_view
>>
>
> Okay, that looks fine. Does
>
> -fieldsplit_0_pc_type lu
> - fieldsplit_1_ksp_rtol 1.0e-10
>
> converge in one Iterate?
>
> What matrix did you attach as the preconditioner matrix for fieldsplit_1_?
>
I used a diagonal matrix with reciprocal of viscosity values of the
corresponding cell centers as the preconditioner.
with the options -fieldsplit_0_pc_type lu - fieldsplit_1_ksp_rtol 1.0e-10
-fieldsplit_1_ksp_converged_reason -ksp_converged_reason
I get the following output which means the outer ksp did converge in one
iterate I guess.
Linear solve converged due to CONVERGED_RTOL iterations 18
Linear solve converged due to CONVERGED_RTOL iterations 18
Linear solve converged due to CONVERGED_RTOL iterations 1
>
> Thanks,
>
> Matt
>
>
>> Linear solve converged due to CONVERGED_RTOL iterations 2
>> KSP Object: 1 MPI processes
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> has attached null space
>> using PRECONDITIONED norm type for convergence test
>> PC Object: 1 MPI processes
>> type: fieldsplit
>> FieldSplit with Schur preconditioner, blocksize = 4, factorization
>> FULL
>> Preconditioner for the Schur complement formed from user provided
>> matrix
>> Split info:
>> Split number 0 Fields 0, 1, 2
>> Split number 1 Fields 3
>> KSP solver for A00 block
>> KSP Object: (fieldsplit_0_) 1 MPI processes
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> using PRECONDITIONED norm type for convergence test
>> PC Object: (fieldsplit_0_) 1 MPI processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=8232, cols=8232
>> package used to perform factorization: petsc
>> total: nonzeros=576000, allocated nonzeros=576000
>> total number of mallocs used during MatSetValues calls =0
>> using I-node routines: found 2744 nodes, limit used is 5
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=8232, cols=8232
>> total: nonzeros=576000, allocated nonzeros=576000
>> total number of mallocs used during MatSetValues calls =0
>> using I-node routines: found 2744 nodes, limit used is 5
>> KSP solver for S = A11 - A10 inv(A00) A01
>> KSP Object: (fieldsplit_1_) 1 MPI processes
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>> Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>> left preconditioning
>> has attached null space
>> using PRECONDITIONED norm type for convergence test
>> PC Object: (fieldsplit_1_) 1 MPI processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=2744, cols=2744
>> package used to perform factorization: petsc
>> total: nonzeros=64000, allocated nonzeros=64000
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix followed by preconditioner matrix:
>> Matrix Object: 1 MPI processes
>> type: schurcomplement
>> rows=2744, cols=2744
>> Schur complement A11 - A10 inv(A00) A01
>> A11
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=2744, cols=2744
>> total: nonzeros=64000, allocated nonzeros=64000
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> A10
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=2744, cols=8232
>> total: nonzeros=192000, allocated nonzeros=192000
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> KSP of A00
>> KSP Object: (fieldsplit_0_) 1
>> MPI processes
>> type: gmres
>> GMRES: restart=30, using Classical (unmodified)
>> Gram-Schmidt Orthogonalization with no iterative refinement
>> GMRES: happy breakdown tolerance 1e-30
>> maximum iterations=10000, initial guess is zero
>> tolerances: relative=1e-05, absolute=1e-50,
>> divergence=10000
>> left preconditioning
>> using PRECONDITIONED norm type for convergence test
>> PC Object: (fieldsplit_0_) 1 MPI
>> processes
>> type: ilu
>> ILU: out-of-place factorization
