[petsc-users] How to run snes ex12 with petsc-3.4.4

Tue May 20 09:20:06 CDT 2014

On Tue, May 20, 2014 at 7:31 AM, Zhang <zyzhang at nuaa.edu.cn> wrote:

> Dear All,
>
> I am trying the PetscFEM solver with petsc-3.4.4.
>
That is changing quickly since it is very new. Can you use 'master'?
http://www.mcs.anl.gov/petsc/developers/index.html
If you use that, Python is no longer required. Also, we will release very
soon, so its not a waste.

  Thanks,

    Matt

> But when I run snes/ex12, I always got run time errors.
>
>
> [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]PETSCERROR: or try
> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> [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
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [1]PETSC ERROR: likely location of problem given in stack below
> [1]PETSC ERROR: --------------------- Stack Frames
> ------------------------------------
> [1]PETSC ERROR: [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
> Note: The EXACT line numbers in the stack are not available,
> [1]PETSC ERROR: INSTEAD the line number of the start of the function
> [1]PETSC ERROR: is given.
> [1]PETSC ERROR: [1] DMPlexProjectFunctionLocal line 230
> /home/zhenyu/petsc-3.4.4/src/dm/impls/plex/plexfem.c
> [1]PETSC ERROR: [1] DMPlexProjectFunction line 338
> /home/zhenyu/petsc-3.4.4/src/dm/impl s/plex/plexfem.c
> [0]PETSC ERROR: is given.
> [0]PETSC ERROR: [0] DMPlexProjectFunctionLocal line 230
> /home/zhenyu/petsc-3.4.4/src/dm/impls/plex/plexfem.c
> [0]PETSC ERROR: [0] DMPlexProjectFunction line 338
> /home/zhenyu/petsc-3.4.4/src/dm/impls/plex/plexfem.c
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13, 2014
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [1]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [1]PETSC ERROR: Signal received!
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13, 2014
> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [1]PETSC ERROR: See docs/index.html for manual pages.
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: [0]PETSC ERROR: See docs/faq.html for hints about trouble
> shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> ex12 on a arch-linux2-c-opt named toshiba by zhenyu Tue May 20 20:26:56
> 2014
> [1]PETSC ERROR: Libraries linked from
> /home/zhenyu/petsc-3.4.4/arch-linux2-c-opt/lib
> [1]PETSC ERROR: Configure run at Mon May 19 23:24:37 2014
> [1]PETSC ERROR: Configure options --download-cmake=1
> --download-fblaslapack=1 --download-f2cblaslapack=1 --download-fftw=1
> --download-ptscotch=1 --download-ctetgen=1 --download-petsc4py=1
> --download-ml=1 --download-parmetis=1 --download-metis=1
> --download-superlu_dist=1 --download-hypre=1 --download-c2html=1
> --download-generator=1 --download-fiat=1 --download-scientificpython=1
> --download-sowing=1 --download -triangle=1 --download-chaco=1
> --download-boost=1 --download-exodusii=1 --download-netcdf=1
> --download-netcdf-shared=1 --download-hdf5=1 --download-moab-shared=1
> --download-suitesparse=1 --with-mpi-dir=/home/zhenyu/deps/openmpi-1.6.5
> --with-pthread=1 --with-valgrind=1
> [1]PETSC ERROR:
> ------------------------------------------------------------------------
> [1]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ex12 on a arch-linux2-c-opt named toshiba by zhenyu Tue
> May 20 20:26:56 2014
> [0]PETSC ERROR: Libraries linked from
> /home/zhenyu/petsc-3.4.4/arch-linux2-c-opt/lib
> [0]PETSC ERROR: Configure run at Mon May 19 23:24:37 2014
> [0]PETSC ERROR: Configure options --download-cmake=1
> --download-fblaslapack=1 --download-f2cblaslapack=1 --download-fftw=1
> --download-ptscotch=1 --download-ctetgen=1 --download-petsc4py=1
> --download-ml=1 --download-parmetis=1 --download-metis=1
> --download-superlu_dist=1 --download-hypre=1 --download-c2html=1
> --download-generator=1 --download-fiat=1 --download-scientificpython=1
> --download-sowing=1 --download-triangle=1 --download-chaco=1
> --download-boost=1 --download-exodusii=1 --download-netcdf=1
> --download-netcdf-shared=1 --download-hdf5=1 --download-moab-shared=1
> --download-suitesparse=1 --with-mpi-dir=/home/zhenyu/deps/openmpi-1.6.5
> --with-pthread=1 --with-valgrind=1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 59.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 3027 on
> node toshiba exiting improperly. There are two reasons this could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> ----------------------------------------------------------- ---------------
> [toshiba:03025] 1 more process has sent help message help-mpi-api.txt /
> mpi-abort
> [toshiba:03025] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
>
> Well, for a smooth compiling, I made two correction to ex12.c
>
> Line 195:   options->fem.bcFuncs = (void (**)(const PetscReal[],
> PetscScalar *)) &options->exactFuncs;
>
> Line 574:   void (*initialGuess[numComponents])(const PetscReal
> x[],PetscScalar* u);
>
> then generate ex12.h by
>
> PETSC_DIR=$HOME/petsc-3.4.4
> DIM=2
> ORDER=1
>
> CASE=ex12
> $PETSC_DIR/bin/pythonscripts/PetscGenerateFEMQuadrature.py \
> $DIM $ORDER $DIM 1 laplacian \
> $DIM $ORDER $DIM 1 boundary \
> $PETSC_DIR/src/snes/examples/tutorials/$CASE.h
>
> Since I am still not fully master the machnism of PetscFEM,
>
> could anyone show me a proper way to run this demo? Many thanks.
>
>
> Zhenyu
>

-- 
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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