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". then ". done" And then nothing. It looks like the program exits before the debugger can attach. after a while I get this: /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 -------------- next part -------------- An HTML attachment was scrubbed... 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