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. 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]PETSCERROR: >>> 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]PETSCERROR: >>> 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 -------------- next part -------------- An HTML attachment was scrubbed... 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