[petsc-users] PETSc Segmentation Violation error

Mon Jun 20 07:56:43 CDT 2022

Glad everything worked out.

(I forgot to reply-all in my initial mail, so the mailing list did not get included, adding it back in now).

Best regards,

Jacob Faibussowitsch
(Jacob Fai - booss - oh - vitch)

> On Jun 20, 2022, at 08:54, Pavankumar Koratikere <kcpkumar33 at gmail.com> wrote:
> 
> Hello Jacob
> 
> Thanks for your reply! As you mentioned, there was a minor discrepancy in the installation of a package which uses PETSc. I changed the version of python with which the package was configured and everything ran as expected.
> 
> Regards,
> Pavan.
> 
> On Sun, Jun 19, 2022 at 9:09 PM Jacob Faibussowitsch <jacob.fai at gmail.com> wrote:
> > [1]PETSC ERROR: #1 User provided function() at unknown file:0
> 
> The error message indicates that the segmentation violation occurs outside of PETSc. PETSc registers a SIGSEGV signal handler on startup, hence why it is the one to catch this. If the error was occurring somewhere within PETSc, or within a user-function called by PETSc then this stack trace would be more complete. 
> 
> Without seeing the code you are running we unfortunately cannot pinpoint the problem.
> 
> Best regards,
> 
> Jacob Faibussowitsch
> (Jacob Fai - booss - oh - vitch)
> 
> > On Jun 19, 2022, at 17:07, Pavankumar Koratikere <kcpkumar33 at gmail.com> wrote:
> > 
> > Hello,
> > I am trying to run a script that uses packages that depend on OpenMPI and PETSC (as shown below).
> > 
> > mpirun -np 4 python test.py
> > I am getting following error:
> > [1]PETSC ERROR: ------------------------------------------------------------------------
> > [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
> > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> > [1]PETSC ERROR: or see 
> > https://petsc.org/release/faq/#valgrind
> > 
> > [1]PETSC ERROR: or try 
> > http://valgrind.org
> >  on GNU/linux and Apple Mac OS X to find memory corruption errors
> > [1]PETSC ERROR: likely location of problem given in stack below
> > [1]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
> > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> > [1]PETSC ERROR:       INSTEAD the line number of the start of the function
> > [1]PETSC ERROR:       is given.
> > [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > [1]PETSC ERROR: Signal received
> > [1]PETSC ERROR: See 
> > https://petsc.org/release/faq/
> >  for trouble shooting.
> > [1]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021 
> > [1]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
> > [1]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
> > [1]PETSC ERROR: #1 User provided function() at unknown file:0
> > [1]PETSC ERROR: Checking the memory for corruption.
> > [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://petsc.org/release/faq/#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.
> > [2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > [2]PETSC ERROR: Signal received
> > [2]PETSC ERROR: See 
> > https://petsc.org/release/faq/
> >  for trouble shooting.
> > [2]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021 
> > [2]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
> > [2]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
> > [2]PETSC ERROR: #1 User provided function() at unknown file:0
> > [2]PETSC ERROR: Checking the memory for corruption.
> > [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://petsc.org/release/faq/#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: --------------------- Error Message --------------------------------------------------------------
> > [3]PETSC ERROR: Signal received
> > [3]PETSC ERROR: See 
> > https://petsc.org/release/faq/
> >  for trouble shooting.
> > [3]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021 
> > [3]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
> > [3]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
> > [3]PETSC ERROR: #1 User provided function() at unknown file:0
> > [3]PETSC ERROR: Checking the memory for corruption.
> > [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://petsc.org/release/faq/#valgrind
> > 
> > [0]PETSC ERROR: or try 
> > http://valgrind.org
> >  on GNU/linux and Apple Mac OS X to find memory corruption errors
> > [0]PETSC ERROR: likely location of problem given in stack below
> > [0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
> > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> > [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> > [0]PETSC ERROR:       is given.
> > [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> > [0]PETSC ERROR: Signal received
> > [0]PETSC ERROR: See 
> > https://petsc.org/release/faq/
> >  for trouble shooting.
> > [0]PETSC ERROR: Petsc Release Version 3.15.5, Sep 29, 2021 
> > [0]PETSC ERROR: Unknown Name on a real-debug named skynet by pavan Sat Jun 18 10:30:04 2022
> > [0]PETSC ERROR: Configure options --PETSC_ARCH=real-debug --with-scalar-type=real --with-debugging=1 --with-mpi-dir=/home/pavan/packages/openmpi-4.0.7/opt-gfortran --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --with-shared-libraries=yes --with-fortran-bindings=1 --with-cxx-dialect=C++11
> > [0]PETSC ERROR: #1 User provided function() at unknown file:0
> > [0]PETSC ERROR: Checking the memory for corruption.
> > 
> > 
> > I am new to PETSc and I don't really know how to debug this. Any help will be much appreciated!
> > Regards,
> > Pavan.
> 