[petsc-users] Caught signal number 11 SEGV

[Matthew Knepley]

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
> <https://discourse.mc-stan.org/t/using-petsc-library-together-with-stan/17550> you
> can find the discussion.
> It has been defined a functor
> <https://github.com/IvanYashchuk/stan-math-petsc/blob/stan-petsc/stan/math/prim/fun/stan_petsc_interface.hpp> to
> convert EigenVector to PetscVec and viceversa, both sequentially and in
> parallel.
> The file
> <https://github.com/IvanYashchuk/stan-math-petsc/blob/stan-petsc/stan/math/rev/functor/petsc_functor.hpp> 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/ <http://www.cse.buffalo.edu/~knepley/>
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