are there any tricks to doing this across ssh? I've attempted it using the method given, but I can't get it to start in the debugger or to attach the debugger, the program just exits or hangs after telling me the error.
-Andrew On Apr 28, 2012, at 4:45 PM, Matthew Knepley wrote: > On Sat, Apr 28, 2012 at 6:39 PM, Andrew Spott <andrew.spott at gmail.com> > wrote: > >-start_in-debugger noxterm -debugger_nodes 14 > > All my cores are on the same machine, is this supposed to start a debugger on > processor 14? or computer 14? > > Neither. This spawns a gdb process on the same node as the process with MPI > rank 14. Then attaches gdb > to process 14. > > Matt > > I don't think I have x11 setup properly for the compute nodes, so x11 isn't > really an option. > > Thanks for the help. > > -Andrew > > > On Apr 27, 2012, at 7:26 PM, Satish Balay wrote: > > > On Fri, 27 Apr 2012, Andrew Spott wrote: > > > >> I'm honestly stumped. > >> > >> I have some petsc code that essentially just populates a matrix in > >> parallel, then puts it in a file. All my code that uses floating point > >> computations is checked for NaN's and infinities and it doesn't seem to > >> show up. However, when I run it on more than 4 cores, I get floating > >> point exceptions that kill the program. I tried turning off the > >> exceptions from petsc, but the program still dies from them, just without > >> the petsc error message. > >> > >> I honestly don't know where to go, I suppose I should attach a debugger, > >> but I'm not sure how to do that for multi-processor code. > > > > assuming you have X11 setup properly from compute nodes you can run > > with the extra option '-start_in_debugger' > > > > If X11 is not properly setup - and you'd like to run gdb on one of the > > nodes [say node 14 where you see SEGV] - you can do: > > > > -start_in-debugger noxterm -debugger_nodes 14 > > > > Or try valgrind > > > > mpiexec -n 16 valgrind --tool=memcheck -q ./executable > > > > > > For debugging - its best to install with --download-mpich [so that its > > valgrind clean] - and run all mpi stuff on a single machine - [usually > > X11 works well from a single machine.] > > > > Satish > > > >> > >> any ideas? (long error message below): > >> > >> -Andrew > >> > >> [14]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [14]PETSC ERROR: Caught signal number 8 FPE: Floating Point > >> Exception,probably divide by zero > >> [14]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > >> [14]PETSC ERROR: or see > >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[14]PETSC > >> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find > >> memory corruption errors > >> [14]PETSC ERROR: likely location of problem given in stack below > >> [14]PETSC ERROR: --------------------- Stack Frames > >> ------------------------------------ > >> [14]PETSC ERROR: Note: The EXACT line numbers in the stack are not > >> available, > >> [14]PETSC ERROR: INSTEAD the line number of the start of the function > >> [14]PETSC ERROR: is given. > >> [14]PETSC ERROR: --------------------- Error Message > >> ------------------------------------ > >> [14]PETSC ERROR: Signal received! > >> [14]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [14]PE[15]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [15]PETSC ERROR: Caught signal number 8 FPE: Floating Point > >> Exception,probably divide by zero > >> [15]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > >> [15]PETSC ERROR: or see > >> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[15]PETSC > >> ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find > >> memory corruption errors > >> [15]PETSC ERROR: likely location of problem given in stack below > >> [15]PETSC ERROR: --------------------- Stack Frames > >> ------------------------------------ > >> [15]PETSC ERROR: Note: The EXACT line numbers in the stack are not > >> available, > >> [15]PETSC ERROR: INSTEAD the line number of the start of the function > >> [15]PETSC ERROR: is given. > >> [15]PETSC ERROR: --------------------- Error Message > >> ------------------------------------ > >> [15]PETSC ERROR: Signal received! > >> [15]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [15]PETSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 > >> CST 2012 > >> [14]PETSC ERROR: See docs/changes/index.html for recent updates. > >> [14]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > >> [14]PETSC ERROR: See docs/index.html for manual pages. > >> [14]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [14]PETSC ERROR: /home/becker/ansp6066/local/bin/finddme on a linux-gnu > >> named photon9.colorado.edu by ansp6066 Fri Apr 27 18:01:55 2012 > >> [14]PETSC ERROR: Libraries linked from > >> /home/becker/ansp6066/local/petsc-3.2-p6/lib > >> [14]PETSC ERROR: Configure run at Mon Feb 27 11:17:14 2012 > >> [14]PETSC ERROR: Configure options > >> --prefix=/home/becker/ansp6066/local/petsc-3.2-p6 --with-c++-support > >> --with-fortran --with-mpi-dir=/usr/local/mpich2 --with-shared-libraries=0 > >> --with-scalar-type=complex > >> --with-blas-lapack-libs=/central/intel/mkl/lib/em64t/libmkl_core.a > >> --with-clanguage=cxx > >> [14]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [14]TSC ERROR: Petsc Release Version 3.2.0, Patch 6, Wed Jan 11 09:28:45 > >> CST 2012 > >> [15]PETSC ERROR: See docs/changes/index.html for recent updates. > >> [15]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > >> [15]PETSC ERROR: See docs/index.html for manual pages. > >> [15]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [15]PETSC ERROR: /home/becker/ansp6066/local/bin/finddme on a linux-gnu > >> named photon9.colorado.edu by ansp6066 Fri Apr 27 18:01:55 2012 > >> [15]PETSC ERROR: Libraries linked from > >> /home/becker/ansp6066/local/petsc-3.2-p6/lib > >> [15]PETSC ERROR: Configure run at Mon Feb 27 11:17:14 2012 > >> [15]PETSC ERROR: Configure options > >> --prefix=/home/becker/ansp6066/local/petsc-3.2-p6 --with-c++-support > >> --with-fortran --with-mpi-dir=/usr/local/mpich2 --with-shared-libraries=0 > >> --with-scalar-type=complex > >> --with-blas-lapack-libs=/central/intel/mkl/lib/em64t/libmkl_core.a > >> --with-clanguage=cxx > >> [15]PETSC ERROR: > >> ------------------------------------------------------------------------ > >> [15]PETSC ERROR: User provided function() line 0 in unknown directory > >> unknown file > >> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 14PETSC ERROR: > >> User provided function() line 0 in unknown directory unknown file > >> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 15[0]0:Return > >> code = 0, signaled with Interrupt > > > > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120428/62e01bf3/attachment.htm>
