[petsc-users] SNES seems not use my matrix-free operation
Yi Hu
y.hu at mpie.de
Wed Jan 10 05:20:19 CST 2024
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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Stay up to date and follow us on LinkedIn, Twitter and YouTube.
Max-Planck-Institut für Eisenforschung GmbH
Max-Planck-Straße 1
D-40237 Düsseldorf
Handelsregister B 2533
Amtsgericht Düsseldorf
Geschäftsführung
Prof. Dr. Gerhard Dehm
Prof. Dr. Jörg Neugebauer
Prof. Dr. Dierk Raabe
Dr. Kai de Weldige
Ust.-Id.-Nr.: DE 11 93 58 514
Steuernummer: 105 5891 1000
Please consider that invitations and e-mails of our institute are
only valid if they end with …@mpie.de.
If you are not sure of the validity please contact rco at mpie.de
Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails
aus unserem Haus nur mit der Endung …@mpie.de gültig sind.
In Zweifelsfällen wenden Sie sich bitte an rco at mpie.de
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Stay up to date and follow us on LinkedIn, Twitter and YouTube.
Max-Planck-Institut für Eisenforschung GmbH
Max-Planck-Straße 1
D-40237 Düsseldorf
Handelsregister B 2533
Amtsgericht Düsseldorf
Geschäftsführung
Prof. Dr. Gerhard Dehm
Prof. Dr. Jörg Neugebauer
Prof. Dr. Dierk Raabe
Dr. Kai de Weldige
Ust.-Id.-Nr.: DE 11 93 58 514
Steuernummer: 105 5891 1000
Please consider that invitations and e-mails of our institute are
only valid if they end with …@mpie.de.
If you are not sure of the validity please contact rco at mpie.de
Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails
aus unserem Haus nur mit der Endung …@mpie.de gültig sind.
In Zweifelsfällen wenden Sie sich bitte an rco at mpie.de
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