[petsc-users] SNESSetFunction and MatMFFDSetFunction
Song Gao
song.gao.mcgill at gmail.com
Sat Mar 1 09:10:55 CST 2014
For the record, I did as Barry suggested, and it worked well for our
problem.
Thank you very much.
On Fri, Jan 17, 2014 at 4:47 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> On Jan 16, 2014, at 10:49 AM, Song Gao <song.gao2 at mail.mcgill.ca> wrote:
>
> > I was looking at the example of MatMFFDSetFunction on website.
> >
> http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex22.c.html
> > I think, the line 312, the last snes should be ctx.
> > 312: MatMFFDSetFunction(*A,(PetscErrorCode
> (*)(void*,Vec,Vec))SNESComputeFunction
> > ,snes);
>
> No the code as in the example is correct. The first argument to
> SNESComputeFunction() is the SNES object
> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/SNESComputeFunction.html#SNESComputeFunction
>
>
> >
> >
> >
> >
> > On Thu, Jan 16, 2014 at 11:04 AM, Song Gao <song.gao2 at mail.mcgill.ca>
> wrote:
> > Thank you.
> >
> > I have found the bug in my codes. SNESSetFunction and MatMFFDSetFunction
> expect functions with different interfaces, but I passed the same function
> to them.
> >
> >
> > On Wed, Jan 8, 2014 at 11:52 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > I suspect the problem is here:
> >
> > >
> > > call MatMFFDSetBase(myJctx%mf, pet_solu_snes, PETSC_NULL_INTEGER,
> > >
> > > @ ierrpet)
> >
> > In fact I am surprised it didn't crash at this line, since we don't
> have code to handle the PETSC_NULL_INTEGER
> >
> > Try adding the
> >
> > > call
> SNESGetFunction(snes,f,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierrpet);
> >
> > before the
> >
> > > MatMFFDSetBase(myJctx%mf,x,f,ierrpet);
> >
> > that I suggested before.
> >
> > Does that change anything?
> >
> > If you still get different values here is how I would debug it next
> >
> > 1) 1 process
> >
> > 2) run each version separately in the debugger (you can use the options
> -start_in_debugger noxterm )
> >
> > 3) put a break point in MatMult(). In most debuggers you just use
> >
> > b MatMult
> >
> > 4) then type c to continue
> >
> > 5) when it stops in MatMult do
> >
> > VecView(x,0)
> >
> > 6) make sure both versions produce the exact same numbers (do they?)
> >
> > 7) then type next several times until it gets to the
> PetscFunctionReturn(0) line
> >
> > 8) do
> >
> > VecView(y,0)
> >
> > again are both answers identical? By all logic they will be different
> since the norms you print are different.
> >
> > If (6) produces the same numbers but (8) produces different ones then
> put a break point in MatMult_MFFD()
> > and call VecView() on ctx->current_u ctx->current_f and a. For both
> versions they should be the same. Are they?
> >
> > Barry
> >
> >
> >
> > On Jan 8, 2014, at 10:47 AM, Song Gao <song.gao2 at mail.mcgill.ca> wrote:
> >
> > > Dear Barry,
> > >
> > > Thanks for reply. I basically implemented your codes. Then I have two
> > > questions.
> > >
> > > The first is I'm working on Fortran. So I can't use MatShellSetContext
> to
> > > set the structure. Therefore I let the variable I want to set, MyJctx,
> to
> > > be global. Is there other way to do that?
> > >
> > > The second question is I did some tests. let the D vec to be zero, I
> > > expect the code which I explicit set the matrix-free jacobian and the
> code
> > > which I use runtime option -snes_mf give the same residual history.
> But it
> > > doesn't.
