No success. Stack trace below. Note that, if I define my variable _only_ on its domain (where there is fluid) it works.
In this case, the problem is in ExodusII_IO::write_discontinuous_timestep. [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Matrix is missing diagonal entry 0 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.7.6, Apr, 24, 2017 [0]PETSC ERROR: obj/bin/abada_sc11 on a linux-gnu-opt named dev-vb by dev Sat Aug 25 09:55:36 2018 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/lib/mpich --with-shared-libraries=1 --with-debugging=yes --download-mumps --download-hypre --download-scalapack --download-spai --download-parms [0]PETSC ERROR: #1 MatLUFactorSymbolic_SeqAIJ() line 301 in /opt/petsc-3.7.6/src/mat/impls/aij/seq/aijfact.c [0]PETSC ERROR: #2 MatLUFactorSymbolic() line 2944 in /opt/petsc-3.7.6/src/mat/interface/matrix.c [0]PETSC ERROR: #3 PCSetUp_LU() line 136 in /opt/petsc-3.7.6/src/ksp/pc/impls/factor/lu/lu.c [0]PETSC ERROR: #4 PCSetUp() line 968 in /opt/petsc-3.7.6/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #5 KSPSetUp() line 390 in /opt/petsc-3.7.6/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #6 KSPSolve() line 599 in /opt/petsc-3.7.6/src/ksp/ksp/interface/itfunc.c Thanks, Renato On Fri, Aug 24, 2018 at 11:49 PM Alexander Lindsay <alexlindsay...@gmail.com> wrote: > If you're using PETSc as your underlying solver, try the options > `-pc_factor_shift_type NONZERO -pc_factor_shift_amount 1e-15` > > On Thu, Aug 23, 2018 at 2:58 PM, Renato Poli <rebp...@gmail.com> wrote: > >> Hi >> >> I am getting trouble here again ... really need some help. >> >> I have part of the domain without flow (and thus without the pressure >> variable defined). >> As I could not export that (could not get write_discontinuous_exodusII to >> work) I just left the matrix empty, without major impact so far. >> However, now I am using LU preconditioning, which does not accept empty >> entries in the diagonal. >> >> How can I get through? >> Any suggestion? >> >> Thanks upfront. >> Renato >> >> >> >> >> >> On Thu, Aug 16, 2018 at 6:47 PM Renato Poli <rebp...@gmail.com> wrote: >> >> > Hi >> > >> > I see the stack trace below when writing a discontinuous timestep >> > (exo.write_discontinuous_timestep). >> > It happens when my variable is set only in part of the domain. >> > No problem arises if I use, instead: exo.write_equation_systems(fname, >> es) >> > >> > Any hint/workaround/idea? >> > >> > Thanks, >> > Renato >> > >> > This is how the variable is set. >> > | std::set<subdomain_id_type> active_subdomains; >> > | active_subdomains.clear(); >> > | active_subdomains.insert(SUBDOMAIN_A); >> > | press_sys.add_variable ("p", SECOND, LAGRANGE, & active_subdomains); >> > >> > 0: libMesh::print_trace(std::ostream&) >> > 1: libMesh::MacroFunctions::report_error(char const*, int, char const*, >> > char const*) >> > 2: >> > >> libMesh::EquationSystems::build_discontinuous_solution_vector(std::__debug::vector<double, >> > std::allocator<double> >&, >> > std::__debug::set<std::__cxx11::basic_string<char, >> std::char_traits<char>, >> > std::allocator<char> >, std::less<std::__cxx11::basic_string<char, >> > std::char_traits<char>, std::allocator<char> > >, >> > std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, >> > std::allocator<char> > > > const*) const >> > 3: >> > >> libMesh::ExodusII_IO::write_discontinuous_exodusII(std::__cxx11::basic_string<char, >> > std::char_traits<char>, std::allocator<char> > const&, >> > libMesh::EquationSystems const&, >> > std::__debug::set<std::__cxx11::basic_string<char, >> std::char_traits<char>, >> > std::allocator<char> >, std::less<std::__cxx11::basic_string<char, >> > std::char_traits<char>, std::allocator<char> > >, >> > std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, >> > std::allocator<char> > > > const*) >> > 4: >> > >> libMesh::ExodusII_IO::write_timestep_discontinuous(std::__cxx11::basic_string<char, >> > std::char_traits<char>, std::allocator<char> > const&, >> > libMesh::EquationSystems const&, int, double, >> > std::__debug::set<std::__cxx11::basic_string<char, >> std::char_traits<char>, >> > std::allocator<char> >, std::less<std::__cxx11::basic_string<char, >> > std::char_traits<char>, std::allocator<char> > >, >> > std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, >> > std::allocator<char> > > > const*) >> > >> > >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Libmesh-users mailing list >> Libmesh-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> > > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
