[CIG-SHORT] Pylith error

[Brad Aagaard]

Jiangning-

Are you sure you are not running out of memory? If you are not running out of 
memory, then rerun with the debugger to get a stacktrace as described below.

In general, if you ever encounter a segmentation fault when running PyLith  
(as you did in this case), you should rerun PyLith and add the command line 
argument --petsc.start_in_debugger. This will open up a debugger window when 
PyLith starts. Enter "c" at the gdb prompt to continue executing PyLith and 
when the error occurs, enter "backtrace" at the gdb prompt to get a 
stacktrace where the segmentation fault occurred. Copy the stacktrace to a 
text file and sent it along with the run log (stderr + stdout).

Brad


On Tuesday 12 February 2008, Jiangning Lu wrote:
> Hi,
>
> I run into some new issue here.  now the pylith did run further until it
> got crashed.  Anyone has a clue what does the following error mean?
> Thanks a lot!!
>
> Where the error info occurred: (Attached is the detailed run log file).
> ......
>  -- implicit(info)
>  -- Creating solution field.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si
>gnal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on
> Apple to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available, [0]PETSC ERROR:       INSTEAD the line number of the start of
> the function [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Development Version 2.3.3, Patch 8, Tue Jan 29
> 00:02:06 CST 2008 HG revision: 4b0f5f032b0655745a4e6a02aa42852564e2854a
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR:
> /chandler/home/jlu/scratch1/pylith_workarea/nemesis/trunk/mpinemesis on a
> linux-gnu named elsasser by jlu Tue Feb 12 11:11:05 2008
> [0]PETSC ERROR: Libraries linked from
> /chandler/home/jlu/scratch1/pylith_workarea/petsc-dev/lib
> [0]PETSC ERROR: Configure run at Tue Jan 29 15:33:02 2008
> [0]PETSC ERROR: Configure options --with-sieve=1 --with-clanguage=C++
> --with-shared=1 --download-f-blas-lapack=1 --with-boost=1
> --download-boost=1 --with-chaco=1 --download-chaco=1 --with-mpi=1
> --download-mpich=1
> --with-mpi-shared=1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [cli_0]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> Jiangning
>
>
> ---
> Jiangning Lü
> 54-521     x3-6389
> Geophysics
> EAPS, MIT
> johnnylu at mit.edu (????