> > >
> > > Here is the histories for
> > >
> > > -snes_monitor -ksp_max_it 5 -snes_converged_reason -snes_max_it 2
> -ksp_converged_reason -ksp_monitor -snes_max_linear_solve_fail 300 -pc_type
> none -snes_view -snes_linesearch_type basic
> > >
> > > 0 SNES Function norm 4.272952196300e-02
> > >
> > > 0 KSP Residual norm 4.272952196300e-02
> > > 1 KSP Residual norm 4.234712668718e-02
> > > 2 KSP Residual norm 3.683301946690e-02
> > >
> > > 3 KSP Residual norm 3.465586805169e-02
> > >
> > > 4 KSP Residual norm 3.452667066800e-02
> > > 5 KSP Residual norm 3.451739518719e-02
> > > Linear solve did not converge due to DIVERGED_ITS iterations 5
> > > 1 SNES Function norm 4.203973403992e-02
> > >
> > > 0 KSP Residual norm 4.203973403992e-02
> > >
> > > 1 KSP Residual norm 4.203070641961e-02
> > > 2 KSP Residual norm 4.202387940443e-02
> > > 3 KSP Residual norm 4.183739347023e-02
> > > 4 KSP Residual norm 4.183629424897e-02
> > >
> > > 5 KSP Residual norm 4.159456024825e-02
> > >
> > > Linear solve did not converge due to DIVERGED_ITS iterations 5
> > > 2 SNES Function norm 4.200901009970e-02
> > > Nonlinear solve did not converge due to DIVERGED_MAX_IT iterations 2
> > >
> > >
> > > Here is the histories for
> > > -snes_mf -snes_monitor -ksp_max_it 5 -snes_converged_reason
> -snes_max_it 2 -ksp_converged_reason -ksp_monitor
> -snes_max_linear_solve_fail 300 -pc_type none -snes_view
> -snes_linesearch_type basic
> > >
> > >
> > > 0 SNES Function norm 4.272952196300e-02
> > > 0 KSP Residual norm 4.272952196300e-02
> > > 1 KSP Residual norm 4.270267664569e-02
> > > 2 KSP Residual norm 3.690026921954e-02
> > >
> > > 3 KSP Residual norm 3.681740616743e-02
> > >
> > > 4 KSP Residual norm 3.464377294985e-02
> > > 5 KSP Residual norm 3.464376048536e-02
> > > Linear solve did not converge due to DIVERGED_ITS iterations 5
> > > 1 SNES Function norm 3.461633424373e-02
> > >
> > > 0 KSP Residual norm 3.461633424373e-02
> > >
> > > 1 KSP Residual norm 3.461632119472e-02
> > > 2 KSP Residual norm 3.406130197963e-02
> > > 3 KSP Residual norm 3.406122155751e-02
> > > 4 KSP Residual norm 3.403393397001e-02
> > >
> > > 5 KSP Residual norm 3.403367748538e-02
> > >
> > > Linear solve did not converge due to DIVERGED_ITS iterations 5
> > > 2 SNES Function norm 3.403367847002e-02
> > > Nonlinear solve did not converge due to DIVERGED_MAX_IT iterations 2
> > >
> > >
> > > We can see that at 0 SNES 1 KSP step, the residual norms are
> different. Did I do something wrong here?
> > >
> > > The codes are like
> > >
> > > type MyJContext
> > > Mat mf
> > > Vec D
> > > Vec work
> > > end type MyJContext
> > >
> > > c
> > >
> > > type(MyJContext) myJctx
> > >
> > >
> --------------------------------------------------------------------------
> > > call SNESCreate(PETSC_COMM_WORLD, snes, ierpetsc)
> > > call SNESSetFunction(snes, pet_rhs_snes, flowsolrhs, ctx,
> > >
> > > @ ierpetsc)
> > >
> > > c
> > > call MatCreateSNESMF(snes, myJctx%mf, ierpetsc)
> > > call MatMFFDSetFunction(myJctx%mf, flowsolrhs, ctx, ierpetsc)
> > > call VecDuplicate(pet_solu_snes, myJctx%D, ierpetsc)
> > >
> > > call VecDuplicate(pet_solu_snes, myJctx%work, ierpetsc)
> > >
> > > call VecSet(myJctx%D, 0.0D-3, ierpetsc)
> > > call MatCreateShell(PETSC_COMM_WORLD, pet_nfff, pet_nfff,
> > > @ PETSC_DETERMINE, PETSC_DETERMINE, ctx, myJ, ierpetsc)
> > >
> > > call MatShellSetOperation(myJ, MATOP_MULT, mymultply,
> > >
> > > @ ierpetsc)
> > > call SNESSetJacobian(snes, myJ, pet_mat_pre,
> > > @ flowsoljac, ctx, ierpetsc)
> > >
> > >
> --------------------------------------------------------------------------
> > >
> > >
> > > subroutine mymultply ( A, x, y, ierpet)
> > > Mat :: A
> > > Vec :: x, y
> > > PetscErrorCode :: ierpet
> > > c
> > > call MatMult(myJctx%mf,x,y, ierpet)
> > > c
> > > end
> > >
> --------------------------------------------------------------------------
> > >
> > >
> > > subroutine flowsoljac ( snes, pet_solu_snes, pet_mat_snes,
> > > @ pet_mat_pre, flag, ctxx, ierrpet )
> > >
> > > c explicitly assemble pet_mat_pre matrix here
> > > c .........
