Build a PETSC_ARCH with -with-debugging=yes as a configure option and run it, preferably in a debugger (for example -start_in_debugger option) to find out where the bus error is taking place.
> On Sep 18, 2025, at 4:42 PM, Riousset, Jeremy via petsc-users > <[email protected]> wrote: > > That helped. I now read my input file correctly. I am getting an error with > the line below: > > DM da; > ierr = > DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DM_BOUNDARY_GHOSTED,DMDA_STENCIL_STAR,21,21,21,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,19,1,PETSC_NULL,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr); > > The error is: > 0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal > memory access > [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!fh2X84CPIXKaFn6PkQPhrXJHX2qplg9tKOZ5R9PVc5RWTkcgK4phevcVoO3P_YgU5vu4GZREF8o52gfFFZ4W1b0$ > > <https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!drLsYfgMTCNAyHHkj7gJrIUzQ9gnkjwyajLeWWqLLyV3mEdA2B7X0fX4pFYTyw9FVWpCJQ7BKm4Ba2f-wE5DJLwP$> > and > https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!fh2X84CPIXKaFn6PkQPhrXJHX2qplg9tKOZ5R9PVc5RWTkcgK4phevcVoO3P_YgU5vu4GZREF8o52gfFoqV6M1A$ > > <https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!drLsYfgMTCNAyHHkj7gJrIUzQ9gnkjwyajLeWWqLLyV3mEdA2B7X0fX4pFYTyw9FVWpCJQ7BKm4Ba2f-wJxIkrms$> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is > causing the crash. > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > Proc: [[44836,1],0] > Errorcode: 59 > > Since the code was running with an old version of PETSc, I am wondering what > I did to break it. > > Jeremy A. Riousset, Ph.D. (he, him, his) > Associate Professor of Engineering Physics > Physical Science > > 1 Aerospace Boulevard > Daytona Beach, FL 32114 > +1 (386) 226-6407 > [email protected] <mailto:[email protected]> > https://urldefense.us/v3/__https://orcid.org/0000-0003-1516-5337__;!!G_uCfscf7eWS!fh2X84CPIXKaFn6PkQPhrXJHX2qplg9tKOZ5R9PVc5RWTkcgK4phevcVoO3P_YgU5vu4GZREF8o52gfFDu9pfak$ > > <https://urldefense.us/v3/__https://orcid.org/0000-0003-1516-5337__;!!G_uCfscf7eWS!drLsYfgMTCNAyHHkj7gJrIUzQ9gnkjwyajLeWWqLLyV3mEdA2B7X0fX4pFYTyw9FVWpCJQ7BKm4Ba2f-wPlXko4P$> > Embry-Riddle Aeronautical University > Florida | Arizona | Worldwide > > >> On Sep 18, 2025, at 3:59 PM, Barry Smith <[email protected]> wrote: >> >> External Sender: Use caution with links, attachments, or when sharing >> information. >> >> >> The PETSc options all begin with a single dash, so it is -options_file >> input/main.in >> >>> On Sep 18, 2025, at 3:44 PM, Riousset, Jeremy via petsc-users >>> <[email protected]> wrote: >>> >>> Hi, >>> >>> I’m updating a code from PETSc 3.4 to run with the latest PETSc. Here is my >>> status: >>> I read the parameters via: mpiexec -n 1 bin/./M4 --options_file >>> input/main.in >>> I’m not opening main.in correctly >>> None of the options are retrieved by e.g., PetscOptionsGetReal >>> Do you have a suggestion to test what file the code is actually trying to >>> access? >>> >>> Thanks >>> >>> Jeremy A. Riousset, Ph.D. (he, him, his) >>> Associate Professor of Engineering Physics >>> Physical Science >>> >>> 1 Aerospace Boulevard >>> Daytona Beach, FL 32114 >>> +1 (386) 226-6407 >>> [email protected] <mailto:[email protected]> >>> https://urldefense.us/v3/__https://orcid.org/0000-0003-1516-5337__;!!G_uCfscf7eWS!fh2X84CPIXKaFn6PkQPhrXJHX2qplg9tKOZ5R9PVc5RWTkcgK4phevcVoO3P_YgU5vu4GZREF8o52gfFDu9pfak$ >>> >>> <https://urldefense.us/v3/__https://orcid.org/0000-0003-1516-5337__;!!G_uCfscf7eWS!YiGxTKiNGs8EnS4pzFoO1YK18z4fx-sCtisUBloRO8dd6sUuh3kfUkimanAH5cJ-jgPhYw-Qk_8q8BBxAtPO0s_6$> >>> Embry-Riddle Aeronautical University >>> Florida | Arizona | Worldwide >>> >>> >> >
