I found my bug. Thanks a lot everyone, I really appreciate the help.
-Andrew On Apr 28, 2012, at 7:16 PM, Andrew Spott wrote: > Yes it did? now I have a bunch of GDB windows open and ready, thanks. > > -Andrew > On Apr 28, 2012, at 7:10 PM, Matthew Knepley wrote: > >> On Sat, Apr 28, 2012 at 8:59 PM, Andrew Spott <andrew.spott at gmail.com> >> wrote: >> What makes it easier if autotools makes it hard? >> >> >> This is a joke, but I do think autotools makes everything hard. >> >> On Apr 28, 2012 6:43 PM, "Matthew Knepley" <knepley at gmail.com> wrote: >> On Sat, Apr 28, 2012 at 8:36 PM, Andrew Spott <andrew.spott at gmail.com> >> wrote: >> When I attach debugger on error on the local machine, I get a bunch of lines >> like this one: >> >> warning: Could not find object file >> "/private/tmp/homebrew-gcc-4.6.2-HNPr/gcc-4.6.2/build/x86_64-apple-darwin11.3.0/libstdc++-v3/src/../libsupc++/.libs/libsupc++convenience.a(cp-demangle.o)" >> - no debug information available for "cp-demangle.c". >> >> It looks like you build with autotools. That just makes things hard :) >> >> then ". done" And then nothing. It looks like the program exits before the >> debugger can attach. after a while I get this: >> >> You can use -debugger_pause 10 to make it wait 10s before continuing after >> spawning the debugger. Make it long >> enough to attach. >> >> Did this work? >> >> Matt >> >> Matt >> >> /Users/spott/Documents/Code/EnergyBasisSchrodingerSolver/data/ebss-input/basis_rmax1.00e+02_rmin1.00e-06_dr1.00e-01/76151: >> No such file or directory >> Unable to access task for process-id 76151: (os/kern) failure. >> >> in the gdb window. In the terminal window, I get >> >> application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3 >> [cli_3]: aborting job: >> >> if I just "start_in_debugger" I just don't' get the "MPI_Abort" thing, but >> everything else is the same. >> >> any ideas? >> >> -Andrew >> >> On Apr 28, 2012, at 6:11 PM, Matthew Knepley wrote: >> >>> On Sat, Apr 28, 2012 at 8:07 PM, Andrew Spott <andrew.spott at gmail.com> >>> wrote: >>> 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. >>> >>> Is there a reason you cannot run this problem on your local machine with 4 >>> processes? >>> >>> Matt >>> >>> -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 >>> >>> >>> >>> >>> -- >>> 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 >> >> >> >> >> -- >> 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 >> >> >> >> -- >> 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... 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