<p>Dear All,</p><p>I am trying the PetscFEM solver with petsc-3.4.4. </p><p><br></p><p>But when I run snes/ex12, I always got run time errors.</p><p><br></p><p>[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>[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<br>[1]PETSC ERROR: ------------------------------------------------------------------------<br>[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>[1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.htm
l#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors<br>[0]PETSC ERROR: likely location of problem given in stack below<br>[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>[1]PETSC ERROR: likely location of problem given in stack below<br>[1]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>[1]PETSC ERROR: [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>[0]PETSC ERROR: INSTEAD the line number of the start of the function<br>Note: The EXACT line numbers in the stack are not available,<br>[1]PETSC ERROR: INSTEAD the line number of the start of the function<br>[1]PETSC ERROR: is given.<br>[1]PETSC ERROR: [1] DMPlexProjectFunctionLocal line 230 /home/zhenyu/petsc-3.4.4/src/dm/impls/plex/plexfem.c<br>[1]PETSC ERROR: [1] DMPlexProjectFunction line 338 /home/zhenyu/petsc-3.4.4/src/dm/impl
s/plex/plexfem.c<br>[0]PETSC ERROR: is given.<br>[0]PETSC ERROR: [0] DMPlexProjectFunctionLocal line 230 /home/zhenyu/petsc-3.4.4/src/dm/impls/plex/plexfem.c<br>[0]PETSC ERROR: [0] DMPlexProjectFunction line 338 /home/zhenyu/petsc-3.4.4/src/dm/impls/plex/plexfem.c<br>[0]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[0]PETSC ERROR: Signal received!<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13, 2014 <br>[0]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[1]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[1]PETSC ERROR: Signal received!<br>[1]PETSC ERROR: ------------------------------------------------------------------------<br>[1]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13, 2014 <br>[1]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[1]PETSC ERROR:
See docs/faq.html for hints about trouble shooting.<br>[1]PETSC ERROR: See docs/index.html for manual pages.<br>[1]PETSC ERROR: ------------------------------------------------------------------------<br>[1]PETSC ERROR: [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[0]PETSC ERROR: See docs/index.html for manual pages.<br>ex12 on a arch-linux2-c-opt named toshiba by zhenyu Tue May 20 20:26:56 2014<br>[1]PETSC ERROR: Libraries linked from /home/zhenyu/petsc-3.4.4/arch-linux2-c-opt/lib<br>[1]PETSC ERROR: Configure run at Mon May 19 23:24:37 2014<br>[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<br>[1]PETSC ERROR: ------------------------------------------------------------------------<br>[1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: ex12 on a arch-linux2-c-opt named toshiba by zhenyu Tue May 20 20:26:56 2014<br>[0]PETSC ERROR: Libraries linked from /home/zhenyu/petsc-3.4.4/arch-linux2-c-opt/lib<br>[0]PETSC ERROR: Configure run at Mon May 19 23:24:37 2014<br>[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<br>[0]PETSC ERROR: ------------------------------------------------------------------------<br>[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file<br>--------------------------------------------------------------------------<br>MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD <br>with errorcode 59.<br><br>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>You may or may not see output from other processes, depending on<br>exactly when Open MPI
kills them.<br>--------------------------------------------------------------------------<br>--------------------------------------------------------------------------<br>mpirun has exited due to process rank 1 with PID 3027 on<br>node toshiba exiting improperly. There are two reasons this could occur:<br><br>1. this process did not call "init" before exiting, but others in<br>the job did. This can cause a job to hang indefinitely while it waits<br>for all processes to call "init". By rule, if one process calls "init",<br>then ALL processes must call "init" prior to termination.<br><br>2. this process called "init", but exited without calling "finalize".<br>By rule, all processes that call "init" MUST call "finalize" prior to<br>exiting or it will be considered an "abnormal termination"<br><br>This may have caused other processes in the application to be<br>terminated by signals sent by mpirun (as reported here).<br>-----------------------------------------------------------
---------------<br>[toshiba:03025] 1 more process has sent help message help-mpi-api.txt / mpi-abort<br>[toshiba:03025] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages<br></p><p><br></p><p>Well, for a smooth compiling, I made two correction to ex12.c</p><p>Line 195: options->fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) &options->exactFuncs;</p><p>Line 574: void (*initialGuess[numComponents])(const PetscReal x[],PetscScalar* u);</p><p>then generate ex12.h by </p><p>PETSC_DIR=$HOME/petsc-3.4.4<br>DIM=2<br>ORDER=1<br><br>CASE=ex12<br>$PETSC_DIR/bin/pythonscripts/PetscGenerateFEMQuadrature.py \<br> $DIM $ORDER $DIM 1 laplacian \<br> $DIM $ORDER $DIM 1 boundary \<br> $PETSC_DIR/src/snes/examples/tutorials/$CASE.h</p><p>Since I am still not fully master the machnism of PetscFEM, </p><p>could anyone show me a proper way to run this demo? Many thanks.</p><p><br></p><p>Zhenyu</p>