>-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?
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 >
