[petsc-users] Caught signal number 11 SEGV
Junchao Zhang
junchao.zhang at gmail.com
Tue Feb 23 20:31:46 CST 2021
Francesco,
If you want to debug the code, why don't you build petsc and your code
in debug mode so that you can see the full error stack?
My favorite debugger is ddt. If not available, then I will try
https://github.com/Azrael3000/tmpi. No need to set DISPLAY. But the
constraint is you have to use OpenMPI.
--Junchao Zhang
On Tue, Feb 23, 2021 at 2:55 PM Francesco Brarda <brardafrancesco at gmail.com>
wrote:
> Thank you for the quick response.
> Sorry, you are right. Here is the complete output:
>
> fbrarda at srvulx13:~/cmdstan-petsc$ $PETSC_DIR/$PETSC_ARCH/bin/mpirun -n
> 2 examples/rosenbrock/rosenbrock optimize -start_in_debugger
> PETSC: Attaching gdb to examples/rosenbrock/rosenbrock of pid 47803
> on display :0.0 on machine srvulx13
> PETSC: Attaching gdb to examples/rosenbrock/rosenbrock of pid 47804
> on display :0.0 on machine srvulx13
> xterm: Xt error: Can't open display: :0.0
> xterm: DISPLAY is not set
> xterm: Xt error: Can't open display: :0.0
> xterm: DISPLAY is not set
> method = optimize
> optimize
> algorithm = lbfgs (Default)
> lbfgs
> method = optimize
> optimize
> algorithm = lbfgs (Default)
> lbfgs
> init_alpha = 0.001 (Default)
> tol_obj = 9.9999999999999998e-13 (Default)
> tol_rel_obj = 10000 (Default)
> tol_grad = 1e-08 (Default)
> init_alpha = 0.001 (Default)
> tol_obj = 9.9999999999999998e-13 (Default)
> tol_rel_obj = 10000 (Default)
> tol_grad = 1e-08 (Default)
> tol_rel_grad = 10000000 (Default)
> tol_param = 1e-08 (Default)
> history_size = 5 (Default)
> tol_rel_grad = 10000000 (Default)
> tol_param = 1e-08 (Default)
> history_size = 5 (Default)
> iter = 2000 (Default)
> iter = 2000 (Default)
> save_iterations = 0 (Default)
> id = 0 (Default)
> data save_iterations = 0 (Default)
> id = 0 (Default)
> data
> file = (Default)
>
> file = (Default)
> init = 2 (Default)
> random
> seed = 3585768430 (Default)
> init = 2 (Default)
> random
> seed = 3585768430 (Default)
> output
> file = output.csv (Default)
> output
> file = output.csv (Default)
> diagnostic_file = (Default)
> refresh = 100 (Default)
> diagnostic_file = (Default)
> refresh = 100 (Default)
>
>
> Initial log joint probability = -731.444
> Iter log prob ||dx|| ||grad|| alpha
> alpha0 # evals Notes
> [1]PETSC ERROR: PetscAbortErrorHandler: main() line 12
> in src/cmdstan/main.cpp
> To prevent termination, change the error handler
> using PetscPushErrorHandler()
>
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = PID 47804 RUNNING AT srvulx13
> = EXIT CODE: 134
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
>
>
>
>
>
> The code inside main.cpp is the following:
>
> #include <cmdstan/command.hpp>
> #include <stan/services/error_codes.hpp>
>
> #include <petsc.h>
>
> int main(int argc, char* argv[]) {
>
> PetscErrorCode ierr;
> ierr = PetscInitialize(&argc, &argv, 0, 0);CHKERRQ(ierr);
>
> try {
> ierr = cmdstan::command(argc, argv);CHKERRQ(ierr);
> } catch (const std::exception& e) {
> std::cout << e.what() << std::endl;
> ierr = stan::services::error_codes::SOFTWARE;CHKERRQ(ierr);
> }
>
> ierr = PetscFinalize();CHKERRQ(ierr);
> return ierr;
> }
>
> I highlighted the line 12. Although I read the page where the command
> PetscPushErrorHandler is explained and the example provided
> (src/ksp/ksp/tutorials/ex27.c), I do not understand how I should
> effectively use the command.
> Should I change the entire try/catch with PetscPushErrorHandler(
> PetscIgnoreErrorHandler,NULL); ?
>
> Best,
> Francesco
>
>
> Il giorno 23 feb 2021, alle ore 11:54, Matthew Knepley <knepley at gmail.com>
> ha scritto:
>
> On Tue, Feb 23, 2021 at 3:54 AM Francesco Brarda <
> brardafrancesco at gmail.com> wrote:
> Hi!
>
> I am very new to the PETSc world. I am working with a GitHub repo that
> uses PETSc together with Stan (a statistics open source software), here you
> can find the discussion.
> It has been defined a functor to convert EigenVector to PetscVec and
> viceversa, both sequentially and in parallel.
> The file using these functions does the conversions with the sequential
> setting. I changed to those using MPI, that is
> from EigenVectorToPetscVecSeq to EigenVectorToPetscVecMPI and so on because
> I want to evaluate the scaling.
> Running the example with mpirun -n 5 examples/rosenbrock/rosenbrock
> optimize in the debug mode I get the error Caught signal number 11 SEGV. I
> therefore used the option -start_in_debugger and I get the following:
>
> For some reason, the -start_in_debuggger option is not being seen. Are you
> showing all the output? Once the debugger is attached,
> you run the program (conr) and then when you hit the SEGV you get a stack
> trace (where).
>
> THanks,
>
> Matt
>
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [2]PETSC ERROR: or see
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [2]PETSC ERROR: likely location of problem given in stack below
> [2]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [2]PETSC ERROR: INSTEAD the line number of the start of the function
> [2]PETSC ERROR: is given.
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [3]PETSC ERROR: or see
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> [3]PETSC ERROR: likely location of problem given in stack below
> [3]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,
> [3]PETSC ERROR: INSTEAD the line number of the start of the function
> [3]PETSC ERROR: is given.
> [3]PETSC ERROR: PetscAbortErrorHandler: User provided function() line 0 in
> unknown file (null)
> To prevent termination, change the error handler using
> PetscPushErrorHandler()
> [2]PETSC ERROR: PetscAbortErrorHandler: User provided function() line 0 in
> unknown file (null)
> To prevent termination, change the error handler using
> PetscPushErrorHandler()
>
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = PID 22939 RUNNING AT srvulx13
> = EXIT CODE: 134
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
>
> I read the documentation regarding the PetscAbortErrorHandler, but I do
> not know where should I use it. How can I solve the problem?
> I hope I have been clear enough.
> Attached you can find also my configure.log and make.log files.
>
> Best,
> Francesco
>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which
> their experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
>
>
>
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