Renato, could you create a minimum example that generates the discontinuous error, and either share it here or create a ticket on github? That would be useful for fixing the issue and adding a test in libmesh to ensure we support the capability.
On Sat, Aug 25, 2018 at 8:33 AM, Alexander Lindsay <alexlindsay...@gmail.com > wrote: > Ah yes...key difference between "empty" and "zero"... > > On Aug 25, 2018, at 7:03 AM, Renato Poli <rebp...@gmail.com> wrote: > > 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
