[petsc-users] SNES seems not use my matrix-free operation
Barry Smith
bsmith at petsc.dev
Thu Jan 11 09:46:49 CST 2024
The following assumes you are not using the shell matrix context for some other purpose
> subroutine formJacobian(snes,F_global,Jac,Jac_pre,dummy,err_PETSc)
>
> SNES :: snes
> Vec :: F_global
>
> ! real(pREAL), dimension(3,3,cells(1),cells(2),cells3), intent(in) :: &
> ! F
> Mat :: Jac, Jac_pre
> PetscObject :: dummy
> PetscErrorCode :: err_PETSc
>
> print*, '@@ start build my jac'
>
> PetscCall(MatShellSetContext(Jac,F_global,ierr)) ! record the current base vector where the Jacobian is to be applied
> print*, '@@ end build my jac'
>
> end subroutine formJacobian
subroutine Gk_op
...
Vec base
PetscCall(MatShellGetContext(Jac,base,ierr))
! use base in the computation of your matrix-free Jacobian vector product
....
> On Jan 11, 2024, at 5:55 AM, Yi Hu <y.hu at mpie.de> wrote:
>
> Now I understand a bit more about the workflow of set jacobian. It seems that the SNES can be really fine-grained. As you point out, J is built via formJacobian() callback, and can be based on previous solution (or the base vector u, as you mentioned). And then KSP can use a customized MATOP_MULT to solve the linear equations J(u)*x=rhs.
>
> So I followed your idea about removing DMSNESSetJacobianLocal() and did the following.
>
> ……
> call MatCreateShell(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,&
> 9*product(cells(1:2))*cells3,9*product(cells(1:2))*cells3,&
> 0,Jac_PETSc,err_PETSc)
> CHKERRQ(err_PETSc)
> call MatShellSetOperation(Jac_PETSc,MATOP_MULT,GK_op,err_PETSc)
> CHKERRQ(err_PETSc)
> call SNESSetJacobian(SNES_mech,Jac_PETSc,Jac_PETSc,formJacobian,0,err_PETSc)
> CHKERRQ(err_PETSc)
> ……
>
> And my formJacobian() is
>
> subroutine formJacobian(snes,F_global,Jac,Jac_pre,dummy,err_PETSc)
>
> SNES :: snes
> Vec :: F_global
>
> ! real(pREAL), dimension(3,3,cells(1),cells(2),cells3), intent(in) :: &
> ! F
> Mat :: Jac, Jac_pre
> PetscObject :: dummy
> PetscErrorCode :: err_PETSc
>
> print*, '@@ start build my jac'
>
> call MatCopy(Jac_PETSc,Jac,SAME_NONZERO_PATTERN,err_PETSc)
> CHKERRQ(err_PETSc)
> call MatCopy(Jac_PETSc,Jac_pre,SAME_NONZERO_PATTERN,err_PETSc)
> CHKERRQ(err_PETSc)
> ! Jac = Jac_PETSc
> ! Jac_pre = Jac_PETSc
>
> print*, '@@ end build my jac'
>
> end subroutine formJacobian
>
> it turns out that no matter by a simple assignment or MatCopy(), the compiled program gives me the same error as before. So I guess the real jacobian is still not set. I wonder how to get around this and let this built jac in formJacobian() to be the same as my shell matrix.
>
> Yi
>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Sent: Wednesday, January 10, 2024 4:27 PM
> To: Yi Hu <y.hu at mpie.de <mailto:y.hu at mpie.de>>
> Cc: petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] SNES seems not use my matrix-free operation
>
>
> By default if SNESSetJacobian() is not called with a function pointer PETSc attempts to compute the Jacobian matrix explicitly with finite differences and coloring. This doesn't makes sense with a shell matrix. Hence the error message below regarding MatFDColoringCreate().
>
> DMSNESSetJacobianLocal() calls SNESSetJacobian() with a function pointer of SNESComputeJacobian_DMLocal() so preventing the error from triggering in your code.
