Looks like something that will be fixed by carefully reconfiguring and recompiling libMesh. I would recommend saving the output of libMesh's configure this way: PETSC_DIR=... PETSC_ARCH=... CC=... ./configure --prefix=... ... 2>&1 | tee configure.log In my experience the resulting configure.log is sometimes more informative and easier to read than the generated config.log.
Dmitry. On Sat Jan 17 2015 at 1:43:09 PM Xujun Zhao <[email protected]> wrote: > Here is the error messages when I run the systems_of_equation ex1: > Memory out of range...... > but this doesn't happen for PETSc examples. > > Xujun > > *************************************************************** > > * Running Example systems_of_equations_ex1: > > * example-opt > > *************************************************************** > > > > Mesh Information: > > mesh_dimension()=2 > > spatial_dimension()=3 > > n_nodes()=961 > > n_local_nodes()=961 > > n_elem()=225 > > n_local_elem()=225 > > n_active_elem()=225 > > n_subdomains()=1 > > n_partitions()=1 > > n_processors()=1 > > n_threads()=1 > > processor_id()=0 > > > EquationSystems > > n_systems()=1 > > System #0, "Stokes" > > Type "LinearImplicit" > > Variables={ "u" "v" } "p" > > Finite Element Types="LAGRANGE", "JACOBI_20_00" "LAGRANGE", > "JACOBI_20_00" > > Infinite Element Mapping="CARTESIAN" "CARTESIAN" > > Approximation Orders="SECOND", "THIRD" "FIRST", "THIRD" > > n_dofs()=2178 > > n_local_dofs()=2178 > > n_constrained_dofs()=0 > > n_local_constrained_dofs()=0 > > n_vectors()=1 > > n_matrices()=1 > > DofMap Sparsity > > Average On-Processor Bandwidth <= 38.4683 > > Average Off-Processor Bandwidth <= 0 > > Maximum On-Processor Bandwidth <= 59 > > Maximum Off-Processor Bandwidth <= 0 > > DofMap Constraints > > Number of DoF Constraints = 0 > > Number of Node Constraints = 0 > > > [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: --------------------- 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 3.5.2, unknown > > [0]PETSC ERROR: ./example-opt on a arch-darwin-c-debug named inl424641 by > xzhao Sat Jan 17 13:40:22 2015 > > [0]PETSC ERROR: Configure options --download-fblaslapack --download-mpich > --download-mumps --download-scalapack --download-hypre > -download-superlu_dist --download-parmetis --download-metis > --with-debugging --with-opencl=0 > > [0]PETSC ERROR: #1 User provided function() line 0 in unknown file > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [unset]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > > > ------------------------------------------------------------------------------------------------------------------ > > | Time: Sat Jan 17 13:40:22 2015 > | > > | OS: Darwin > | > > | HostName: inl424641 > | > > | OS Release: 14.0.0 > | > > | OS Version: Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT > 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 | > > | Machine: x86_64 > | > > | Username: xzhao > | > > | Configuration: ./configure '-prefix=/Users/xzhao/software/libmesh_dbg' > | > > | '--enable-everything' > | > > | '--disable-strict-lgpl' > | > > | 'PETSC_DIR=/Users/xzhao/software/petsc/petsc_352_dbg_gcc49' > | > > | 'PETSC_ARCH=arch-darwin-c-debug' > | > > > > ------------------------------------------------------------------------------------------------------------------ > > On Sat, Jan 17, 2015 at 11:59 AM, Dmitry Karpeyev <[email protected]> > wrote: > >> Sounds like something went wrong during configure/build. >> Can you send the complete PETSc error messages you get when running >> libMesh examples? >> Can you build with METHOD=dbg and see if the problem persists and whether >> this gives more information >> to work with? This is also required if you end up having to go after >> this with a debugger, but >> this behavior is most likely due to some build incompatibility. Could you >> capture the output of >> libMesh configure (and/or the resulting config.log) and send that? >> >> Thanks. >> Dmitry. >> >> On Sat Jan 17 2015 at 11:13:56 AM Xujun Zhao <[email protected]> wrote: >> >>> Hi folks, >>> >>> I have a strange situation. The PETSc and libmesh