Re: [petsc-users] Example of SNES using matrix free jacobian

[Daniel Pino Munoz]

That's what I thought, so I replaced its content by:

VecZeroEntries(f);

and the result is the same...


On 29/10/2024 21:31, Barry Smith wrote:

   This
   [0]PETSC ERROR: #1 SNES callback function
    indicates the crash is in your computeResidual function and thus you need 
to debug your function

    Barry

On Oct 29, 2024, at 4:28 PM, Daniel Pino Munoz 
<daniel.pino_mu...@mines-paristech.fr> wrote:

I ran it with -malloc_debug and it does not change anything.

The output is the following:

he absolute tolerance is 0.001
The relative tolerance is 0.001
The divergence tolerance is 10000
The maximum iterations is 10000
Initial load !
[0]PETSC ERROR: 
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!Z0ifVNZaie3VDyNzpdW9w-vk0Aw1cEjqvlrJcp_-d2R06pFj_9PAlB2x6azoU8bjbqzaGXlVlziswk5eBSowDWMil2MSKYzGXNx6bzkEpw$ and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!Z0ifVNZaie3VDyNzpdW9w-vk0Aw1cEjqvlrJcp_-d2R06pFj_9PAlB2x6azoU8bjbqzaGXlVlziswk5eBSowDWMil2MSKYzGXNxyzMy5Zw$ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------

[0]PETSC ERROR: The line numbers in the error traceback are not always exact.
[0]PETSC ERROR: #1 SNES callback function
[0]PETSC ERROR: #2 SNESComputeFunction() at 
/home/daniel-pino/Software/Dependencies/petsc/src/snes/interface/snes.c:2489
[0]PETSC ERROR: #3 SNESSolve_KSPONLY() at 
/home/daniel-pino/Software/Dependencies/petsc/src/snes/impls/ksponly/ksponly.c:27
[0]PETSC ERROR: #4 SNESSolve() at 
/home/daniel-pino/Software/Dependencies/petsc/src/snes/interface/snes.c:4841
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
   Proc: [[27669,1],0]
   Errorcode: 59

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------



On 29/10/2024 20:17, Barry Smith wrote:

    Hmm, cut and paste the output when it crashes.

     Also run with -malloc_debug and see what happens


     Barry

On Oct 29, 2024, at 3:13 PM, Daniel Pino Munoz 
<daniel.pino_mu...@mines-paristech.fr> wrote:

Hi Barry,

Thanks for getting back to me!

I tried replacing KSPSetOperators(ksp, J, J); by SNESSetJacobian(snes,J,J, 
MatMFFDComputeJacobian)

and I get the same result = It works in Debug mode but not in Release. I also 
ran valgrind and it did not catch any memory problem.

Any ideas?

PS : You are right regarding the number of iterations of the non preconditioned 
problem. In the previous version of the code that only used a KSP, I already 
had to set -ksp_gmres_restart 100. But thanks for the heads up.

Best,

   Daniel

On 29/10/2024 20:01, Barry Smith wrote:

    Don't call

    KSPSetOperators(ksp, J, J);


     instead call

     SNESSetJacobian(snes,J,J, MatMFFDComputeJacobian)

     but I am not sure that would explain the crash.

     BTW: since you are applying no preconditioner if the matrix is 
ill-conditioned it may take many iterations or not converge. You can try 
something like -ksp_gmres_restart 100 or similar value to try to improve 
convergence (default is 30).

     Barry

On Oct 29, 2024, at 12:37 PM, Daniel Pino Munoz 
<daniel.pino_mu...@mines-paristech.fr> wrote:

Dear all,

I have a linear problem that I am currently solving with a KSP matrix-free.

I would like to move on to a non linear problem, so figure I could start by 
solving the same linear problem using SNES. So I am setting the problem as 
follows:

SNESCreate(PETSC_COMM_WORLD, &snes);
MatCreateShell(PETSC_COMM_WORLD, n_dofs, n_dofs, PETSC_DETERMINE, PETSC_DETERMINE, 
&ctx, &J);
MatCreateShell(PETSC_COMM_WORLD, n_dofs, n_dofs, PETSC_DETERMINE, PETSC_DETERMINE, 
&ctx, &B);
MatShellSetOperation(J, MATOP_MULT, (void (*)(void))(Multiplication));
MatCreateVecs(J, &x_sol, &b);
VecDuplicate(x_sol, &r);
SNESSetFromOptions(snes);
SNESSetFunction(snes, r, &(computeResidual), &ctx);
SNESSetUseMatrixFree(snes, PETSC_FALSE, PETSC_TRUE);
SNESGetLineSearch(snes, &linesearch);
SNESGetKSP(snes, &ksp);
KSPSetOperators(ksp, J, J);
KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);

I tested it with a small problem (compiled in debug) and it works.

When I compiled it in Release, it crashes with a segfault. I tried running the 
Debug version through valgrind, but even for a small problem, it is too slow. 
So I was wondering if you guys could see any rocky mistake on the lines I used 
above?

Otherwise, is there any example that uses a SNES combined with a matrix free 
KSP operator?

Thank you,

   Daniel