> > > c .........
> > >
> > > call MatMFFDSetBase(myJctx%mf, pet_solu_snes, PETSC_NULL_INTEGER,
> > >
> > > @ ierrpet)
> > >
> > > end
> > >
> > >
> > >
> > >
> > > On Fri, Jan 3, 2014 at 6:46 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > >
> > > Dario,
> > >
> > > Your discussion below (SOR, ILU(200)) seems to imply that you are
> providing some actual explicit representation of the Jacobian, not just
> doing something completely matrix free. Is this correct? But the PETSc
> MatMFFD() is completely matrix free, it provides only a matrix-vector
> product and no access to the matrix entries, hence I am slightly confused.
> > >
> > > If you wish to use for the Jacobian something like D + J and do it
> completely matrix free then rather than than monkeying with "changing the
> function" I would
> > > use the "correct" function to compute J x using matrix free multiply
> and then apply the D to as an additional operation. Hence you would do
> something like
> > >
> > > typedef struct { /* data structure to store the usual matrix
> free matrix and the additional diagonal matrix */
> > > Mat mf;
> > > Vec D;
> > > Vec work;
> > > } MyJContext;
> > >
> > > MyJContext myJctx;
> > >
> > > MatCreateSNESMF(SNES,&myJctx.mf); /* create the usual MFFD
> matrix using the real nonlinear function */
> > >
> MatMFFDSetFunction(myJctx.mf,yournonlinearfunction,nonlinearfunctionctx);
> > > VecCreate(comm,&myJctx.D);
> > > /* set the correct sizes for D and fill up with your diagonal
> matrix entries */
> > > VecDuplicate(&myJctx.D,&myJCtx.work);
> > > MatCreateShell(comm,.... &myJ);
> > > MatShellSetOperation(myJ,MATOP_MULT, mymultiply);
> > > MatShellSetContext(myJ,&myJctx);
> > > SNESSetJacobian(snes,myJ,myJ, myJFunction,NULL);
> > >
> > > where
> > >
> > > PetscErrorCode mymultply(Mat A,Vec x,Vec y) /* computes y = J x
> + D x
> > > {
> > > MyJContext *myJctx;
> > >
> > > MatShellGetContext(A,&myJctx);
> > > MatMult(myJctx->mf,x,y);
> > > VecPointwiseMult(myJctx->D,x,myJctx->work);
> > > VecAXPY(y,1.myJctx->work);
> > > }
> > >
> > > and
> > >
> > > PetscErrorCode myJFunction(SNES snes,Vec x,Mat *A,Mat
> *B,MatStructure *str,void* ctx)
> > >
> > > /* this is called for each new "Jacobian" to set the point at
> which it is computed */
> > > {
> > > MyJContext *myJctx;
> > > Vec f;
> > > MatShellGetContext(*A,&myJctx);
> > > SNESGetFunction(snes,&f);
> > > MatMFFDSetBase(myJctx->mf,x,f);
> > >
> > > /* change the D entries if they depend on the current
> solution etc */
> > > return 0;
> > > }
> > >
> > > Sorry now that I have typed it out it looks a bit more
> complicated then it really is. It does what you want but without any
> trickery or confusing code.
> > >
> > > But, of course, since it is completely matrix free you cannot
> use SOR with it. Of course by making D suitably large you can make it as
> well conditioned as you want and thus get rapid linear convergence (though
> that may slow down or ruin the nonlinear convergence).
> > >
> > > Hope this helps,
> > >
> > > Barry
> > >
> > >
> > >
> > >
> > >
> > > On Jan 3, 2014, at 12:18 PM, Dario Isola <dario.isola at newmerical.com>
> wrote:
> > >
> > > > Dear, Barry and Jed,
> > > >
> > > > Thanks for your replies.
