Yes it is On Mon, Aug 27, 2018 at 3:59 PM, Renato Poli <[email protected]> wrote:
> Is that "p"? > > On Mon, Aug 27, 2018 at 5:51 PM Alexander Lindsay < > [email protected]> wrote: > >> Like this? This is how it looks for me. >> >> On Mon, Aug 27, 2018 at 12:21 PM, Renato Poli <[email protected]> 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/ >>> 126feb954ba89c5739794dd286ed8a47c2735be8) >>> >>> rgds, >>> Renato >>> >>> >>> >>> On Mon, Aug 27, 2018 at 12:35 PM Alexander Lindsay < >>> [email protected]> wrote: >>> >>>> Renato, please check to see whether https://github.com/ >>>> libMesh/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 <[email protected]> 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 <[email protected]> >>>>> wrote: >>>>> >>>>>> Sure.... please give me a couple of hours. >>>>>> >>>>>> On Sat, Aug 25, 2018 at 12:04 PM Alexander Lindsay < >>>>>> [email protected]> 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 < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Ah yes...key difference between "empty" and "zero"... >>>>>>>> >>>>>>>> On Aug 25, 2018, at 7:03 AM, Renato Poli <[email protected]> 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 < >>>>>>>> [email protected]> 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 <[email protected]> >>>>>>>>> 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 <[email protected]> >>>>>>>>>> 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 >>>>>>>>>> [email protected] >>>>>>>>>> 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 [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
