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

Andrew Spott andrew.spott at gmail.com
Sat Apr 28 19:59:03 CDT 2012 

What makes it easier if autotools makes it 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.
>
>    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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