Hi Xujun, It will be a lot more helpful if you rebuild with METHOD=dbg. In fact, it might be impossible to identify the error without it. It shouldn't be difficult at all provided you configured with that METHOD. If not, it's a good idea to reconfigure, since you might need it repeatedly in the future. Let me know if you need help reconfiguring/rebuilding. I would even recommend using a separate debugging build with a debugging version of PETSc - stack traces will be much more useful that way.
Dmitry On Fri, Feb 20, 2015, 13:05 Xujun Zhao <[email protected]> wrote: > I currently only have opt mode, the errors are as follows. > It can pass those lines, but stopped and output error at > equation_systems.init ();, which is the next line of the above codes. > If I use serial mesh: SerialMesh mesh(init.comm()); Then there is no > problem. > > > > [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: configure using --with-debugging=yes, recompile, link, and > run > > [0]PETSC ERROR: to get more information on the crash. > > [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 > 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: configure using --with-debugging=yes, recompile, link, and > run > > [1]PETSC ERROR: to get more information on the crash. > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [0]PETSC ERROR: Signal received > > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for > trouble shooting. > > [0]PETSC ERROR: Petsc Release Version 3.5.3, unknown > > [0]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named > mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015 > > [0]PETSC ERROR: Configure options --download-fblaslapack --download-mpich > --download-mumps --download-scalapack --download-hypre > -download-superlu_dist --download-parmetis --download-metis > --download-triangle -download-chaco --download-ml --with-opencl=0 > --with-debugging=0 > > [0]PETSC ERROR: #1 User provided function() line 0 in unknown file > > [1]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [1]PETSC ERROR: Signal received > > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for > trouble shooting. > > [1]PETSC ERROR: [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 > 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: configure using --with-debugging=yes, recompile, link, and > run > > [2]PETSC ERROR: to get more information on the crash. > > [2]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [2]PETSC ERROR: Signal received > > [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for > trouble shooting. > > [2]PETSC ERROR: Petsc Release Version 3.5.3, unknown > > [2]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named > mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015 > > [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 > 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: configure using --with-debugging=yes, recompile, link, and > run > > [3]PETSC ERROR: to get more information on the crash. > > [3]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [3]PETSC ERROR: Signal received > > [3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for > trouble shooting. > > [3]PETSC ERROR: Petsc Release Version 3.5.3, unknown > > [3]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named > mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015 > > [3]PETSC ERROR: Configure options --download-fblaslapack --download-mpich > --download-mumps --download-scalapack --download-hypre > -download-superlu_dist --download-parmetis --download-metis > --download-triangle -download-chaco --download-ml --with-opencl=0 > --with-debugging=0 > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [cli_0]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > Petsc Release Version 3.5.3, unknown > > [1]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named > mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015 > > [1]PETSC ERROR: Configure options --download-fblaslapack --download-mpich > --download-mumps --download-scalapack --download-hypre > -download-superlu_dist --download-parmetis --download-metis > --download-triangle -download-chaco --download-ml --with-opencl=0 > --with-debugging=0 > > [1]PETSC ERROR: #1 User provided function() line 0 in unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > [2]PETSC ERROR: Configure options --download-fblaslapack --download-mpich > --download-mumps --download-scalapack --download-hypre > -download-superlu_dist --download-parmetis --download-metis > --download-triangle -download-chaco --download-ml --with-opencl=0 > --with-debugging=0 > > [2]PETSC ERROR: #1 User provided function() line 0 in unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > [3]PETSC ERROR: #1 User provided function() line 0 in unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > [cli_1]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1 > > [cli_2]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2 > > [cli_3]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3 > > > ------------------------------------------------------------ > ------------------------------------------------------- > > | Processor id: 0 > | > > | Num Processors: 4 > | > > | Time: Fri Feb 20 13:58:43 2015 > | > > | OS: Darwin > | > > | HostName: mcswl094.mcs.anl.gov > | > > | OS Release: 14.1.0 > | > > | OS Version: Darwin Kernel Version 14.1.0: Mon Dec 22 23:10:38 PST > 2014; root:xnu-2782.10.72~2/RELEASE_X86_64 | > > | Machine: x86_64 > | > > | Username: xzhao > | > > | Configuration: ./configure '-prefix=/Users/xzhao/software/libmesh' > | > > | '--enable-everything' > | > > | '--disable-strict-lgpl' > | > > | '--enable-parmesh' > | > > | 'PETS > > ============================================================ > ======================= > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = PID 50290 RUNNING AT mcswl094.mcs.anl.gov > > = EXIT CODE: 59 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > ============================================================ > ======================= > > On Fri, Feb 20, 2015 at 1:56 PM, Roy Stogner <[email protected]> > wrote: > > > > > On Fri, 20 Feb 2015, Xujun Zhao wrote: > > > > Sorry for the incomplete message. I am simulating a channel flow with > >> periodic boundary conditions. See the codes below. It seems to work well > >> for serial run, but fails for the mpirun. I am curious if the PBC is > >> supported for the parallel implementation. > >> > > > > It's definitely supported in parallel. > > > > What's the exact error? (in dbg mode, with stack trace, please) > > --- > > Roy > > > ------------------------------------------------------------ > ------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=190641631&; > iu=/4140/ostg.clktrk > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users > ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
