[petsc-users] PETSc Segmentation Violation error

Sun Jun 19 16:07:43 CDT 2022

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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