Dear Libmesh developers, I upgrarded from 1.2.1 to 1.4.0
My code stopped working. The first error is as follows: [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Not for unassembled vector [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.8.4, Mar, 24, 2018 [0]PETSC ERROR: /home/mpovolot/NEMO5/prototype/bug1/Bell/nemo on a linux named brown-a302.rcac.purdue.edu by mpovolot Tue Mar 26 18:58:29 2019 [0]PETSC ERROR: Configure options --with-scalar-type=real --with-x=0 --with-hdf5 --download-hdf5=1 --with-single-library=1 --with-pic=1 --with-shared-libraries=0 --with-log=0 --with-clanguage=C++ --CXXFLAGS="-fopenmp -fPIC" --CFLAGS="-fopenmp -fPIC" --with-fortran=0 --FFLAGS="-fopenmp -fPIC" --with-debugging=0 --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx COPTFLAGS= CXXOPTFLAGS= FOPTFLAGS= --download-metis=1 --download-parmetis=1 --with-valgrind-dir=/apps/brown/valgrind/3.13.0_gcc-4.8.5 --download-mumps=1 --with-fortran-kernels=0 --download-superlu_dist=1 --with-blaslapack-lib="-L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core " --with-blacs-lib=/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so --with-blacs-include=/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/include --with-scalapack-lib="-Wl,-rpath,/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64 -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64 -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lpthread -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" --with-scalapack-include=/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/include [0]PETSC ERROR: #1 VecCopy() line 1562 in /depot/kildisha/apps/brown/nemo5/libs/petsc/build-real/src/vec/vec/interface/vector.c terminate called after throwing an instance of 'libMesh::PetscSolverException' what(): Object is in wrong state Program received signal SIGABRT, Aborted. 0x00002aaab14ea207 in raise () from /usr/lib64/libc.so.6 Missing separate debuginfos, use: debuginfo-install glibc-2.17-260.el7.x86_64 libibumad-43.1.1.MLNX20180612.87b4d9b-0.1.45101.x86_64 libibverbs-41mlnx1-OFED.4.5.0.1.0.45101.x86_64 libicu-50.1.2-17.el7.x86_64 libmlx4-41mlnx1-OFED.4.5.0.0.3.45101.x86_64 libmlx5-41mlnx1-OFED.4.5.0.3.8.45101.x86_64 libnl3-3.2.28-4.el7.x86_64 librdmacm-41mlnx1-OFED.4.2.0.1.3.45101.x86_64 numactl-libs-2.0.9-7.el7.x86_64 opensm-libs-5.3.0.MLNX20181108.33944a2-0.1.45101.x86_64 python-libs-2.7.5-76.el7.x86_64 zlib-1.2.7-18.el7.x86_64 (gdb) up #1 0x00002aaab14eb8f8 in abort () from /usr/lib64/libc.so.6 (gdb) #2 0x00002aaab087086d in __gnu_cxx::__verbose_terminate_handler () at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/vterminate.cc:95 95 /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/vterminate.cc: No such file or directory. (gdb) #3 0x00002aaab086e8b6 in __cxxabiv1::__terminate (handler=<optimized out>) at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:47 47 /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc: No such file or directory. (gdb) #4 0x00002aaab086e901 in std::terminate () at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:57 57 in /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc (gdb) #5 0x00002aaab086eb18 in __cxxabiv1::__cxa_throw (obj=0x5f95400, tinfo=0x2aaab00a41e0 <typeinfo for libMesh::PetscSolverException>, dest= 0x2aaaad2c0a42 <libMesh::PetscSolverException::~PetscSolverException()>) at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_throw.cc:87 87 /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_throw.cc: No such file or directory. (gdb) #6 0x00002aaabe208304 in libMesh::PetscVector<double>::operator= (this=0x373fc60, v=...) at src/numerics/petsc_vector.C:581 581 LIBMESH_CHKERR(ierr); (gdb) #7 0x00002aaabe208cb3 in libMesh::PetscVector<double>::operator= (this=0x373fc60, v_in=...) at src/numerics/petsc_vector.C:552 552 *this = *v; (gdb) #8 0x00002aaabe20c6ae in libMesh::PetscVector<double>::localize (this=0x373fba0, v_local_in=..., send_list=...) at src/numerics/petsc_vector.C:723 723 v_local_in = *this; (gdb) #9 0x00002aaabe43f570 in libMesh::System::update (this=0x3734120) at src/systems/system.C:424 424 solution->localize (*current_local_solution, send_list); (gdb) #10 0x00002aaabe3bbb33 in libMesh::libmesh_petsc_snes_residual_helper (snes=0x58daf60, x=0x3628680, ctx=0x373fdb0) at src/solvers/petsc_nonlinear_solver.C:98 98 sys.update(); (gdb) #11 0x00002aaabe3bbe56 in libMesh::libmesh_petsc_snes_residual (snes=0x58daf60, x=0x3628680, r=0x36b70d0, ctx=0x373fdb0) at src/solvers/petsc_nonlinear_solver.C:152 152 ResidualContext rc = libmesh_petsc_snes_residual_helper(snes, x, ctx); (gdb) #12 0x00002aaaaeae4dff in SNESComputeFunction () from /home/mpovolot/NEMO5/prototype/lib/libnemo.so (gdb) #13 0x00002aaaaefd4fe6 in SNESSolve_NEWTONTR(_p_SNES*) () from /home/mpovolot/NEMO5/prototype/lib/libnemo.so (gdb) #14 0x00002aaaaeaeed40 in SNESSolve () from /home/mpovolot/NEMO5/prototype/lib/libnemo.so (gdb) #15 0x00002aaabe3bf889 in libMesh::PetscNonlinearSolver<double>::solve (this=0x373fdb0, pre_in=..., x_in=..., r_in=...) at src/solvers/petsc_nonlinear_solver.C:926 926 ierr = SNESSolve (_snes, PETSC_NULL, x->vec()); (gdb) #16 0x00002aaabe4367ad in libMesh::NonlinearImplicitSystem::solve (this=0x3734120) at src/systems/nonlinear_implicit_system.C:183 183 nonlinear_solver->max_linear_iterations); (gdb) #17 0x00002aaaadb45bb2 in NonlinearPoisson::execute_for_single_replica (this=0x2cbaa90, my_system=0x3734120) at NonlinearPoisson.cpp:1359 1359 system->solve(); (gdb) #18 0x00002aaaadb66dc4 in NonlinearPoisson::execute_solver (this=0x2cbaa90) at NonlinearPoisson.cpp:1247 1247 execute_for_single_replica(my_system); (gdb) In order to solve it, I had to compile with disable-ghosted After that, I have got another similar error: #1 0x00002aaab14eb8f8 in abort () from /usr/lib64/libc.so.6 (gdb) #2 0x00002aaab087086d in __gnu_cxx::__verbose_terminate_handler () at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/vterminate.cc:95 95 in /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/vterminate.cc (gdb) #3 0x00002aaab086e8b6 in __cxxabiv1::__terminate (handler=<optimized out>) at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:47 47 /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc: No such file or directory. (gdb) #4 0x00002aaab086e901 in std::terminate () at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc:57 57 in /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_terminate.cc (gdb) #5 0x00002aaab086eb18 in __cxxabiv1::__cxa_throw (obj=0x5fe1060, tinfo=0x2aaab0059a20 <typeinfo for libMesh::LogicError>, dest=0x2aaaacc4de4a <libMesh::LogicError::~LogicError()>) at /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_throw.cc:87 87 /tmp/aai/gcc-5.2.0/libstdc++-v3/libsupc++/eh_throw.cc: No such file or directory. (gdb) #6 0x00002aaabda5c5b4 in libMesh::DofMap::enforce_constraints_exactly (this=0x382c3e0, system=..., v=0x382ab70, homogeneous=false) at src/base/dof_map_constraints.C:2108 2108 libmesh_assert (v_local->closed()); (gdb) #7 0x00002aaabe3bbb0b in libMesh::libmesh_petsc_snes_residual_helper (snes=0x58f21f0, x=0x3713590, ctx=0x382ac80) at src/solvers/petsc_nonlinear_solver.C:105 105 sys.get_dof_map().enforce_constraints_exactly(sys, sys.current_local_solution.get()); (gdb) #8 0x00002aaabe3bbde2 in libMesh::libmesh_petsc_snes_residual (snes=0x58f21f0, x=0x3713590, r=0x37a0560, ctx=0x382ac80) at src/solvers/petsc_nonlinear_solver.C:152 152 ResidualContext rc = libmesh_petsc_snes_residual_helper(snes, x, ctx); (gdb) #9 0x00002aaaaeae4dff in SNESComputeFunction () from /home/mpovolot/NEMO5/prototype/lib/libnemo.so (gdb) #10 0x00002aaaaefd4fe6 in SNESSolve_NEWTONTR(_p_SNES*) () from /home/mpovolot/NEMO5/prototype/lib/libnemo.so (gdb) #11 0x00002aaaaeaeed40 in SNESSolve () from /home/mpovolot/NEMO5/prototype/lib/libnemo.so (gdb) #12 0x00002aaabe3bf815 in libMesh::PetscNonlinearSolver<double>::solve (this=0x382ac80, pre_in=..., x_in=..., r_in=...) at src/solvers/petsc_nonlinear_solver.C:926 926 ierr = SNESSolve (_snes, PETSC_NULL, x->vec()); (gdb) #13 0x00002aaabe4365bd in libMesh::NonlinearImplicitSystem::solve (this=0x381f030) at src/systems/nonlinear_implicit_system.C:183 183 nonlinear_solver->max_linear_iterations); Please advise. Michael. _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
