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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