Re: [Libmesh-users] parallel run of periodic boundary conditions

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I currently only have opt mode, the errors are as follows.
It can pass those lines, but stopped and output error at
equation_systems.init ();, which is the next line of the above codes.
If I use serial mesh: SerialMesh mesh(init.comm()); Then there is no
problem.

[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: configure using --with-debugging=yes, recompile, link, and
run

[0]PETSC ERROR: to get more information on the crash.

[1]PETSC ERROR:
------------------------------------------------------------------------

[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range

[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[1]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors

[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run

[1]PETSC ERROR: to get more information on the crash.

[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 Release Version 3.5.3, unknown

[0]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015

[0]PETSC ERROR: Configure options --download-fblaslapack --download-mpich
--download-mumps --download-scalapack --download-hypre
-download-superlu_dist --download-parmetis --download-metis
--download-triangle -download-chaco --download-ml --with-opencl=0
--with-debugging=0

[0]PETSC ERROR: #1 User provided function() line 0 in  unknown file

[1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------

[1]PETSC ERROR: Signal received

[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.

[1]PETSC ERROR: [2]PETSC ERROR:
------------------------------------------------------------------------

[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range

[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[2]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors

[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run

[2]PETSC ERROR: to get more information on the crash.

[2]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------

[2]PETSC ERROR: Signal received

[2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.

[2]PETSC ERROR: Petsc Release Version 3.5.3, unknown

[2]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015

[3]PETSC ERROR:
------------------------------------------------------------------------

[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range

[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[3]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind

[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors

[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run

[3]PETSC ERROR: to get more information on the crash.

[3]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------

[3]PETSC ERROR: Signal received

[3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.

[3]PETSC ERROR: Petsc Release Version 3.5.3, unknown

[3]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015

[3]PETSC ERROR: Configure options --download-fblaslapack --download-mpich
--download-mumps --download-scalapack --download-hypre
-download-superlu_dist --download-parmetis --download-metis
--download-triangle -download-chaco --download-ml --with-opencl=0
--with-debugging=0

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

[cli_0]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

Petsc Release Version 3.5.3, unknown

[1]PETSC ERROR: ./example-opt on a arch-darwin-c-opt named
mcswl094.mcs.anl.gov by xzhao Fri Feb 20 13:58:43 2015

[1]PETSC ERROR: Configure options --download-fblaslapack --download-mpich
--download-mumps --download-scalapack --download-hypre
-download-superlu_dist --download-parmetis --download-metis
--download-triangle -download-chaco --download-ml --with-opencl=0
--with-debugging=0

[1]PETSC ERROR: #1 User provided function() line 0 in  unknown file

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1

[2]PETSC ERROR: Configure options --download-fblaslapack --download-mpich
--download-mumps --download-scalapack --download-hypre
-download-superlu_dist --download-parmetis --download-metis
--download-triangle -download-chaco --download-ml --with-opencl=0
--with-debugging=0

[2]PETSC ERROR: #1 User provided function() line 0 in  unknown file

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2

[3]PETSC ERROR: #1 User provided function() line 0 in  unknown file

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3

[cli_1]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1

[cli_2]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2

[cli_3]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3

 -------------------------------------------------------------------------------------------------------------------

| Processor id:   0
                                        |

| Num Processors: 4
                                        |

| Time:           Fri Feb 20 13:58:43 2015
                                         |

| OS:             Darwin
                                         |

| HostName:       mcswl094.mcs.anl.gov
                                         |

| OS Release:     14.1.0
                                         |

| OS Version:     Darwin Kernel Version 14.1.0: Mon Dec 22 23:10:38 PST
2014; root:xnu-2782.10.72~2/RELEASE_X86_64  |

| Machine:        x86_64
                                         |

| Username:       xzhao
                                        |

| Configuration:  ./configure  '-prefix=/Users/xzhao/software/libmesh'
                                         |

|  '--enable-everything'
                                         |

|  '--disable-strict-lgpl'
                                         |

|  '--enable-parmesh'
                                        |

|  'PETS

===================================================================================

=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

=   PID 50290 RUNNING AT mcswl094.mcs.anl.gov

=   EXIT CODE: 59

=   CLEANING UP REMAINING PROCESSES

=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

===================================================================================

On Fri, Feb 20, 2015 at 1:56 PM, Roy Stogner <roy...@ic...>
wrote:

>
> On Fri, 20 Feb 2015, Xujun Zhao wrote:
>
>  Sorry for the incomplete message. I am simulating a channel flow with
>> periodic boundary conditions. See the codes below. It seems to work well
>> for serial run, but fails for the mpirun. I am curious if the PBC is
>> supported for the parallel implementation.
>>
>
> It's definitely supported in parallel.
>
> What's the exact error? (in dbg mode, with stack trace, please)
> ---
> Roy
>