[petsc-users] snes matrix-free jacobian fails with preconditioner shape mismatch

Mon Mar 11 07:10:57 CDT 2024

I think you misunderstand "global" vector. The global solution is never on
one processor. A global vector in this case seems to have 81 global values
and 27 local values.
It looks like you create a "global" vector that has 81 local values that
should never be created other than for debigging.
GlobalToLocal refers to a "local" vector with ghost cells, so it would have
> 27 values in this case and you use it for local operations only (its
communicator is PETSC_COMM_SELF).
Hope this helps,
Mark

On Mon, Mar 11, 2024 at 4:48 AM Yi Hu <y.hu at mpie.de> wrote:

> Dear Barry,
>
>
>
> Thanks for your response. Now I am doing simple debugging for my
> customized mat_mult_op of my shell jacobian matrix. As far as I understand,
> because the input and output of shell jacobian are all global vectors, I
> need to do the global to local mapping of my input vector (dF) by myself.
> Before starting debugging the mapping, I first try to verify the size match
> of input and output.
>
>
>
> Because the input and output of a mat_mult_op of my shell matrix should
> have the same size. So I tried just equating them in my customized
> mat_mult_op. Basically like this
>
>
>
> subroutine GK_op(Jac,dF_global,output_global,err_PETSc)
>
>
>
>   DM                                   :: dm_local ! Yi: later for is,ie
>
>   Vec                                  :: dF_global
>
>   Vec                                  :: output_global
>
>   PetscErrorCode                       :: err_PETSc
>
>
>
>   real(pREAL), pointer,dimension(:,:,:,:) :: dF_scal, output_scal
>
>
>
>   call SNESGetDM(SNES_mech,dm_local,err_PETSc)
>
>   CHKERRQ(err_PETSc)
>
>
>
>   output_global = dF_global
>
>
>
> end subroutine GK_op
>
>
>
> When I run with mpirun -np 3, it gives me similar error like previous,
> “Preconditioner number of local rows 27 does not equal input vector size
> 81”, (I changed my problem size so the numbers are different).
>
>
>
> Maybe simple equating input and output is not valid (due to ownership of
> different portion of a global vector). Then it may give me different error
> message. In fact my global dF has size 9*3*3*3, when running on 3
> processors, the local dF has size 9*3*3*1 (I split my domain in z
> direction). The error message seems to suggest I am using a local dF rather
> than a global dF. And the output and input vector sizes seems to be
> different. Do I miss something here?
>
>
>
> Best regards,
>
> Yi
>
>
>
>
>
> *From:* Barry Smith <bsmith at petsc.dev>
> *Sent:* Sunday, March 10, 2024 6:45 PM
> *To:* Yi Hu <y.hu at mpie.de>
> *Cc:* Mark Adams <mfadams at lbl.gov>; petsc-users <petsc-users at mcs.anl.gov>
> *Subject:* Re: [petsc-users] snes matrix-free jacobian fails with
> preconditioner shape mismatch
>
>
>
>
>
>
>
> On Mar 10, 2024, at 10:16 AM, Yi Hu <y.hu at mpie.de> wrote:
>
>
>
> This Message Is From an External Sender
>
> This message came from outside your organization.
>
> Dear Mark,
>
> Thanks for your reply. I see this mismatch. In fact my global DoF is 324.
> It seems like I always get the local size = global Dof / np^2, np is my
> processor number. By the way, I used DMDASNESsetFunctionLocal() to set my
> form function. Is it eligible to mix DMDASNESsetFunctionLocal() and a
> native SNESSetJacobian()?
>
>
>
> Yes
>
>
>
> Best,
>
> Yi
>
> On 3/10/24 13:55, Mark Adams wrote:
>
> It looks like your input vector is the global vector, size 162, and the local matrix size is 81.
>
> Mark
>
> [1]PETSC ERROR: Preconditioner number of local rows 81 does not equal
>
> input vector size 162
>
>
>
> On Sun, Mar 10, 2024 at 7:21 AM Yi Hu <y.hu at mpie.de> wrote:
>
> *This Message Is From an External Sender *
>
> This message came from outside your organization.
