Hi Alexander, Please find attached the example you asked. I used introduction_ex3 as a basis... it got a little messy, I hope it is enough. Please let me know otherwise.
Thanks Renato On Sat, Aug 25, 2018 at 12:42 PM Renato Poli <rebp...@gmail.com> wrote: > Sure.... please give me a couple of hours. > > On Sat, Aug 25, 2018 at 12:04 PM Alexander Lindsay < > alexlindsay...@gmail.com> wrote: > >> 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
