Also you would have to call MPI_Init() before the first PetscInitialize() [and similarly MPI_Finalize() after the last call to PetscFinalize()]
Satish On Tue, 3 Sep 2013, Barry Smith wrote: > > There is a problem with the 3.3 series when reinitializing PETSc. Can you > switch to PETSc 3.4 which properly supports calling PetscInitialize() several > times. > > Barry > > On Sep 3, 2013, at 1:58 PM, Suraj Prabhakaran <[email protected]> > wrote: > > > Hello, > > > > Again, this relates to finalizing and initializing petsc in my application. > > I basically want to finalize petsc and initialize it again with a different > > MPI communicator. A rough sketch of my quite huge application is as follows. > > > > > > main() > > { > > PetscInitialize() > > ... > > ... > > AOCreate().. > > AO operations.. > > AODestroy().. > > ... > > ... > > PetscFinalize() > > PETSC_COMM_WORLD = A new communicator (which includes more processes) > > PetscInitialize() > > ... > > ... > > AOCreate().. > > AO operations.. > > AODestroy() > > ... > > ... > > PetscFinalize() > > } > > > > So after finalizing and initializing it back, I always get an error with > > one of the AO calls. Given below is the complete error I get when running > > with 8 procs. Can anyone give me a hint what the problem could be? I was > > told earlier, that finalizing and initializing petsc should not be a > > problem! > > > > Best, > > Suraj > > > > -------------------------ERROR starts here------------------------------- > > [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 > > http://www.mcs.anl.gov/petsc/documentation/faq.html#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: [0] PetscStrcmp line 414 > > /root/petsc/petsc-3.3-p7/src/sys/utils/str.c > > [0]PETSC ERROR: [0] PetscFListAdd line 202 > > /root/petsc/petsc-3.3-p7/src/sys/dll/reg.c > > [0]PETSC ERROR: [0] AORegister line 99 > > /root/petsc/petsc-3.3-p7/src/dm/ao/interface/aoreg.c > > [0]PETSC ERROR: [0] AORegisterAll line 28 > > /root/petsc/petsc-3.3-p7/src/dm/ao/interface/aoregall.c > > [0]PETSC ERROR: [0] AOInitializePackage line 49 > > /root/petsc/petsc-3.3-p7/src/dm/ao/interface/dlregisdm.c > > [0]PETSC ERROR: [0] AOCreate line 530 > > /root/petsc/petsc-3.3-p7/src/dm/ao/interface/ao.c > > [0]PETSC ERROR: [0] AOCreateBasicIS line 381 > > /root/petsc/petsc-3.3-p7/src/dm/ao/impls/basic/aobasic.c > > [0]PETSC ERROR: [0] AOCreateBasic line 336 > > /root/petsc/petsc-3.3-p7/src/dm/ao/impls/basic/aobasic.c > > [0]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [0]PETSC ERROR: Signal received! > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [0]PETSC ERROR: See docs/index.html for manual pages. > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > [0]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [0]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [0]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > [0]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > -------------------------------------------------------------------------- > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > with errorcode 59. > > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > You may or may not see output from other processes, depending on > > exactly when Open MPI kills them. > > -------------------------------------------------------------------------- > > [1]PETSC ERROR: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [1]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#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: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [1]PETSC ERROR: See docs/index.html for manual pages. > > [1]PETSC ERROR: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [1]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [1]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [1]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [1]PETSC ERROR: > > ------------------------------------------------------------------------ > > [1]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > [2]PETSC ERROR: > > ------------------------------------------------------------------------ > > [2]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [2]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#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: > > ------------------------------------------------------------------------ > > [2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [2]PETSC ERROR: See docs/changes/index.html for recent updates. > > [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [2]PETSC ERROR: See docs/index.html for manual pages. > > [2]PETSC ERROR: > > ------------------------------------------------------------------------ > > [2]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [2]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [2]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [2]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [2]PETSC ERROR: > > ------------------------------------------------------------------------ > > [2]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > [3]PETSC ERROR: > > ------------------------------------------------------------------------ > > [3]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [3]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#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: > > ------------------------------------------------------------------------ > > [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [3]PETSC ERROR: See docs/changes/index.html for recent updates. > > [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [3]PETSC ERROR: See docs/index.html for manual pages. > > [3]PETSC ERROR: > > ------------------------------------------------------------------------ > > [3]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [3]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [3]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [3]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [3]PETSC ERROR: > > ------------------------------------------------------------------------ > > [3]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > [4]PETSC ERROR: > > ------------------------------------------------------------------------ > > [4]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [4]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[4]PETSC ERROR: > > or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > > corruption errors > > [4]PETSC ERROR: likely location of problem given in stack below > > [4]PETSC ERROR: --------------------- Stack Frames > > ------------------------------------ > > [4]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [4]PETSC ERROR: INSTEAD the line