>> 0 levels of fill
>> tolerance for zero pivot 2.22045e-14
>> using diagonal shift on blocks to prevent zero pivot
>> matrix ordering: natural
>> factor fill ratio given 1, needed 1
>> Factored matrix follows:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=8232, cols=8232
>> package used to perform factorization: petsc
>> total: nonzeros=576000, allocated nonzeros=576000
>> total number of mallocs used during MatSetValues
>> calls =0
>> using I-node routines: found 2744 nodes, limit
>> used is 5
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=8232, cols=8232
>> total: nonzeros=576000, allocated nonzeros=576000
>> total number of mallocs used during MatSetValues calls
>> =0
>> using I-node routines: found 2744 nodes, limit used
>> is 5
>> A01
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=8232, cols=2744
>> total: nonzeros=192000, allocated nonzeros=192000
>> total number of mallocs used during MatSetValues calls =0
>> using I-node routines: found 2744 nodes, limit used is 5
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=2744, cols=2744
>> total: nonzeros=64000, allocated nonzeros=64000
>> total number of mallocs used during MatSetValues calls =0
>> not using I-node routines
>> linear system matrix = precond matrix:
>> Matrix Object: 1 MPI processes
>> type: seqaij
>> rows=10976, cols=10976, bs=4
>> total: nonzeros=1024000, allocated nonzeros=1024000
>> total number of mallocs used during MatSetValues calls =0
>> using I-node routines: found 2744 nodes, limit used is 5
>>
>>
>>
>>
>>> Matt
>>>
>>>
>>>> I am testing a small problem with CONSTANT viscosity for grid size of
>>>> 14^3 with the run time option:
>>>> -ksp_type gcr -pc_type fieldsplit -pc_fieldsplit_type schur
>>>> -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2
>>>> -pc_fieldsplit_1_fields 3 -ksp_converged_reason -ksp_view
>>>> -fieldsplit_0_ksp_type gcr -fieldsplit_0_pc_type gamg
>>>> -fieldsplit_0_ksp_monitor_true_residual -fieldsplit_0_ksp_converged_reason
>>>> -fieldsplit_1_ksp_monitor_true_residual
>>>>
>>>> Here is my relevant code of the solve function:
>>>> PetscErrorCode ierr;
>>>> PetscFunctionBeginUser;
>>>> ierr = DMKSPSetComputeRHS(mDa,computeRHSTaras3D,this);CHKERRQ(ierr);
>>>> ierr =
>>>> DMKSPSetComputeOperators(mDa,computeMatrixTaras3D,this);CHKERRQ(ierr);
>>>> ierr = KSPSetDM(mKsp,mDa);CHKERRQ(ierr); //mDa with
>>>> dof = 4, vx,vy,vz and p.
>>>> ierr = KSPSetNullSpace(mKsp,mNullSpace);CHKERRQ(ierr);//nullSpace
>>>> for the main system
>>>> ierr = KSPSetFromOptions(mKsp);CHKERRQ(ierr);
>>>> ierr = KSPSetUp(mKsp);CHKERRQ(ierr); //register
>>>> the fieldsplits obtained from options.
>>>>
>>>> //Setting up user PC for Schur Complement
>>>> ierr = KSPGetPC(mKsp,&mPc);CHKERRQ(ierr);
>>>> ierr =
>>>> PCFieldSplitSchurPrecondition(mPc,PC_FIELDSPLIT_SCHUR_PRE_USER,mPcForSc);CHKERRQ(ierr);
>>>>
>>>> KSP *subKsp;
>>>> PetscInt subKspPos = 0;
>>>> //Set up nearNullspace for A00 block.
>>>> ierr = PCFieldSplitGetSubKSP(mPc,&subKspPos,&subKsp);CHKERRQ(ierr);
>>>> MatNullSpace rigidBodyModes;
>>>> Vec coords;
>>>> ierr = DMGetCoordinates(mDa,&coords);CHKERRQ(ierr);
>>>> ierr =
>>>> MatNullSpaceCreateRigidBody(coords,&rigidBodyModes);CHKERRQ(ierr);
>>>> Mat matA00;
>>>> ierr = KSPGetOperators(subKsp[0],&matA00,NULL,NULL);CHKERRQ(ierr);
>>>> ierr = MatSetNearNullSpace(matA00,rigidBodyModes);CHKERRQ(ierr);
>>>> ierr = MatNullSpaceDestroy(&rigidBodyModes);CHKERRQ(ierr);
>>>>
>>>> //Position 1 => Ksp corresponding to Schur complement S on pressure
>>>> space
>>>> subKspPos = 1;
>>>> ierr = PCFieldSplitGetSubKSP(mPc,&subKspPos,&subKsp);CHKERRQ(ierr);
>>>> //Set up the null space of constant pressure.
