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
