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 <[email protected]> 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. > > > >
