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. >