>>>> ierr = KSPSetNullSpace(subKsp[1],mNullSpaceP);CHKERRQ(ierr);
>>>> PetscBool isNull;
>>>> Mat matSc;
>>>> ierr = KSPGetOperators(subKsp[1],&matSc,NULL,NULL);CHKERRQ(ierr);
>>>> ierr = MatNullSpaceTest(mNullSpaceP,matSc,&isNull);
>>>> if(!isNull)
>>>> SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"not a valid pressure
>>>> null space \n");
>>>> ierr = KSPGetOperators(mKsp,&mA,NULL,NULL);CHKERRQ(ierr);
>>>> ierr = MatNullSpaceTest(mNullSpace,mA,&isNull);CHKERRQ(ierr);
>>>> if(!isNull)
>>>> SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"not a valid system
>>>> null space \n");
>>>>
>>>> ierr = PetscFree(subKsp);CHKERRQ(ierr);
>>>> ierr = KSPSolve(mKsp,NULL,NULL);CHKERRQ(ierr);
>>>> ierr = KSPGetSolution(mKsp,&mX);CHKERRQ(ierr);
>>>> ierr = KSPGetRhs(mKsp,&mB);CHKERRQ(ierr);
>>>>
>>>>
>>>> PetscFunctionReturn(0);
>>>>
>>>>
>>>> On Wed, Aug 7, 2013 at 2:15 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>
>>>>> On Wed, Aug 7, 2013 at 7:07 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Aug 6, 2013 at 11:34 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>>
>>>>>>> On Tue, Aug 6, 2013 at 10:59 AM, Bishesh Khanal <bisheshkh at gmail.com
>>>>>>> > wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Aug 6, 2013 at 4:40 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>>>>>
>>>>>>>>> On Tue, Aug 6, 2013 at 8:06 AM, Bishesh Khanal <
>>>>>>>>> bisheshkh at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Aug 5, 2013 at 4:14 PM, Matthew Knepley <
>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> On Mon, Aug 5, 2013 at 8:48 AM, Bishesh Khanal <
>>>>>>>>>>> bisheshkh at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Mon, Aug 5, 2013 at 3:17 PM, Matthew Knepley <
>>>>>>>>>>>> knepley at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> On Mon, Aug 5, 2013 at 7:54 AM, Bishesh Khanal <
>>>>>>>>>>>>> bisheshkh at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Wed, Jul 17, 2013 at 9:48 PM, Jed Brown <
>>>>>>>>>>>>>> jedbrown at mcs.anl.gov> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Bishesh Khanal <bisheshkh at gmail.com> 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);
>>>>>>>>
>>>>>>>
>>>>>>> Sorry, you need to return to the old DMDA behavior, so you want
>>>>>>>
>>>>>>> -pc_fieldsplit_dm_splits 0
>>>>>>>
>>>>>>
>>>>>> Thanks, with this it seems I can attach the null space properly, but
>>>>>> I have a question regarding whether the Schur complement ksp solver is
>>>>>> actually using the preconditioner matrix I provide.
>>>>>> When using -ksp_view, the outer level pc object of type fieldsplit
>>>>>> does report that: "Preconditioner for the Schur complement formed from user
>>>>>> provided matrix", but in the KSP solver for Schur complement S, the pc
>>>>>> object (fieldsplit_1_) is of type ilu and doesn't say that it is using the
>>>>>> matrix I provide. Am I missing something here ?
>>>>>> Below are the relevant commented code snippet and the output of the
>>>>>> -ksp_view
>>>>>> (The options I used: -pc_type fieldsplit -pc_fieldsplit_type schur
>>>>>> -pc_fieldsplit_dm_splits 0 -pc_fieldsplit_0_fields 0,1,2
>>>>>> -pc_fieldsplit_1_fields 3 -ksp_converged_reason -ksp_view )
>>>>>>
>>>>>
>>>>> If ILU does not error, it means it is using your matrix, because the
>>>>> Schur complement matrix cannot be factored, and FS says it is using your
>>>>> matrix.
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Code snippet:
>>>>>> ierr = KSPSetNullSpace(mKsp,mNullSpaceSystem);CHKERRQ(ierr); //The
>>>>>> nullspace for the whole system
>>>>>> ierr = KSPSetFromOptions(mKsp);CHKERRQ(ierr);
>>>>>> ierr = KSPSetUp(mKsp);CHKERRQ(ierr); //Set up
>>>>>> mKsp with the options provided with fieldsplit and the fields associated
>>>>>> with the two splits.
