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!eQxllmSvw4WuVrXfPz5uK3h9cSjVYg1fCeWM8bhtm4NwaGhghQVhAMg18ppPqOQxe2lkX-UQyOXgJx91MV6-KqE$ > and > https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!eQxllmSvw4WuVrXfPz5uK3h9cSjVYg1fCeWM8bhtm4NwaGhghQVhAMg18ppPqOQxe2lkX-UQyOXgJx910VEZbZQ$ > > [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 >>>>>
