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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> > > 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. >
