[petsc-users] PETSc Segmentation Violation error

Mon Jun 20 09:22:18 CDT 2022

Hello Satish

Thanks for your email! 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.

The package which I am using requires me to use a specific version of
PETSc, so I am using an old version.

Regards,
Pavan.

On Sun, Jun 19, 2022 at 9:59 PM Satish Balay <balay at mcs.anl.gov> wrote:

> As the below message indicates - you can try running this code via
> valgrind or gdb to determine the location of error.
>
> https://petsc.org/release/faq/#valgrind
> i.e
> mpirun -np 4 valgrind --tool=memcheck python test.py
>
> One way to specify option  -start_in_debugger is:
>
> PETSC_OPTION=-start_in_debugger mpirun -np 4 python test.py
>
> Also good to use latest petsc version - currently its 3.17
>
> Satish
>
> On Sun, 19 Jun 2022, Pavankumar Koratikere 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.
> >
>
>
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