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

[Daniel Pino Munoz]

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!ecHZVRiYJFEV3Ru8URyFbEGJ2vXQ2KQNNyMC0E_KEclprR38CfKltYBqj_PQOatAvKs-QLz5Xh161SwNgfph8H2kFhfcV5HZZemMgh7IVw$  and 
https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ecHZVRiYJFEV3Ru8URyFbEGJ2vXQ2KQNNyMC0E_KEclprR38CfKltYBqj_PQOatAvKs-QLz5Xh161SwNgfph8H2kFhfcV5HZZekrkUwXlA$ 
[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_munoz at 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_munoz at 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
>>>>