[petsc-users] Caught signal number 11 SEGV
Francesco Brarda
brardafrancesco at gmail.com
Tue Feb 23 15:46:49 CST 2021
Using the command you suggested I got
fbrarda at srvulx13:~/cmdstan-petsc$ $PETSC_DIR/$PETSC_ARCH/bin/mpirun -n 2 examples/rosenbrock/rosenbrock optimize -start_in_debugger noxterm -debugger_nodes 3
** PETSc DEPRECATION WARNING ** : the option -debugger_nodes is deprecated as of version 3.14 and will be removed in a future release. Please use the option -debugger_ranks instead. (Silence this warning with -options_suppress_deprecated_warnings)
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)
init_alpha = 0.001 (Default)
tol_obj = 9.9999999999999998e-13 (Default)
tol_rel_obj = 10000 (Default)
tol_grad = 1e-08 (Default) tol_rel_obj = 10000 (Default)
tol_grad = 1e-08 (Default)
tol_rel_grad = 10000000 (Default)
tol_rel_grad = 10000000 (Default)
tol_param = 1e-08 (Default) tol_param = 1e-08 (Default)
history_size = 5 (Default)
iter = 2000 (Default)
history_size = 5 (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 = 3623621468 (Default)
output
file = output.csv (Default)init = 2 (Default)
random
seed = 3623621468 (Default)
output
file = output.csv (Default)
diagnostic_file = (Default)
refresh = 100 (Default)
diagnostic_file = (Default)
refresh = 100 (Default)
Initial log joint probability = -195.984
Iter log prob ||dx|| ||grad|| alpha alpha0 # evals Notes
10 -0.97101 0.00292919 1.65855 0.001 0.001 46 LS failed, Hessian reset
12 -0.483952 0.001316 1.18542 0.001 0.001 77 LS failed, Hessian reset
13 -0.477916 0.0118542 0.163518 0.01 0.001 106 LS failed, Hessian reset
[1]PETSC ERROR: #1 main() line 12 in src/cmdstan/main.cpp
[1]PETSC ERROR: PETSc Option Table entries:
[1]PETSC ERROR: -debugger_nodes 3
[1]PETSC ERROR: -start_in_debugger noxterm
[1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov—————
And then it does not go further. With the -debugger_ranks suggested, the output is the same. What do you think, please?
I am using a cluster (one node, dual-socket system with twelve-core-CPUs), but when I do the ssh I do not use the -X flag, if that's what you mean.
Thank you,
Francesco
> Il giorno 23 feb 2021, alle ore 21:59, Matthew Knepley <knepley at gmail.com> ha scritto:
>
> On Tue, Feb 23, 2021 at 3:55 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
>
> Do you have an Xserver running? If not, you can use
>
> -start_in_debugger noxterm -debugger_nodes 3
>
> and try to get a stack trace from one node.
>
> Thanks,
>
> Matt
>
> 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/
>
>
>
> --
> 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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