[petsc-users] Error running DMPlex example

[Matthew Knepley]

On Tue, Aug 4, 2015 at 11:27 PM, Gautam Bisht <gbisht at lbl.gov> wrote:

> Hi,
>
> I'm getting the following error while running the following DMPlex
> example. Any suggestion what is going wrong? Attached are example.log and
> configure.log.
>

Can you run the test by hand either with the debugger and get a stack trace:

/opt/local/bin/mpiexec-mpich-gcc49 -host localhost -n 1
darwin-gnu-fort-debug/lib/ex12-obj/ex12 -run_type test -refinement_limit
0.0    -bc_type dirichlet -interpolate 0 -petscspace_order 1 -show_initial
-dm_plex_print_fem 1 -start_in_debugger

or using valgrind? I cannot reproduce the problem here.

  Thanks,

     Matt


> python2.7 ./config/builder2.py check src/snes/examples/tutorials/ex12.c
> Namespace(args=[], files=['src/snes/examples/tutorials/ex12.c'],
> func=<function check at 0x10d874c80>, numProcs=None, regParams=None,
> replace=False, retain=False, testnum=None)
> Running 52 tests
> Building
> ['/Users/gbisht/projects/petsc/petsc_f0284fa/src/snes/examples/tutorials/ex12.c']
> Running #0: /opt/local/bin/mpiexec-mpich-gcc49 -host localhost -n 1
> darwin-gnu-fort-debug/lib/ex12-obj/ex12 -run_type test -refinement_limit
> 0.0    -bc_type dirichlet -interpolate 0 -petscspace_order 1 -s
> TEST ERROR: Failed to execute darwin-gnu-fort-debug/lib/ex12-obj/ex12
> ===================================================================================
>
>
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>
>
> =   PID 69451 RUNNING AT localhost
>
>
> =   EXIT CODE: 59
>
>
> =   CLEANING UP REMAINING PROCESSES
>
>
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
>
>
> ===================================================================================
> [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/documentation/faq.html#valgrind
>
>
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X 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: [0] DMPlexGenerate_Triangle line 217
> src/dm/impls/plex/plexgenerate.c
>
> [0]PETSC ERROR: [0] DMPlexGenerate line 1056
> src/dm/impls/plex/plexgenerate.c
>
>
> [0]PETSC ERROR: [0] DMPlexCreateBoxMesh line 897
> src/dm/impls/plex/plexcreate.c
>
>
> [0]PETSC ERROR: [0] CreateMesh line 347 src/snes/examples/tutorials/ex12.c
>
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
>
> [0]PETSC ERROR: Signal received
>
>
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [0]PETSC ERROR: Petsc Development GIT revision: v3.6.1-238-gf0284fa  GIT
> Date: 2015-07-27 13:34:26 -0500
>
> [0]PETSC ERROR: darwin-gnu-fort-debug/lib/ex12-obj/ex12 on a
> darwin-gnu-fort-debug named gautam-laptop by gbisht Tue Aug  4 21:09:37
> 2015
> [0]PETSC ERROR: Configure options --download-hdf5=1
> --with-blas-lapack-lib=/System/Library/Frameworks/Accelerate.framework/Versions/Current/Accelerate
> --download-parmetis=yes --download-metis=yes --with-c
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
>
>
>
>
> TEST RUN FAILED (check example.log for details)
>
>
> -Gautam.
>
>


-- 
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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