[petsc-users] SNES seems not use my matrix-free operation

Tue Jan 16 03:47:52 CST 2024

Dear Barry,

Thanks for your reply. In fact, this still does not work, giving the error “code not yet written for matrix type shell”. I also tried recording F_global as base in my global shell matrix Jac_PETSc. And fetch it in my GK_op, but the same error occurs. So the question is still, how can I assign the Jac in my formJacobian() to my global defined Jac_PETSc when set up with SNESSetJacobian(snes,Jac_PETSc,Jac_PETSc,formJacobian,0,ierr). As far as I understand, when using SNESSetJacobian() the jac argument is only for reserving memory. And the matrix is not written yet. Only a valid formJacobian() can lead to a write to the matrix. My formJacobian maybe not valid (because the output not gives me print), so the Jac_PETSc is never written for the SNES. Maybe I am wrong about it.  

Best wishes,
Yi

From: Barry Smith <bsmith at petsc.dev> 
Sent: Thursday, January 11, 2024 4:47 PM
To: Yi Hu <y.hu at mpie.de>
Cc: petsc-users <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] SNES seems not use my matrix-free operation

   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> 
Sent: Wednesday, January 10, 2024 4:27 PM
To: Yi Hu <y.hu at mpie.de>
Cc: petsc-users <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> 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> 
Sent: Tuesday, January 9, 2024 4:49 PM
To: Yi Hu <y.hu at mpie.de>
Cc: petsc-users <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> 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> 
Sent: Monday, January 8, 2024 6:41 PM
To: Yi Hu <y.hu at mpie.de>
Cc: 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> 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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