> > > >
> > > > We understand your doubts, so let me to put our question into
> context. In CFD it is standard practice to solve non-linear equations of
> conservation for steady flows by means of a inexact Newton method. The
> original Jacobian matrix is modified by adding terms on the diagonal which
> are proportional to the Courant number and to the lumped mass matrix. This
> allows us to obtain two things, "relax" the solution update and increase
> the diagonal dominance of the matrix itself.
> > > >
> > > > The latter is key when simple preconditioners are adopted, in our
> case point Jacobi or SOR. Indeed, if the original matrix was to be used,
> the GMRES method would converge only on very regular meshes and only when
> adopting ILU preconditioners with a very high level of fill-in. As result a
> higher number of non-linear iterations is traded with a simpler linear
> system to be solved.
> > > >
> > > > While exploring the SNES+MF capabilities we found out that we could
> successfully solve the linear system only with ILU(200) or so. Of course we
> do not want to touch the function used to evaluate the residual, which
> determines the final solution. However we think that a suitable
> modification of the function that Petsc differences to compute the matrix
> vector product would allow us to obtain a behavior similar to the inexact
> Newton method.
> > > >
> > > > Best regards,
> > > > Dario
> > > >
> > > >
> > > > On 01/03/2014 12:32 PM, Song Gao wrote:
> > > >>
> > > >>
> > > >> ---------- Forwarded message ----------
> > > >> From: Jed Brown <jedbrown at mcs.anl.gov>
> > > >> Date: Thu, Jan 2, 2014 at 10:20 AM
> > > >> Subject: Re: [petsc-users] SNESSetFunction and MatMFFDSetFunction
> > > >> To: Song Gao <song.gao2 at mail.mcgill.ca>, Barry Smith <
> bsmith at mcs.anl.gov>
> > > >> Cc: petsc-users <petsc-users at mcs.anl.gov>
> > > >>
> > > >>
> > > >> Song Gao <song.gao2 at mail.mcgill.ca> writes:
> > > >>
> > > >> > Thanks, Barry.
> > > >> >
> > > >> > I mean 2) providing a function that I want PETSc to difference to
> evaluate
> > > >> > the matrix vector product.
> > > >> >
> > > >> > I want to make a slight modification of the matrix after PETSc
> evaluate the
> > > >> > matrix vector product.
> > > >>
> > > >> Performing a matrix-vector product is not supposed to modify the
> matrix.
> > > >> It's unlikely that you really want this.
> > > >>
> > > >>
> > > >> On Wed, Jan 1, 2014 at 3:01 PM, Barry Smith <bsmith at mcs.anl.gov>
> wrote:
> > > >>
> > > >> On Jan 1, 2014, at 11:09 AM, Song Gao <song.gao2 at mail.mcgill.ca>
> wrote:
> > > >>
> > > >> > Dear all,
> > > >> >
> > > >> > Happy new year!
> > > >> >
> > > >> > I'm using the matrix-free method to solve NS equations. I call
> the SNESSetFunction to set the RHS function. I think SNES also uses that
> RHS function to evaluate the matrix vector product.
> > > >>
> > > >> Yes, PETSc differences this function to evaluate the matrix
> vector product.
> > > >>
> > > >> >
> > > >> > But I want to set one function to evaluate the residual, and
> another different function to evaluate the matrix vector product.
> > > >>
> > > >> Are you providing a function that
> > > >>
> > > >> 1) actually evaluates the matrix vector product or are you
> > > >>
> > > >> 2) providing a function that you want PETSc to difference to
> evaluate the matrix vector product?
> > > >>
> > > >> > How can I do that? Does MatMFFDSetFunction do this job?
> > > >>
> > > >> For 2) yes, but if the function you provide is different than
> the function provided with SNESSetFunction then the matrix-vector product
> obtained from differencing it will not be "correct" Jacobian for the
> SNESSetFunction() you are providing so I don't see why you would do it.
> > > >>
> > > >> For 1) you should use MatCreateShell() and
> MatShellSetOperation(mat,MATOP_MULT, ....) and then pass that matrix to
> SNESSetJacobian(), then PETSc will use that "matrix" to do its
> matrix-vector products.
> > > >>
> > > >> Barry
> > > >>
> > > >>
> > > >>
> > > >> >
> > > >> > Any suggestion is appreciated. Thank you.
> > > >> >
> > > >> >
> > > >> > Song
> > > >>
> > > >
> > >
> > >
> >
> >
> >
>
>
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