>
> You can provide your own function to SNESSetJacobian() and thus not need to call DMSNESSetJacobianLocal(). What you do depends on how you want to record the "base" vector that tells your matrix-free multiply routine where the Jacobian matrix vector product is being applied, that is J(u)*x. u is the "base" vector which is passed to the function provided with SNESSetJacobian().
>
> Barry
>
>
>
> On Jan 10, 2024, at 6:20 AM, Yi Hu <y.hu at mpie.de <mailto:y.hu at mpie.de>> wrote:
>
> Thanks for the clarification. It is more clear to me now about the global to local processes after checking the examples, e.g. ksp/ksp/tutorials/ex14f.F90.
>
> And for using Vec locally, I followed your advice of VecGet.. and VecRestore… In fact I used DMDAVecGetArrayReadF90() and some other relevant subroutines.
>
> For your comment on DMSNESSetJacobianLocal(). It seems that I need to use both SNESSetJacobian() and then DMSNESSetJacobianLocal() to get things working. When I do only SNESSetJacobian(), it does not work, meaning the following does not work
>
> ……
> call DMDASNESsetFunctionLocal(DM_mech,INSERT_VALUES,formResidual,PETSC_NULL_SNES,err_PETSc)
> CHKERRQ(err_PETSc)
> call MatCreateShell(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,&
> 9*product(cells(1:2))*cells3,9*product(cells(1:2))*cells3,&
> 0,Jac_PETSc,err_PETSc)
> CHKERRQ(err_PETSc)
> call MatShellSetOperation(Jac_PETSc,MATOP_MULT,GK_op,err_PETSc)
> CHKERRQ(err_PETSc)
> call SNESSetJacobian(SNES_mech,Jac_PETSc,Jac_PETSc,PETSC_NULL_FUNCTION,0,err_PETSc)
> CHKERRQ(err_PETSc)
> !call DMSNESsetJacobianLocal(DM_mech,formJacobian,PETSC_NULL_SNES,err_PETSc)
> !CHKERRQ(err_PETSc)
> call SNESsetConvergenceTest(SNES_mech,converged,PETSC_NULL_SNES,PETSC_NULL_FUNCTION,err_PETSc)
> CHKERRQ(err_PETSc)
> call SNESSetDM(SNES_mech,DM_mech,err_PETSc)
> CHKERRQ(err_PETSc)
> ……
>
> It gives me the message
> [0]PETSC ERROR: No support for this operation for this object type
> [0]PETSC ERROR: Code not yet written for matrix type shell
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.16.4, Feb 02, 2022
> [0]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu --with-fortran-bindings --with-mpi-f90module-visibility=0 --download-fftw --download-hdf5 --download-hdf5-fortran-bindings --download-fblaslapack --download-ml --download-zlib
> [0]PETSC ERROR: #1 MatFDColoringCreate() at /home/yi/app/petsc-3.16.4/src/mat/matfd/fdmatrix.c:471
> [0]PETSC ERROR: #2 SNESComputeJacobian_DMDA() at /home/yi/app/petsc-3.16.4/src/snes/utils/dmdasnes.c:173[0]PETSC ERROR: #3 SNESComputeJacobian() at /home/yi/app/petsc-3.16.4/src/snes/interface/snes.c:2864
> [0]PETSC ERROR: #4 SNESSolve_NEWTONLS() at /home/yi/app/petsc-3.16.4/src/snes/impls/ls/ls.c:222
> [0]PETSC ERROR: #5 SNESSolve() at /home/yi/app/petsc-3.16.4/src/snes/interface/snes.c:4809
> [0]PETSC ERROR: #6 User provided function() at User file:0
> [0]PETSC ERROR: #7 VecSetErrorIfLocked() at /home/yi/app/petsc-3.16.4/include/petscvec.h:623
> [0]PETSC ERROR: #8 VecGetArray() at /home/yi/app/petsc-3.16.4/src/vec/vec/interface/rvector.c:1769
> [0]PETSC ERROR: #9 User provided function() at User file:0
> [0]PETSC ERROR: #10 MatFDColoringCreate() at /home/yi/app/petsc-3.16.4/src/mat/matfd/fdmatrix.c:471
> [0]PETSC ERROR: #11 SNESComputeJacobian_DMDA() at /home/yi/app/petsc-3.16.4/src/snes/utils/dmdasnes.c:173
> [0]PETSC ERROR: #12 SNESComputeJacobian() at /home/yi/app/petsc-3.16.4/src/snes/interface/snes.c:2864
> [0]PETSC ERROR: #13 SNESSolve_NEWTONLS() at /home/yi/app/petsc-3.16.4/src/snes/impls/ls/ls.c:222
> [0]PETSC ERROR: #14 SNESSolve() at /home/yi/app/petsc-3.16.4/src/snes/interface/snes.c:4809
>
> It seems that I have to use a DMSNESSetJacobianLocal() to “activate” the use of my shell matrix, although the formJacobian() in the DMSNESSetJacobianLocal() is doing nothing.
