[petsc-users] discontinuous viscosity stokes equation 3D staggered grid
Bishesh Khanal
bisheshkh at gmail.com
Fri Aug 23 08:42:32 CDT 2013
On Fri, Aug 23, 2013 at 3:34 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Aug 23, 2013 at 8:30 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>
>>
>>
>>
>> On Fri, Aug 23, 2013 at 3:16 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Fri, Aug 23, 2013 at 8:01 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>
>>>>
>>>>
>>>>
>>>> On Fri, Aug 23, 2013 at 2:53 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>>>
>>>>> On Fri, Aug 23, 2013 at 7:46 AM, Bishesh Khanal <bisheshkh at gmail.com>wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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
>>>>>>
>>>>>
>>>>> Okay, so A_00 is nonsingular, and the system seems to solve alright.
>>>>> What do you get for
>>>>>
>>>>> -fieldsplit_0_ksp_max_it 30
>>>>> -fieldsplit_0_pc_type gamg
>>>>> -fieldsplit_0_ksp_converged_reason
>>>>> -fieldsplit_1_ksp_converged_reason
>>>>>
>>>>>
>>>>
>>>> It fieldsplit_0_ does not converge in 30 iterations. It gives:
>>>> Linear solve converged due to CONVERGED_ATOL iterations 0
>>>> Linear solve did not converge due to DIVERGED_ITS iterations 30
>>>>
>>>> and continues with the same message.
>>>>
>>>
>>> So what would you do? Give up?
>>>
>>> No, I don't want to give up :)
>>
>>
>>> -fieldsplit_0_ksp_gmres_restart 200
>>>
>>> The idea is to figure out what is going on:
>>>
>>> -fieldsplit_0_ksp_monitor_true_residual
>>>
>>> I have tried these options before too, the residual is decreasing very
>> very slowly, but I've not been able to figure out why. (using hypre does
>> converge although slowly again, but I had problems using hypre with
>> multiple nodes in a cluster with segmentation fault (we discussed that in
>> another thread!) )
>>
>
> Put in the Laplacian instead of the operator you have now. It should
> converge in a few iterates. If not, you have a problem
> in the specification.
>
> If so, put in linear elasticity. If it is slow, you have made a mistake
> specifiying the near null space. Also, you need to check
> that the near null space made it to GAMG using the ksp_view output.
>
Which operator are you referring to ? The one in A00 block ? I'm testing
currently with the constant viscosity case which means the A00 block has
\mu div(grad(v)) which is a Laplacian.
And Is it possible to view the ksp_view output before the solver actually
converges to check if GAMG took the near null space ?
>
> Matt
>
>
>> e.g a snapshot of the output:
>>
>> Residual norms for fieldsplit_0_ solve.
>> 0 KSP preconditioned resid norm 0.000000000000e+00 true resid norm
>> 0.000000000000e+00 ||r(i)||/||b|| -nan
>> Linear solve converged due to CONVERGED_ATOL iterations 0
>> Residual norms for fieldsplit_0_ solve.
>> 0 KSP preconditioned resid norm 2.619231455875e-01 true resid norm
>> 3.637306695895e+02 ||r(i)||/||b|| 1.000000000000e+00
>> 1 KSP preconditioned resid norm 9.351491725479e-02 true resid norm
>> 6.013334574957e+01 ||r(i)||/||b|| 1.653238255038e-01
>> 2 KSP preconditioned resid norm 6.010357491087e-02 true resid norm
>> 3.664473273769e+01 ||r(i)||/||b|| 1.007468871928e-01
>> 3 KSP preconditioned resid norm 6.006968012944e-02 true resid norm
>> 3.696451770148e+01 ||r(i)||/||b|| 1.016260678353e-01
>> 4 KSP preconditioned resid norm 4.418407037098e-02 true resid norm
>> 3.184810838034e+01 ||r(i)||/||b|| 8.755959022176e-02
>> ...
>> ...
>> 93 KSP preconditioned resid norm 4.549506047737e-04 true resid norm
>> 2.877594552685e+00 ||r(i)||/||b|| 7.911333283864e-03
>> 94 KSP preconditioned resid norm 4.515424416235e-04 true resid norm
>> 2.875249044668e+00 ||r(i)||/||b|| 7.904884809172e-03
>> 95 KSP preconditioned resid norm 4.277647876573e-04 true resid norm
>> 2.830418831358e+00 ||r(i)||/||b|| 7.781633686685e-03
>> 96 KSP preconditioned resid norm 4.244529173876e-04 true resid norm
>> 2.807041401408e+00 ||r(i)||/||b|| 7.717362422521e-03
>> 97 KSP preconditioned resid norm 4.138326570674e-04 true resid norm
>> 2.793663020386e+00 ||r(i)||/||b|| 7.680581413547e-03
>> 98 KSP preconditioned resid norm 3.869979433609e-04 true resid norm
>> 2.715150386650e+00 ||r(i)||/||b|| 7.464727650583e-03
>> 99 KSP preconditioned resid norm 3.847873979265e-04 true resid norm
>> 2.706008990336e+00 ||r(i)||/||b|| 7.439595328571e-03
>>
>> ....
>> ....
>> 294 KSP preconditioned resid norm 1.416482289961e-04 true resid norm
>> 2.735750748819e+00 ||r(i)||/||b|| 7.521363958412e-03
>> 295 KSP preconditioned resid norm 1.415389087364e-04 true resid norm
>> 2.742638608355e+00 ||r(i)||/||b|| 7.540300661064e-03
>> 296 KSP preconditioned resid norm 1.414967651105e-04 true resid norm
>> 2.747224243968e+00 ||r(i)||/||b|| 7.552907889424e-03
>> 297 KSP preconditioned resid norm 1.413843018303e-04 true resid norm
>> 2.752574248710e+00 ||r(i)||/||b|| 7.567616587891e-03
>> 298 KSP preconditioned resid norm 1.411747949695e-04 true resid norm
>> 2.765459647367e+00 ||r(i)||/||b|| 7.603042246859e-03
>> 299 KSP preconditioned resid norm 1.411609742082e-04 true resid norm
>> 2.765900464868e+00 ||r(i)||/||b|| 7.604254180683e-03
>> 300 KSP preconditioned resid norm 1.409844332838e-04 true resid norm
>> 2.771790506811e+00 ||r(i)||/||b|| 7.620447596402e-03
>> Linear solve did not converge due to DIVERGED_ITS iterations 300
>> Residual norms for fieldsplit_0_ solve.
>> 0 KSP preconditioned resid norm 1.294272083271e-03 true resid norm
>> 1.776945075651e+00 ||r(i)||/||b|| 1.000000000000e+00
>> ...
>> ...
>>
>>
>>
>>
>>> Matt
>>>
>>>
>>>>
>>>>
>>>>
>>>>> This is the kind of investigation you msut be comfortable with if you
>>>>> want to experiment with these solvers.
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>>
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20130823/d9a632b9/attachment-0001.html>
More information about the petsc-users
mailing list