Run in the debugger, even though there will not be full debugging support with the optimizations it should still provide you some information
> On Oct 29, 2024, at 4:35 PM, Daniel Pino Munoz > <daniel.pino_mu...@mines-paristech.fr> wrote: > > 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!dibDYt_ZFa-6FBchlzMndWYg1NqvsEIZOJlfOEQkpzMOqyVUFiiumr5JERY5e-jjXiKd8sI5HQxEi-65JQwqWxc$ >>> and >>> https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dibDYt_ZFa-6FBchlzMndWYg1NqvsEIZOJlfOEQkpzMOqyVUFiiumr5JERY5e-jjXiKd8sI5HQxEi-65GdSV720$ >>> >>> [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 >>>>>>>