>
> Best wishes,
> Yi
>
>
>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Sent: Tuesday, January 9, 2024 4:49 PM
> To: Yi Hu <y.hu at mpie.de <mailto:y.hu at mpie.de>>
> Cc: petsc-users <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] SNES seems not use my matrix-free operation
>
> However, my GK_op (which is the reloaded MATOP_MULT) gives me some problem. It is entered but then crashed with Segmentation Violation error. So I guess my indices may be wrong. I wonder do I need to use the local Vec (of dF), and should my output Vec also be in the correct shape (i.e. after calculation I need to transform back into a Vec)? As you can see here, my dF is a tensor defined on every grid point.
>
>
> The input for the matrix-vector product is a global vector, as is the result. (Not like the arguments to DMSNESSetJacobianLocal).
>
> This means that your MATOP_MULT function needs to do the DMGlobalToLocal() vector operation first then the "unwrapping" from the vector to the array format at the beginning of the routine. Similarly it needs to "unwrap" the result vector as an array. See src/snes/tutorials/ex14f.F90 and in particular the code block
>
> PetscCall(DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX,ierr))
> PetscCall(DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX,ierr))
>
> ! Get pointers to vector data
>
> PetscCall(VecGetArrayReadF90(localX,xx,ierr))
> PetscCall(VecGetArrayF90(F,ff,ierr))
>
> Barry
>
> You really shouldn't be using DMSNESSetJacobianLocal() for your code. Basically all the DMSNESSetJacobianLocal() gives you is that it automatically handles the global to local mapping and unwrapping of the vector to an array, but it doesn't work for shell matrices.
>
>
>
>
> On Jan 9, 2024, at 6:30 AM, Yi Hu <y.hu at mpie.de <mailto:y.hu at mpie.de>> wrote:
>
> Dear Barry,
>
> Thanks for your help.
>
> It works when doing first SNESSetJacobian() with my created shell matrix Jac in the main (or module) and then DMSNESSetJacobianLocal() to associate with my DM and an dummy formJacobian callback (which is doing nothing). My SNES can now recognize my shell matrix and do my customized operation.
>
> However, my GK_op (which is the reloaded MATOP_MULT) gives me some problem. It is entered but then crashed with Segmentation Violation error. So I guess my indices may be wrong. I wonder do I need to use the local Vec (of dF), and should my output Vec also be in the correct shape (i.e. after calculation I need to transform back into a Vec)? As you can see here, my dF is a tensor defined on every grid point.
>
> Best wishes,
> Yi
>
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Sent: Monday, January 8, 2024 6:41 PM
> To: Yi Hu <y.hu at mpie.de <mailto:y.hu at mpie.de>>
> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>
> Subject: Re: [petsc-users] SNES seems not use my matrix-free operation
>
>
> "formJacobian" should not be __creating__ the matrices. Here "form" means computing the numerical values in the matrix (or when using a shell matrix it means keeping a copy of X so that your custom matrix-free multiply knows the base location where the matrix free Jacobian-vector products are computed.)
>
> You create the shell matrices up in your main program and pass them in with SNESSetJacobian().
>
> Try first calling SNESSetJacobian() to provide the matrices (provide a dummy function argument) and then call DMSNESSetJacobianLocal() to provide your "formjacobian" function (that does not create the matrices).
