How did you apply my patch? On Mon, Aug 27, 2018 at 4:00 PM, Alexander Lindsay <alexlindsay...@gmail.com > wrote:
> Yes it is > > On Mon, Aug 27, 2018 at 3:59 PM, Renato Poli <rebp...@gmail.com> wrote: > >> Is that "p"? >> >> On Mon, Aug 27, 2018 at 5:51 PM Alexander Lindsay < >> alexlindsay...@gmail.com> wrote: >> >>> Like this? This is how it looks for me. >>> >>> On Mon, Aug 27, 2018 at 12:21 PM, Renato Poli <rebp...@gmail.com> wrote: >>> >>>> Hi Alexander, >>>> >>>> It did run, but the values were not assigned at the right elements. >>>> Please find a paraview figure attached. >>>> It was produced by the example I sent (open mesh.e in paraview). >>>> The pressure subdomain should be a circle in the center. >>>> >>>> I would guess the problem lies in lines 1141-2 below (just a guess): >>>> soln[nv*(nn++) + (var + var_num)] += >>>> nodal_soln[n]; >>>> (https://github.com/libMesh/libmesh/pull/1836/files/126feb95 >>>> 4ba89c5739794dd286ed8a47c2735be8) >>>> >>>> rgds, >>>> Renato >>>> >>>> >>>> >>>> On Mon, Aug 27, 2018 at 12:35 PM Alexander Lindsay < >>>> alexlindsay...@gmail.com> wrote: >>>> >>>>> Renato, please check to see whether https://github.com/lib >>>>> Mesh/libmesh/pull/1836 fixes your issue. It appears to work to me on >>>>> the example you sent >>>>> >>>>> On Sat, Aug 25, 2018 at 3:16 PM, Renato Poli <rebp...@gmail.com> >>>>> wrote: >>>>> >>>>>> 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_vecto >>>>>>>>>>> r(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::__cx >>>>>>>>>>> x11::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::__cx >>>>>>>>>>> x11::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