>
>
>
> Dear petsc team,
>
>
>
> I implemented a matrix-free jacobian, and it can run sequentially. But
>
> running parallel I got the pc error like this (running with mpirun -np
>
> 2, only error from rank1 is presented here)
>
>
>
> [1]PETSC ERROR: --------------------- Error Message
>
> --------------------------------------------------------------
>
> [1]PETSC ERROR: Nonconforming object sizes
>
> [1]PETSC ERROR: Preconditioner number of local rows 81 does not equal
>
> input vector size 162
>
> [1]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ahmistzr4wD3TJ0OvI0JWxB9aVSIbP78Jcs2X_6KMb4LdoR8drLB_DkHvaguhrca22RgFer0PlyUrtdfCA$ <https://urldefense.us/v3/__https:/petsc.org/release/faq/__;!!G_uCfscf7eWS!ahmistzr4wD3TJ0OvI0JWxB9aVSIbP78Jcs2X_6KMb4LdoR8drLB_DkHvaguhrca22RgFer0PlyUrtdfCA$> for trouble shooting.
>
> [1]PETSC ERROR: Petsc Release Version 3.17.3, Jun 29, 2022
>
> [1]PETSC ERROR: /home/yi/workspace/DAMASK_yi/bin/DAMASK_grid on a
>
> arch-linux-c-opt named carbon-x1 by yi Sun Mar 10 12:01:46 2024
>
> [1]PETSC ERROR: Configure options --download-fftw --download-hdf5
>
> --with-hdf5-fortran-bindings --download-fblaslapack --download-chaco
>
> --download-hypre --download-metis --download-mumps --download-parmetis
>
> --download-scalapack --download-suitesparse --download-superlu
>
> --download-superlu_dist --download-triangle --download-zlib
>
> --download-cmake --with-cxx-dialect=C++11 --with-c2html=0
>
> --with-debugging=0 --with-ssl=0 --with-x=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
>
> FOPTFLAGS=-O3
>
> [1]PETSC ERROR: #1 PCApply() at
>
> /home/yi/App/petsc-3.17.3/src/ksp/pc/interface/precon.c:424
>
> [1]PETSC ERROR: #2 KSP_PCApply() at
>
> /home/yi/App/petsc-3.17.3/include/petsc/private/kspimpl.h:376
>
> [1]PETSC ERROR: #3 KSPInitialResidual() at
>
> /home/yi/App/petsc-3.17.3/src/ksp/ksp/interface/itres.c:64
>
> [1]PETSC ERROR: #4 KSPSolve_GMRES() at
>
> /home/yi/App/petsc-3.17.3/src/ksp/ksp/impls/gmres/gmres.c:242
>
> [1]PETSC ERROR: #5 KSPSolve_Private() at
>
> /home/yi/App/petsc-3.17.3/src/ksp/ksp/interface/itfunc.c:902
>
> [1]PETSC ERROR: #6 KSPSolve() at
>
> /home/yi/App/petsc-3.17.3/src/ksp/ksp/interface/itfunc.c:1078
>
> [1]PETSC ERROR: #7 SNESSolve_NEWTONLS() at
>
> /home/yi/App/petsc-3.17.3/src/snes/impls/ls/ls.c:222
>
> [1]PETSC ERROR: #8 SNESSolve() at
>
> /home/yi/App/petsc-3.17.3/src/snes/interface/snes.c:4756
>
> [1]PETSC ERROR: #9 User provided function() at User file:0
>
>
>
> However, from snes matrix-free documentation
>
> (https://urldefense.us/v3/__https://petsc.org/release/manual/snes/*matrix-free-methods__;Iw!!G_uCfscf7eWS!ahmistzr4wD3TJ0OvI0JWxB9aVSIbP78Jcs2X_6KMb4LdoR8drLB_DkHvaguhrca22RgFer0Ply6ZbywOw$ <https://urldefense.us/v3/__https:/petsc.org/release/manual/snes/*matrix-free-methods__;Iw!!G_uCfscf7eWS!ahmistzr4wD3TJ0OvI0JWxB9aVSIbP78Jcs2X_6KMb4LdoR8drLB_DkHvaguhrca22RgFer0Ply6ZbywOw$>), it is said
>
> matrix-free is used with pcnone. So I assume it would not apply
>
> preconditioner, but it did use preconditioning probably the same as my
>
> matrix-free shell matrix. Here is how i initialize my shell matrix and
>
> the corresponding customized multiplication.