number of the start of the function > > [4]PETSC ERROR: is given. > > [4]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [4]PETSC ERROR: Signal received! > > [4]PETSC ERROR: > > ------------------------------------------------------------------------ > > [4]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [4]PETSC ERROR: See docs/changes/index.html for recent updates. > > [4]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [4]PETSC ERROR: See docs/index.html for manual pages. > > [4]PETSC ERROR: > > ------------------------------------------------------------------------ > > [4]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [4]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [4]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [4]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [4]PETSC ERROR: > > ------------------------------------------------------------------------ > > [4]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > [5]PETSC ERROR: > > ------------------------------------------------------------------------ > > [5]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [5]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[5]PETSC ERROR: > > or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > > corruption errors > > [5]PETSC ERROR: likely location of problem given in stack below > > [5]PETSC ERROR: --------------------- Stack Frames > > ------------------------------------ > > [5]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [5]PETSC ERROR: INSTEAD the line number of the start of the function > > [5]PETSC ERROR: is given. > > [5]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [5]PETSC ERROR: Signal received! > > [5]PETSC ERROR: > > ------------------------------------------------------------------------ > > [5]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [5]PETSC ERROR: See docs/changes/index.html for recent updates. > > [5]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [5]PETSC ERROR: See docs/index.html for manual pages. > > [5]PETSC ERROR: > > ------------------------------------------------------------------------ > > [5]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [5]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [5]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [5]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [5]PETSC ERROR: > > ------------------------------------------------------------------------ > > [5]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > [6]PETSC ERROR: > > ------------------------------------------------------------------------ > > [6]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [6]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[6]PETSC ERROR: > > or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > > corruption errors > > [6]PETSC ERROR: likely location of problem given in stack below > > [6]PETSC ERROR: --------------------- Stack Frames > > ------------------------------------ > > [6]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [6]PETSC ERROR: INSTEAD the line number of the start of the function > > [6]PETSC ERROR: is given. > > [6]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [6]PETSC ERROR: Signal received! > > [6]PETSC ERROR: > > ------------------------------------------------------------------------ > > [6]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [6]PETSC ERROR: See docs/changes/index.html for recent updates. > > [6]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [6]PETSC ERROR: See docs/index.html for manual pages. > > [6]PETSC ERROR: > > ------------------------------------------------------------------------ > > [6]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [6]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [6]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [6]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [6]PETSC ERROR: > > ------------------------------------------------------------------------ > > [6]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > [7]PETSC ERROR: > > ------------------------------------------------------------------------ > > [7]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the > > batch system) has told this process to end > > [7]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [7]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[7]PETSC ERROR: > > or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory > > corruption errors > > [7]PETSC ERROR: likely location of problem given in stack below > > [7]PETSC ERROR: --------------------- Stack Frames > > ------------------------------------ > > [7]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [7]PETSC ERROR: INSTEAD the line number of the start of the function > > [7]PETSC ERROR: is given. > > [7]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [7]PETSC ERROR: Signal received! > > [7]PETSC ERROR: > > ------------------------------------------------------------------------ > > [7]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 > > CDT 2013 > > [7]PETSC ERROR: See docs/changes/index.html for recent updates. > > [7]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [7]PETSC ERROR: See docs/index.html for manual pages. > > [7]PETSC ERROR: > > ------------------------------------------------------------------------ > > [7]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue > > Sep 3 20:56:21 2013 > > [7]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib > > [7]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013 > > [7]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 > > --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 > > --with-debugging > > [7]PETSC ERROR: > > ------------------------------------------------------------------------ > > [7]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > -------------------------------------------------------------------------- > > mpiexec has exited due to process rank 0 with PID 2670 on > > node grsacc17 exiting improperly. There are two reasons this could occur: > > > > 1. this process did not call "init" before exiting, but others in > > the job did. This can cause a job to hang indefinitely while it waits > > for all processes to call "init". By rule, if one process calls "init", > > then ALL processes must call "init" prior to termination. > > > > 2. this process called "init", but exited without calling "finalize". > > By rule, all processes that call "init" MUST call "finalize" prior to > > exiting or it will be considered an "abnormal termination" > > > > This may have caused other processes in the application to be > > terminated by signals sent by mpiexec (as reported here). > >
