[petsc-users] floating point exception… but only when >4 cores are used...

Sat Apr 28 19:42:54 CDT 2012

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
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