>
>
>
>    call MatCreateShell(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,&
>
> int(9*product(cells(1:2))*cells3,pPETSCINT),&
>
> int(9*product(cells(1:2))*cells3,pPETSCINT),&
>
>                        F_PETSc,Jac_PETSc,err_PETSc)
>
>    call MatShellSetOperation(Jac_PETSc,MATOP_MULT,GK_op,err_PETSc)
>
>    call SNESSetDM(SNES_mech,DM_mech,err_PETSc)
>
>    call
>
> SNESSetJacobian(SNES_mech,Jac_PETSc,Jac_PETSc,PETSC_NULL_FUNCTION,0,err_PETSc)
>
>    call SNESGetKSP(SNES_mech,ksp,err_PETSc)
>
>    call PCSetType(pc,PCNONE,err_PETSc)
>
>
>
> And my GK_op is like
>
>
>
> subroutine GK_op(Jac,dF_global,output_local,err_PETSc)
>
>
>
>    DM                                   :: dm_local
>
>    Vec                                  :: dF_global, dF_local, output_local
>
>    Mat                                  :: Jac
>
>    PetscErrorCode                       :: err_PETSc
>
>
>
>    real(pREAL), pointer,dimension(:,:,:,:) :: dF_scal, output_scal
>
>
>
>    real(pREAL), dimension(3,3,cells(1),cells(2),cells3) :: &
>
>      dF
>
>    real(pREAL), dimension(3,3,cells(1),cells(2),cells3) :: &
>
>      output
>
>
>
>    call SNESGetDM(SNES_mech,dm_local,err_PETSc)
>
>
>
>    call DMGetLocalVector(dm_local,dF_local,err_PETSc)
>
>    call
>
> DMGlobalToLocalBegin(dm_local,dF_global,INSERT_VALUES,dF_local,err_PETSc)
>
>    call
>
> DMGlobalToLocalEnd(dm_local,dF_global,INSERT_VALUES,dF_local,err_PETSc)
>
>
>
>    call DMDAVecGetArrayReadF90(dm_local,dF_local,dF_scal,err_PETSc)
>
>    dF = reshape(dF_scal, [3,3,cells(1),cells(2),cells3])
>
>
>
> .......
>
>
>
>
>
>    call DMDAVecRestoreArrayF90(dm_local,output_local,output_scal,err_PETSc)
>
>    CHKERRQ(err_PETSc)
>
>
>
>    call DMDAVecRestoreArrayF90(dm_local,dF_local,dF_scal,err_PETSc)
>
>    CHKERRQ(err_PETSc)
>
>
>
> end subroutine GK_op
>
>
>
> I checked my cells3, it corresponds to my local size, and it seems the
>
> local size of dF_local is ok.
>
>
>
> I am a bit lost here to find the reason for the preconditioner bug.
>
> Could you help me on this? Thanks.
>
>
>
> Best regards,
>
>
>
> Yi
>
>
>
>
>
>
>
>
>
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>
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>
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> Steuernummer: 105 5891 1000
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>
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>
> Handelsregister B 2533
> Amtsgericht Düsseldorf
>
> Geschäftsführung
> Prof. Dr. Gerhard Dehm
> Prof. Dr. Jörg Neugebauer
> Prof. Dr. Dierk Raabe
> Dr. Kai de Weldige
>
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