[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_munoz at 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_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
>>>>>>