are installed >>> successfully, and I didn't see anything wrong during installation. when I >>> run libmesh examples, they pass the 'make', but some errors came out >>> immediately during run, like this: >>> >>> inl424641:ex1 xzhao$ make >>> >>> Compiling C++ (in optimized mode) introduction_ex1.C... >>> >>> mpicxx -DNDEBUG -std=gnu++11 -O2 -felide-constructors -funroll-loops >>> -fstrict-aliasing -Wdisabled-optimization -fopenmp >>> -I/Users/xzhao/software/libmesh_xzhao/include -D_THREAD_SAFE -pthread >>> -I/Users/xzhao/software/petsc/petsc_352_opt_gcc49/include >>> -I/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/include >>> -I./contrib/boost/include -c introduction_ex1.C -o >>> introduction_ex1.x86_64-apple-darwin14.0.0.opt.o >>> >>> Linking example-opt... >>> >>> libtool: link: mpicxx -std=gnu++11 -O2 -felide-constructors >>> -funroll-loops >>> -fstrict-aliasing -Wdisabled-optimization -fopenmp >>> introduction_ex1.x86_64-apple-darwin14.0.0.opt.o -o example-opt >>> -Wl,-rpath >>> -Wl,/Users/xzhao/software/libmesh_xzhao/lib -Wl,-bind_at_load >>> -L/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch-darwin-c-opt/lib >>> -L/usr/local/Cellar/gcc/4.9.2/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2 >>> -L/usr/local/Cellar/gcc/4.9.2/lib >>> -L/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/externalpackages/mpich-3.1/src/mpl >>> -L/Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/externalpackages/mpich-3.1/src/openpa/src >>> -L/Users/xzhao/software/libmesh_xzhao/lib >>> /Users/xzhao/software/libmesh_xzhao/lib/libmesh_opt.dylib >>> /Users/xzhao/software/libmesh_xzhao/lib/libnetcdf.dylib -lcurl -lz >>> -lpetsc >>> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack >>> -lsuperlu_dist_3.3 -lHYPRE -lflapack -lfblas -lparmetis -lmetis -lssl >>> -lcrypto >>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/lib/libmpichf90.dylib >>> -lgfortran -lquadmath -lm >>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/lib/libmpichcxx.dylib >>> -lstdc++ >>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/lib/libpmpich.dylib >>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/lib/libmpich.dylib >>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/lib/libopa.dylib >>> -lpthread >>> /Users/xzhao/software/petsc/petsc_352_opt_gcc49/arch- >>> darwin-c-opt/lib/libmpl.dylib >>> -lSystem -lgcc_ext.10.5 -ldl -fopenmp >>> >>> inl424641:ex1 xzhao$ sh run.sh >>> >>> *************************************************************** >>> >>> * Running Example introduction_ex1: >>> >>> * example-opt -d 3 >>> /Users/xzhao/software/libmesh_xzhao/reference_elements/3D/one_hex27.xda >>> >>> *************************************************************** >>> >>> >>> >>> Stack frames: 2 >>> >>> 0: 0 libmesh_opt.0.dylib 0x0000000109843730 >>> libMesh::print_trace(std::ostream&) + 1520 >>> >>> 1: 1 libmesh_opt.0.dylib 0x0000000109841b0c >>> libMesh::MacroFunctions::report_error(char const*, int, char const*, >>> char >>> const*) + 124 >>> >>> [0] src/utils/xdr_cxx.C, line 227, compiled Jan 17 2015 at 10:13:44 >>> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 >>> >>> [unset]: aborting job: >>> >>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 >>> >>> >>> >>> I also tried some other examples, unfortunately, all failed! For some of >>> them, it showed PETSc errors, although there were no problems when I run >>> several PETSc examples. Can anyone help me figure out why? >>> >>> thanks a lot. >>> >>> Xujun >>> ------------------------------------------------------------ >>> ------------------ >>> New Year. New Location. New Benefits. New Data Center in Ashburn, VA. >>> GigeNET is offering a free month of service with a new server in Ashburn. >>> Choose from 2 high performing configs, both with 100TB of bandwidth. >>> Higher redundancy.Lower latency.Increased capacity.Completely compliant. >>> http://p.sf.net/sfu/gigenet >>> _______________________________________________ >>> Libmesh-users mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/libmesh-users >>> >> > ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