>
> Barry
>
>
> Yes, "form" is a bad word that should not have been used in our code.
>
>
>
>
>
>
> On Jan 8, 2024, at 12:24 PM, Yi Hu <y.hu at mpie.de <mailto:y.hu at mpie.de>> wrote:
>
> Dear PETSc Experts,
>
> I am implementing a matrix-free jacobian for my SNES solver in Fortran. (command line option -snes_type newtonls -ksp_type gmres)
>
> In the main program, I define my residual and jacobian and matrix-free jacobian like the following,
>
> …
> call DMDASNESSetFunctionLocal(DM_mech, INSERT_VALUES, formResidual, PETSC_NULL_SNES, err_PETSc)
> call DMSNESSetJacobianLocal(DM_mech, formJacobian, PETSC_NULL_SNES, err_PETSc)
> …
>
> subroutine formJacobian(residual_subdomain,F,Jac_pre,Jac,dummy,err_PETSc)
>
> #include <petsc/finclude/petscmat.h>
> use petscmat
> implicit None
> DMDALocalInfo, dimension(DMDA_LOCAL_INFO_SIZE) :: &
> residual_subdomain !< DMDA info (needs to be named "in" for macros like XRANGE to work)
> real(pREAL), dimension(3,3,cells(1),cells(2),cells3), intent(in) :: &
> F !< deformation gradient field
> Mat :: Jac, Jac_pre
> PetscObject :: dummy
> PetscErrorCode :: err_PETSc
> PetscInt :: N_dof ! global number of DoF, maybe only a placeholder
>
> N_dof = 9*product(cells(1:2))*cells3
>
> print*, 'in my jac'
>
> call MatCreateShell(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,N_dof,N_dof,0,Jac,err_PETSc)
> CHKERRQ(err_PETSc)
> call MatShellSetOperation(Jac,MATOP_MULT,GK_op,err_PETSc)
> CHKERRQ(err_PETSc)
>
> print*, 'in my jac'
>
> ! for jac preconditioner
> call MatCreateShell(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,N_dof,N_dof,0,Jac_pre,err_PETSc)
> CHKERRQ(err_PETSc)
> call MatShellSetOperation(Jac_pre,MATOP_MULT,GK_op,err_PETSc)
> CHKERRQ(err_PETSc)
>
> print*, 'in my jac'
>
> end subroutine formJacobian
>
> subroutine GK_op(Jac,dF,output,err_PETSc)
> real(pREAL), dimension(3,3,cells(1),cells(2),cells3), intent(in) :: &
> dF
> real(pREAL), dimension(3,3,cells(1),cells(2),cells3), intent(out) :: &
> output
> real(pREAL), dimension(3,3) :: &
> deltaF_aim = 0.0_pREAL
>
> Mat :: Jac
> PetscErrorCode :: err_PETSc
>
> integer :: i, j, k, e
>
> … a lot of calculations …
>
> print*, 'in GK op'
>
> end subroutine GK_op
>
> The first question is that: it seems I still need to explicitly define the interface of MatCreateShell() and MatShellSetOperation() to properly use them, even though I include them via “use petscmat”. It is a little bit strange to me, since some examples do not perform this step.
>
> Then the main issue is that I can build my own Jacobian from my call back function formJacobian, and confirm my Jacobian is a shell matrix (by MatView). However, my customized operator GK_op is not called when solving the nonlinear system (not print my “in GK op”). When I try to monitor my SNES, it gives me some conventional output not mentioning my matrix-free operations. So I guess my customized MATOP_MULT may be not associated with Jacobian. Or my configuration is somehow wrong. Could you help me solve this issue?
>
> Thanks,
> Yi
>
>
>
>
>
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> D-40237 Düsseldorf
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> Handelsregister B 2533
> Amtsgericht Düsseldorf
>
> Geschäftsführung
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> D-40237 Düsseldorf
>
> Handelsregister B 2533
> Amtsgericht Düsseldorf
>
> Geschäftsführung
> Prof. Dr. Gerhard Dehm
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