>>>>>>
>>>>>> ierr = KSPGetPC(mKsp,&mPcOuter);CHKERRQ(ierr);
>>>>>> //Get the fieldsplit pc set up from the options
>>>>>>
>>>>>> ierr =
>>>>>> PCFieldSplitSchurPrecondition(mPcOuter,PC_FIELDSPLIT_SCHUR_PRE_USER,mPcForSc);CHKERRQ(ierr);
>>>>>> //Use mPcForSc as the preconditioner for Schur Complement
>>>>>>
>>>>>> KSP *kspSchur;
>>>>>> PetscInt kspSchurPos = 1;
>>>>>> ierr =
>>>>>> PCFieldSplitGetSubKSP(mPcOuter,&kspSchurPos,&kspSchur);CHKERRQ(ierr);
>>>>>> ierr =
>>>>>> KSPSetNullSpace(kspSchur[1],mNullSpacePressure);CHKERRQ(ierr);
>>>>>> //Attach the null-space for the Schur complement ksp solver.
>>>>>> ierr = PetscFree(kspSchur);CHKERRQ(ierr);
>>>>>>
>>>>>> ierr = KSPSolve(mKsp,NULL,NULL);CHKERRQ(ierr);
>>>>>>
>>>>>>
>>>>>>
>>>>>> the output of the -ksp_view
>>>>>> KSP Object: 1 MPI processes
>>>>>> type: gmres
>>>>>> GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>>>>>> Orthogonalization with no iterative refinement
>>>>>> GMRES: happy breakdown tolerance 1e-30
>>>>>> maximum iterations=10000, initial guess is zero
>>>>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>>>>>> left preconditioning
>>>>>> has attached null space
>>>>>> using PRECONDITIONED norm type for convergence test
>>>>>> PC Object: 1 MPI processes
>>>>>> type: fieldsplit
>>>>>> FieldSplit with Schur preconditioner, blocksize = 4,
>>>>>> factorization FULL
>>>>>> Preconditioner for the Schur complement formed from user provided
>>>>>> matrix
>>>>>> Split info:
>>>>>> Split number 0 Fields 0, 1, 2
>>>>>> Split number 1 Fields 3
>>>>>> KSP solver for A00 block
>>>>>> KSP Object: (fieldsplit_0_) 1 MPI processes
>>>>>> type: gmres
>>>>>> GMRES: restart=30, using Classical (unmodified)
>>>>>> Gram-Schmidt Orthogonalization with no iterative refinement
>>>>>> GMRES: happy breakdown tolerance 1e-30
>>>>>> maximum iterations=10000, initial guess is zero
>>>>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>>>>>> left preconditioning
>>>>>> using PRECONDITIONED norm type for convergence test
>>>>>> PC Object: (fieldsplit_0_) 1 MPI processes
>>>>>> type: ilu
>>>>>> ILU: out-of-place factorization
>>>>>> 0 levels of fill
>>>>>> tolerance for zero pivot 2.22045e-14
>>>>>> using diagonal shift on blocks to prevent zero pivot
>>>>>> matrix ordering: natural
>>>>>> factor fill ratio given 1, needed 1
>>>>>> Factored matrix follows:
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=2187, cols=2187
>>>>>> package used to perform factorization: petsc
>>>>>> total: nonzeros=140625, allocated nonzeros=140625
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> using I-node routines: found 729 nodes, limit used
>>>>>> is 5
>>>>>> linear system matrix = precond matrix:
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=2187, cols=2187
>>>>>> total: nonzeros=140625, allocated nonzeros=140625
>>>>>> total number of mallocs used during MatSetValues calls =0
>>>>>> using I-node routines: found 729 nodes, limit used is 5
>>>>>> KSP solver for S = A11 - A10 inv(A00) A01
>>>>>> KSP Object: (fieldsplit_1_) 1 MPI processes
>>>>>> type: gmres
>>>>>> GMRES: restart=30, using Classical (unmodified)
>>>>>> Gram-Schmidt Orthogonalization with no iterative refinement
>>>>>> GMRES: happy breakdown tolerance 1e-30
>>>>>> maximum iterations=10000, initial guess is zero
>>>>>> tolerances: relative=1e-05, absolute=1e-50, divergence=10000
>>>>>> left preconditioning
>>>>>> has attached null space
>>>>>> using PRECONDITIONED norm type for convergence test
>>>>>> PC Object: (fieldsplit_1_) 1 MPI processes
>>>>>> type: ilu
>>>>>> ILU: out-of-place factorization
>>>>>> 0 levels of fill
>>>>>> tolerance for zero pivot 2.22045e-14
>>>>>> using diagonal shift on blocks to prevent zero pivot
>>>>>> matrix ordering: natural
>>>>>> factor fill ratio given 1, needed 1
>>>>>> Factored matrix follows:
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=729, cols=729
>>>>>> package used to perform factorization: petsc
>>>>>> total: nonzeros=15625, allocated nonzeros=15625
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> not using I-node routines
>>>>>> linear system matrix followed by preconditioner matrix:
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: schurcomplement
>>>>>> rows=729, cols=729
>>>>>> Schur complement A11 - A10 inv(A00) A01
>>>>>> A11
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=729, cols=729
>>>>>> total: nonzeros=15625, allocated nonzeros=15625
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> not using I-node routines
>>>>>> A10
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=729, cols=2187
>>>>>> total: nonzeros=46875, allocated nonzeros=46875
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> not using I-node routines
>>>>>> KSP of A00
>>>>>> KSP Object: (fieldsplit_0_)
>>>>>> 1 MPI processes
>>>>>> type: gmres
>>>>>> GMRES: restart=30, using Classical (unmodified)
>>>>>> Gram-Schmidt Orthogonalization with no iterative refinement
>>>>>> GMRES: happy breakdown tolerance 1e-30
>>>>>> maximum iterations=10000, initial guess is zero
>>>>>> tolerances: relative=1e-05, absolute=1e-50,
>>>>>> divergence=10000
>>>>>> left preconditioning
>>>>>> using PRECONDITIONED norm type for convergence test
>>>>>> PC Object: (fieldsplit_0_) 1
>>>>>> MPI processes
>>>>>> type: ilu
>>>>>> ILU: out-of-place factorization
>>>>>> 0 levels of fill
>>>>>> tolerance for zero pivot 2.22045e-14
>>>>>> using diagonal shift on blocks to prevent zero pivot
>>>>>> matrix ordering: natural
>>>>>> factor fill ratio given 1, needed 1
>>>>>> Factored matrix follows:
>>>>>> Matrix Object: 1 MPI
>>>>>> processes
>>>>>> type: seqaij
>>>>>> rows=2187, cols=2187
>>>>>> package used to perform factorization: petsc
>>>>>> total: nonzeros=140625, allocated
>>>>>> nonzeros=140625
>>>>>> total number of mallocs used during
>>>>>> MatSetValues calls =0
>>>>>> using I-node routines: found 729 nodes,
>>>>>> limit used is 5
>>>>>> linear system matrix = precond matrix:
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=2187, cols=2187
>>>>>> total: nonzeros=140625, allocated nonzeros=140625
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> using I-node routines: found 729 nodes, limit
>>>>>> used is 5
>>>>>> A01
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=2187, cols=729
>>>>>> total: nonzeros=46875, allocated nonzeros=46875
>>>>>> total number of mallocs used during MatSetValues
>>>>>> calls =0
>>>>>> using I-node routines: found 729 nodes, limit used
>>>>>> is 5
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=729, cols=729
>>>>>> total: nonzeros=15625, allocated nonzeros=15625
>>>>>> total number of mallocs used during MatSetValues calls =0
>>>>>> not using I-node routines
>>>>>> linear system matrix = precond matrix:
>>>>>> Matrix Object: 1 MPI processes
>>>>>> type: seqaij
>>>>>> rows=2916, cols=2916, bs=4
>>>>>> total: nonzeros=250000, allocated nonzeros=250000
>>>>>> total number of mallocs used during MatSetValues calls =0
>>>>>> using I-node routines: found 729 nodes, limit used is 5
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> or
>>>>>>>
>>>>>>> PCFieldSplitSetDMSplits(pc, PETSC_FALSE)
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Matt
>>>>>>>
>>>>>>>
>>>>>>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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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